GSM2564321 Embryo NA GSE97425 N2 Embryo Mid-Embryogenesis (roughly 40 cell stage) N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 Embryo Dnase-seq Biological Replicate D bw_0_1_2_4_ce10 GSM2564321_merged.embryo.ce10.D.positive.bw GSM2564320 Embryo NA GSE97425 N2 Embryo Mid-Embryogenesis (roughly 40 cell stage) N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 Embryo Dnase-seq Biological Replicate C bw_0_1_2_4_ce10 GSM2564320_merged.embryo.ce10.C.total.bw GSM2564319 Embryo NA GSE97425 N2 Embryo Mid-Embryogenesis (roughly 40 cell stage) N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 Embryo Dnase-seq Biological Replicate B bw_0_1_2_4_ce10 GSM2564319_merged.embryo.ce10.B.negative.bw GSM2564318 Embryo NA GSE97425 N2 Embryo Mid-Embryogenesis (roughly 40 cell stage) N2 DNase WS220 Reads were analyzed using FastQC and filtered using quality threshold Q20. N2 Embryo Dnase-seq Biological Replicate A bw_0_1_2_4_ce10 GSM2564318_merged.embryo.ce10.A.negative.bw GSM1825721 Embryo NA GSE67650 whole worms embryo SET4 AMA1 Q2357 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 SET4 MxEmb Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1825720 Embryo NA GSE67650 whole worms embryo CB428 AMA1 Q2357 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 CB428 MxEmb Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1825722 Embryo NA GSE67650 whole worms embryo SET4 AMA1 Q2357 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 SET4 MxEmb Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1825718 Embryo NA GSE67650 whole worms embryo CB428 AMA1 Q2357 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 CB428 MxEmb Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1825719 Embryo NA GSE67650 whole worms embryo CB428 AMA1 Q2357 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 CB428 MxEmb Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1825717 Embryo NA GSE67650 whole worms embryo N2 AMA1 Q2357 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 N2 MxEmb Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1652675 Embryo NA GSE67650 whole worms embryo MT14911 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 SET4 MxEmb Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1652674 Embryo NA GSE67650 whole worms embryo MT14911 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 SET4 MxEmb Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1652673 Embryo NA GSE67650 whole worms embryo CB428 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 CB428 MxEmb Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1652672 Embryo NA GSE67650 whole worms embryo CB428 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 CB428 MxEmb Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1652671 Embryo NA GSE67650 whole worms embryo CB428 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 CB428 MxEmb Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1440293 Embryo NA GSE59716 mixed stage embryos embryo N2 SDC-3 ChIP-Seq 50 base single end Illumina sequences were sorted by the bar code in the first 4 or 6 sequenced bases, then bar codes were removed ECMB09_w4_N2-embryo_SDC3-IP bd_0_1_2_6_ce10 UsingSRR GSM1089275 Embryo NA GSE44412 embryo crosslinked chromatin MNase-Seq WS220 1. We used Novoalign (2.07.00 - Aug 5 2010) to map paired-end 25bp reads to release WS220 (Feb 2011) of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads mapped only to C. elegans (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group. WT_input_FCL_(20120817_3_12) bd_0_1_2_6_ce10 UsingSRR GSM1089271 Embryo NA GSE44412 embryo soluble chromatin MNase-Seq WS220 1. We used Novoalign (2.07.00 - Aug 5 2010) to map paired-end 25bp reads to release WS220 (Feb 2011) of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads mapped only to C. elegans (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group. WT_input_1min_(20110706_1) bd_0_1_2_6_ce10 UsingSRR GSM1089269 Embryo NA GSE44412 embryo crosslinked ChIPed chromatin CENP-C ChIP-Seq WS220 1. We used Novoalign (2.07.00 - Aug 5 2010) to map paired-end 25bp reads to release WS220 (Feb 2011) of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads mapped only to C. elegans (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group. WT_HCP4_FCL_(20120817_3_4) bd_0_1_2_6_ce10 UsingSRR GSM1111802 Embryo NA GSE45678 whole worms embryo N2 PQN-85 SDQ4481 is the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. PQN85 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111801 Embryo NA GSE45678 whole worms embryo N2 PQN-85 SDQ4481 is the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. PQN85 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111800 Embryo NA GSE45678 whole worms embryo N2 MIX-1 SDQ3892 is the antigen MHIKSIHLDGFKSYQKHTDILDFSPTFNAITGYNGSGKSNILDSICFIMGINKLDNIRAKSMHELISHGGTKAIVQVRFDNTDKRCSPFGMEHLDEIVVQ May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. MIX1 Rep5 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111799 Embryo NA GSE45678 whole worms embryo N2 MIX-1 SDQ3892 is the antigen MHIKSIHLDGFKSYQKHTDILDFSPTFNAITGYNGSGKSNILDSICFIMGINKLDNIRAKSMHELISHGGTKAIVQVRFDNTDKRCSPFGMEHLDEIVVQ May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. MIX1 Rep4 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111798 Embryo NA GSE45678 whole worms embryo N2 MIX-1 SDQ4107 is the antigen MHIKSIHLDGFKSYQKHTDILDFSPTFNAITGYNGSGKSNILDSICFIMGINKLDNIRAKSMHELISHGGTKAIVQVRFDNTDKRCSPFGMEHLDEIVVQ. May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. MIX1 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111797 Embryo NA GSE45678 whole worms embryo N2 MIX-1 SDQ4107 is the antigen MHIKSIHLDGFKSYQKHTDILDFSPTFNAITGYNGSGKSNILDSICFIMGINKLDNIRAKSMHELISHGGTKAIVQVRFDNTDKRCSPFGMEHLDEIVVQ. May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. MIX1 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111796 Embryo NA GSE45678 whole worms embryo N2 MIX-1 JL0004 to 837-1244 aa. ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. MIX1 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111794 Embryo NA GSE45678 whole worms embryo N2 KLE-2 SDQ3942 is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. KLE2 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111792 Embryo NA GSE45678 whole worms embryo N2 HTZ1 BK00001 ascites HTZ-1 specific peptide N-PGKPGAPGQGPQ-C ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HTZ Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111793 Embryo NA GSE45678 whole worms embryo N2 KLE-2 SDQ3898 is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. KLE2 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111791 Embryo NA GSE45678 whole worms embryo N2 HTZ1 BK00001 ascites HTZ-1 specific peptide N-PGKPGAPGQGPQ-C ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HTZ Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111782 Embryo NA GSE45678 whole worms embryo N2 DPY-28 SDQ4564 is the antigen QQQPTRNNDGLSGFKSITEIIAEADNNIPSEQIDKDIDSFSSYSDISDWRGIPKFFPSLSSLSRRASTYENWENRFKVVDYLVSCSGALKDSVSDYVADY May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY28 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111781 Embryo NA GSE45678 whole worms embryo N2 DPY-28 SDQ4564 is the antigen QQQPTRNNDGLSGFKSITEIIAEADNNIPSEQIDKDIDSFSSYSDISDWRGIPKFFPSLSSLSRRASTYENWENRFKVVDYLVSCSGALKDSVSDYVADY May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY28 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111777 Embryo NA GSE45678 whole worms embryo N2 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111774 Embryo NA GSE45678 whole worms embryo N2 DPY-26 SDQ4561 is the antigen RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY26 Rep5 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111773 Embryo NA GSE45678 whole worms embryo N2 DPY-26 SDQ4561 is the antigen RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY26 Rep4 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111772 Embryo NA GSE45678 whole worms embryo N2 DPY-26 SDQ4496 is the antigen RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY26 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111771 Embryo NA GSE45678 whole worms embryo N2 DPY-26 SDQ4496 is the antigen RVDRLHHDVRQIDSALSSGTVMRDSNGEEIHLTLESRKAKKKMAVVDGMNGMLDFLNNMDDALTTTELDADNDKNWKEDEENIAGEPRIDFKANSKDVDA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY26 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111764 Embryo NA GSE45678 whole worms embryo N2 CAPG-1 SDQ3990 is the antigen MPPKKRIRGPKLPALREEKSTGTDVASDESFNESADFLNNEELNNDQNDAENTVLSEGVSTLRINENMTKEDRACISAALFIKKRVVESIRTVFQSRDDI May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG1 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111763 Embryo NA GSE45678 whole worms embryo N2 CAPG-1 SDQ3967 is the antigen MPPKKRIRGPKLPALREEKSTGTDVASDESFNESADFLNNEELNNDQNDAENTVLSEGVSTLRINENMTKEDRACISAALFIKKRVVESIRTVFQSRDDI May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG1 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111762 Embryo NA GSE45678 whole worms embryo N2 CAPG-1 SDQ3967 is the antigen MPPKKRIRGPKLPALREEKSTGTDVASDESFNESADFLNNEELNNDQNDAENTVLSEGVSTLRINENMTKEDRACISAALFIKKRVVESIRTVFQSRDDI May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG1 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1171493 Embryo NA GSE45678 whole worms embryo TY1072 PQN-85 SDQ4481 is the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. PQN85 TY1072 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1171492 Embryo NA GSE45678 whole worms embryo TY1072 KLE-2 SDQ3942 is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. KLE2 TY1072 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1171491 Embryo NA GSE45678 whole worms embryo TY1072 KLE-2 SDQ3942 is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. KLE2 TY1072 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111808 Embryo NA GSE45678 whole worms embryo N2 SMC-4 KH-SMC4 to 1519-1549 aa sequence CGSTPKRSPMKPLTPSSKKKEKAIVDDDDDME ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SMC4 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111806 Embryo NA GSE45678 whole worms embryo N2 SMC-4 OD0039 from Arshad Desai Lab ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SMC4 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111807 Embryo NA GSE45678 whole worms embryo N2 SMC-4 OD0039 from Arshad Desai Lab ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. SMC4 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111804 Embryo NA GSE45678 whole worms embryo TY1072 PQN-85 SDQ4481 is the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. PQN85 TY1072 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111805 Embryo NA GSE45678 whole worms embryo TY1072 PQN-85 SDQ4481 is the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. PQN85 TY1072 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111803 Embryo NA GSE45678 whole worms embryo N2 PQN-85 SDQ4481 is the antigen QQQPVQQIQRQQPIAQPIPQHTIPPSTSNQFQQQIQSAASSIFDSSVISSHQKLYEEQCRQIEKERKEQEERKRKQELEEQRKRNEELKRLRIAEEKRLL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. PQN85 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111790 Embryo NA GSE45678 whole worms embryo TY1072 HCP-6 KH-HCP6 to 1708-1722 aa sequence CKSAQAYHLHNIFEEDEES ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HCP6 TY1072 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111795 Embryo NA GSE45678 whole worms embryo N2 KLE-2 SDQ3942 is the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. KLE2 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111789 Embryo NA GSE45678 whole worms embryo TY1072 HCP-6 KH-HCP6 to 1708-1722 aa sequence CKSAQAYHLHNIFEEDEES ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HCP6 TY1072 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111788 Embryo NA GSE45678 whole worms embryo N2 HCP-6 KH-HCP6 to 1708-1722 aa sequence CKSAQAYHLHNIFEEDEES ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HCP6 Rep4 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111787 Embryo NA GSE45678 whole worms embryo N2 HCP-6 KH-HCP6 to 1708-1722 aa sequence CKSAQAYHLHNIFEEDEES ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HCP6 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111786 Embryo NA GSE45678 whole worms embryo N2 HCP-6 KH-HCP6 to 1708-1722 aa sequence CKSAQAYHLHNIFEEDEES ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HCP6 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111785 Embryo NA GSE45678 whole worms embryo N2 HCP-6 KH-HCP6 to 1708-1722 aa sequence CKSAQAYHLHNIFEEDEES ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. HCP6 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111784 Embryo NA GSE45678 whole worms embryo N2 DPY-28 KH-DPY28 to 1484-1499 aa sequence CKSAVADDDSDSDEFMLDD ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY28 Rep4 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111783 Embryo NA GSE45678 whole worms embryo N2 DPY-28 SDQ4564 is the antigen QQQPTRNNDGLSGFKSITEIIAEADNNIPSEQIDKDIDSFSSYSDISDWRGIPKFFPSLSSLSRRASTYENWENRFKVVDYLVSCSGALKDSVSDYVADY May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY28 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111780 Embryo NA GSE45678 whole worms embryo N2 DPY-27 SDQ3995 is the antigen LSNGLSNVVIAPKRKQRRLEMLKLSDFGLDDDSDLPEFNRFPPATRRELSVEDSDEDDEPVRRRPRRQVEEEDEEDELIEEATPSPPPIVVQRRVRRSRH May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 Rep4 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111779 Embryo NA GSE45678 whole worms embryo N2 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111778 Embryo NA GSE45678 whole worms embryo N2 DPY-27 JL00001 to 1-409 aa. is the antigen 1-409 aa ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY27 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111776 Embryo NA GSE45678 whole worms embryo TY1072 DPY-26 JL00003 to 40-1262 aa. ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY26 TY1072 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111775 Embryo NA GSE45678 whole worms embryo TY1072 DPY-26 JL00003 to 40-1262 aa. ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY26 TY1072 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111770 Embryo NA GSE45678 whole worms embryo N2 DPY-26 JL00003 to 40-1262 aa. ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. DPY26 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111769 Embryo NA GSE45678 whole worms embryo N2 CAPG-2 SDQ4484 to 808-907 aa is the antigen IPKWMNKQCDLMEDDEENIFKNHREIVESLRQFHKRVSETDYWDEDSAKRMMHHFMLFSIVSASSKNDDEAYDDPRDEDYKPPHFISLALIKFILKEKSL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG2 Rep5 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111768 Embryo NA GSE45678 whole worms embryo N2 CAPG-2 SDQ4567 to 808-907 aa is the antigen IPKWMNKQCDLMEDDEENIFKNHREIVESLRQFHKRVSETDYWDEDSAKRMMHHFMLFSIVSASSKNDDEAYDDPRDEDYKPPHFISLALIKFILKEKSL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG2 Rep4 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111766 Embryo NA GSE45678 whole worms embryo N2 CAPG-2 SDQ4484 to 808-907 aa is the antigen IPKWMNKQCDLMEDDEENIFKNHREIVESLRQFHKRVSETDYWDEDSAKRMMHHFMLFSIVSASSKNDDEAYDDPRDEDYKPPHFISLALIKFILKEKSL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG2 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111767 Embryo NA GSE45678 whole worms embryo N2 CAPG-2 SDQ4567 to 808-907 aa is the antigen IPKWMNKQCDLMEDDEENIFKNHREIVESLRQFHKRVSETDYWDEDSAKRMMHHFMLFSIVSASSKNDDEAYDDPRDEDYKPPHFISLALIKFILKEKSL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG2 Rep3 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111765 Embryo NA GSE45678 whole worms embryo N2 CAPG-2 SDQ4484 to 808-907 aa is the antigen IPKWMNKQCDLMEDDEENIFKNHREIVESLRQFHKRVSETDYWDEDSAKRMMHHFMLFSIVSASSKNDDEAYDDPRDEDYKPPHFISLALIKFILKEKSL May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. CAPG2 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111761 Embryo NA GSE45678 whole worms embryo N2 AMA1 Q2357 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 Rep2 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1111760 Embryo NA GSE45678 whole worms embryo N2 AMA1 Q2358 is the antigen DLVLDVEKCKYGMEIPQNVVMGGGFYGSFAGSPSNREFSPAHSPWNSGVTPTYAGAAWSPTTGGMSPGAGFSPAGNTDGGASPFNEGGWSPASPGDPLGA May be available as part of modENCODE antibodies from Novus Biologicals "http ChIP-Seq WS220 Basecalls were performed using CASAVA version 1.8. AMA1 Rep1 ChIPSeq bd_0_1_2_6_ce10 UsingSRR GSM1183844 Embryo NA GSE48753 MED-1_GFP_MIDEMB_ChIP_Rep2 embryo OP391(official name : OP391 genotype : unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The MED-1::EGFP fusion protein is expressed in the correct med-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MED-1 transcription factor. made_by : Unknown ) Snyder_MED-1_GFP_MIDEMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_MED-1_GFP_MIDEMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183844_Snyder_MED-1_GFP_MIDEMB_GFP_rep_2_120213_ROCKFORD_00128_FC63BAJ_L6_CATT.bedgraph.gz GSM1183842 Embryo NA GSE48753 MED-1_GFP_MIDEMB_ChIP_Rep1 embryo OP391(official name : OP391 genotype : unc-119(ed3) III; wgIs391(med-1::TY1 EGFP FLAG C; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The MED-1::EGFP fusion protein is expressed in the correct med-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MED-1 transcription factor. made_by : Unknown ) Snyder_MED-1_GFP_MIDEMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_MED-1_GFP_MIDEMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183842_Snyder_MED-1_GFP_MIDEMB_GFP_rep_1_120213_ROCKFORD_00128_FC63BAJ_L6_GTAT.bedgraph.gz GSM1183816 Embryo NA GSE48746 ZTF-11_GFP_EMB_ChIP_Rep2 embryo OP236(official name : OP236 genotype : unc-119(ed3) III; wgIs236(ekl-2::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ) Snyder_ZTF-11_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_ZTF-11_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183816_Snyder_ZTF-11_GFP_EMB_GFP_rep_2_120120_SPADE_00132_FC63A5M_L7_CATT.bedgraph.gz GSM1183814 Embryo NA GSE48746 ZTF-11_GFP_EMB_ChIP_Rep1 embryo OP236(official name : OP236 genotype : unc-119(ed3) III; wgIs236(ekl-2::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ) Snyder_ZTF-11_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_ZTF-11_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183814_Snyder_ZTF-11_GFP_EMB_GFP_rep_1_120120_SPADE_00132_FC63A5M_L7_GTAT.bedgraph.gz GSM1183808 Embryo NA GSE48744 GEI-11_GFP_Emb_ChIP_Rep2 embryo OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ) Snyder_GEI-11_GFP_Emb_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_GEI-11_GFP_Emb_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183808_Snyder_GEI-11_GFP_Emb_GFP_rep_2_110104_ROCKFORD_00045_FC70FLC_L6_TGCT.bedgraph.gz GSM1183806 Embryo NA GSE48744 GEI-11_GFP_Emb_ChIP_Rep1 embryo OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ) Snyder_GEI-11_GFP_Emb_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_GEI-11_GFP_Emb_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183806_Snyder_GEI-11_GFP_Emb_GFP_rep_1_110104_ROCKFORD_00045_FC70FLC_L6_ACGT.bedgraph.gz GSM1183804 Embryo NA GSE48743 BLMP-1_GFP_Emb_ChIP_Rep2 embryo OP109(official name : OP109 genotype : unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. made_by : R Waterston ) Snyder_BLMP-1_GFP_Emb_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_BLMP-1_GFP_Emb_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183804_Snyder_BLMP-1_GFP_Emb_GFP_rep_2_111004_MAGNUM_00100_FC64KG3_L4_CATT.bedgraph.gz GSM1183802 Embryo NA GSE48743 BLMP-1_GFP_Emb_ChIP_Rep1 embryo OP109(official name : OP109 genotype : unc-119 (ed3) III; wgIs109 [blmp-1::TY1::EGFP::FLAG; unc-119 (+)] outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The BLMP-1::EGFP fusion protein is expressed in the correct blmp-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the BLMP-1 transcription factor. made_by : R Waterston ) Snyder_BLMP-1_GFP_Emb_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_BLMP-1_GFP_Emb_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183802_Snyder_BLMP-1_GFP_Emb_GFP_rep_1_111004_MAGNUM_00100_FC64KG3_L4_GTAT.bedgraph.gz GSM1183756 Embryo NA GSE48732 NHR-28_GFP_EMB_ChIP_Rep2 embryo OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston ) Snyder_NHR-28_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-28_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183756_Snyder_NHR-28_GFP_EMB_GFP_rep_2_110915_SPADE_00108_FC631JC_L8_TGCT.bedgraph.gz GSM1183754 Embryo NA GSE48732 NHR-28_GFP_EMB_ChIP_Rep1 embryo OP317(official name : OP317 genotype : unc119(ed3);wgIs317(nhr-28::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-28::EGFP fusion protein is expressed in the correct nhr-28 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-28 transcription factor. made_by : R Waterston ) Snyder_NHR-28_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_NHR-28_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183754_Snyder_NHR-28_GFP_EMB_GFP_rep_1_110915_SPADE_00108_FC631JC_L8_ACGT.bedgraph.gz GSM1183752 Embryo NA GSE48731 UNC_62_GFP_EMB_ChIP_Rep2 embryo OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ) Snyder_UNC_62_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_UNC_62_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183752_Snyder_UNC_62_GFP_EMB_GFP_rep_2_110915_SPADE_00108_FC631JC_L7_TGCT.bedgraph.gz GSM1183750 Embryo NA GSE48731 UNC_62_GFP_EMB_ChIP_Rep1 embryo OP600(official name : OP600 genotype : unc119(ed3);wgIs600(unc-62::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-62::EGFP fusion protein is expressed in the correct unc-62 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-62 transcription factor. made_by : S Kim ) Snyder_UNC_62_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_UNC_62_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183750_Snyder_UNC_62_GFP_EMB_GFP_rep_1_110915_SPADE_00108_FC631JC_L7_ACGT.bedgraph.gz GSM1183728 Embryo NA GSE48725 NHR-2_GFP_EMB_ChIP_Rep2 embryo OP99(official name : OP99 genotype : unc119(ed3);wgIs99(nhr-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-2::EGFP fusion protein is expressed in the correct nhr-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-2 transcription factor. made_by : Unknown ) Snyder_NHR-2_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_NHR-2_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183728_Snyder_NHR-2_GFP_EMB_rep2-1.bedgraph.gz GSM1183726 Embryo NA GSE48725 NHR-2_GFP_EMB_ChIP_Rep1 embryo OP99(official name : OP99 genotype : unc119(ed3);wgIs99(nhr-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-2::EGFP fusion protein is expressed in the correct nhr-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-2 transcription factor. made_by : Unknown ) Snyder_NHR-2_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_NHR-2_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183726_Snyder_NHR-2_GFP_EMB_rep1.bedgraph.gz GSM1183724 Embryo NA GSE48724 CEH-39_GFP_EMB_ChIP_Rep2 embryo OP169(official name : OP169 genotype : unc119(ed3);wgIs169(ceh-39::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-39::EGFP fusion protein is expressed in the correct ceh-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-39 transcription factor. made_by : Unknown ) Snyder_CEH-39_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_CEH-39_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183724_Snyder_CEH-39_GFP_EMB_rep2-1.bedgraph.gz GSM1183722 Embryo NA GSE48724 CEH-39_GFP_EMB_ChIP_Rep1 embryo OP169(official name : OP169 genotype : unc119(ed3);wgIs169(ceh-39::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CEH-39::EGFP fusion protein is expressed in the correct ceh-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-39 transcription factor. made_by : Unknown ) Snyder_CEH-39_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_CEH-39_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183722_Snyder_CEH-39_GFP_EMB_rep1.bedgraph.gz GSM1183720 Embryo NA GSE48723 CES-1_GFP_EMB_ChIP_Rep2 embryo OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ) Snyder_CES-1_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_CES-1_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183720_Snyder_CES-1_GFP_EMB_rep2.bedgraph.gz GSM1183718 Embryo NA GSE48723 CES-1_GFP_EMB_ChIP_Rep1 embryo OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ) Snyder_CES-1_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_CES-1_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183718_Snyder_CES-1_GFP_EMB_rep1-1.bedgraph.gz GSM1183716 Embryo NA GSE48722 PAX-1_GFP_EMB_ChIP_Rep2 embryo OP117(official name : OP117 genotype : unc119(ed3);wgIs117(pax-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PAX-1::EGFP fusion protein is expressed in the correct pax-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PAX-1 transcription factor. made_by : Unknown ) Snyder_PAX-1_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_PAX-1_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183716_Snyder_PAX-1_GFP_EMB_rep2-1.bedgraph.gz GSM1183714 Embryo NA GSE48722 PAX-1_GFP_EMB_ChIP_Rep1 embryo OP117(official name : OP117 genotype : unc119(ed3);wgIs117(pax-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PAX-1::EGFP fusion protein is expressed in the correct pax-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PAX-1 transcription factor. made_by : Unknown ) Snyder_PAX-1_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_PAX-1_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183714_Snyder_PAX-1_GFP_EMB_rep1-1.bedgraph.gz GSM1183712 Embryo NA GSE48721 NHR-237_GFP_EMB_ChIP_Rep2 embryo OP228(official name : OP228 genotype : unc119(ed3);wgIs228(nhr-237:TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-237::EGFP fusion protein is expressed in the correct nhr-237 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-237 transcription factor. made_by : Unknown ) Snyder_NHR-237_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_NHR-237_GFP_EMB_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183712_Snyder_nhr-237_GFP_EMB_rep2-1.bedgraph.gz GSM1183710 Embryo NA GSE48721 NHR-237_GFP_EMB_ChIP_Rep1 embryo OP228(official name : OP228 genotype : unc119(ed3);wgIs228(nhr-237:TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-237::EGFP fusion protein is expressed in the correct nhr-237 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-237 transcription factor. made_by : Unknown ) Snyder_NHR-237_GFP_EMB_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_NHR-237_GFP_EMB_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183710_Snyder_nhr-237_GFP_EMB_rep1.bedgraph.gz GSM1183688 Embryo NA GSE48715 LSY-2_GFP_Embryo_ChIP_Rep2 embryo OP367(official name : OP367 genotype : unc-119(ed3); wgIs367(lsy-2::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_LSY-2_GFP_Embryo_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_LSY-2_GFP_Embryo_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183688_Snyder_LSY-2_GFP_Emb_rep2.bedgraph.gz GSM1183686 Embryo NA GSE48715 LSY-2_GFP_Embryo_ChIP_Rep1 embryo OP367(official name : OP367 genotype : unc-119(ed3); wgIs367(lsy-2::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The LSY-2::EGFP fusion protein is expressed in the correct lsy-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LSY-2 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_LSY-2_GFP_Embryo_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_LSY-2_GFP_Embryo_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183686_Snyder_LSY-2_GFP_Emb_rep1.bedgraph.gz GSM1183674 Embryo NA GSE48712 MAB-5_GFP_Embryo_ChIP_Rep2 embryo OP27(official name : OP27 genotype : unc-119(ed3); wgIs27(mab-5::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_MAB-5_GFP_Embryo_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_MAB-5_GFP_Embryo_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183674_Snyder_MAB-5_GFP_Emb_rep2-1.bedgraph.gz GSM1183672 Embryo NA GSE48712 MAB-5_GFP_Embryo_ChIP_Rep1 embryo OP27(official name : OP27 genotype : unc-119(ed3); wgIs27(mab-5::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The MAB-5::EGFP fusion protein is expressed in the correct mab-5 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MAB-5 transcription factor. made_by : Bob Waterston's lab from UW ) Snyder_MAB-5_GFP_Embryo_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 Snyder_MAB-5_GFP_Embryo_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183672_Snyder_MAB-5_GFP_Emb_rep1.bedgraph.gz GSM1183670 Embryo NA GSE48711 F23F12.9_GFP_Emb_ChIP_Rep2 embryo OP327(official name : OP327 genotype : unc327(ed3);wgIs102(F23F12.::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ) Snyder_F23F12.9_GFP_Emb_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_F23F12.9_GFP_Emb_ChIP_Rep2 bg_0_1_2_4_ce10 GSM1183670_Snyder_F23F12.9_GFP_Emb_rep2-1.bedgraph.gz GSM1183668 Embryo NA GSE48711 F23F12.9_GFP_Emb_ChIP_Rep1 embryo OP327(official name : OP327 genotype : unc327(ed3);wgIs102(F23F12.::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ) Snyder_F23F12.9_GFP_Emb_ChIP ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Skip Illumina Data Merging protocol. Two biological replicates of ChIPed samples and one replicate of Input sample(total genomic DNA) were individually sequenced, and then the sequencing files from different biological replicates will be merged for Peak calling. Th sequencing file from one Input sample will serve as an input control for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS180 Snyder_F23F12.9_GFP_Emb_ChIP_Rep1 bg_0_1_2_4_ce10 GSM1183668_Snyder_F23F12.9_GFP_Emb_rep1.bedgraph.gz GSM1056281 Embryo NA GSE43087 sdc-2(y93) fed with sdc-2(RNAi)sdc-2(y93) mutant embryos fed with sdc-2(RNAi) bacteria Embryo GRO-seq WS230 Libraries were sequenced with Illumina¡¯s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further. GRO-seq_y93.sdc2RNAi_Emb other GSM1056281.bigwig GSM1056280 Embryo NA GSE43087 Wild-Type (N2) fed with L4440 Control RNAiWild-type embryos fed with L4440 control RNAi bacteria Embryo GRO-seq WS230 Libraries were sequenced with Illumina¡¯s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further. GRO-seq_controlRNAi_Emb other GSM1056280.bigwig GSM1056292 Embryo NA GSE43087 Wild-type embryos Embryo DPY-27 rabbit was generated in ChIP-Seq WS190 Libraries were sequenced on the Illumina GA2 and HiSeq 2000 platforms. After barcode removal, 32 bp reads were aligned uniquely to the C. elegans WS190 genome using bowtie. DPY-27_ChIP-seq bd_0_1_2_6_ce10 UsingSRR GSM1056279 Embryo NA GSE43087 Wild-Type (N2)Wild-type embryos Embryo GRO-seq WS230 Libraries were sequenced with Illumina¡¯s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further. GRO-seq_N2_Emb other GSM1056279.bigwig GSM1138403 Embryo NA GSE46779 NHR-12 EMB ChIPRep2 embryo OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW ) NHR-12 GFP EMB C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 NHR-12 GFP EMB C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138403_Snyder_NHR-12_GFP_EMB_GFP_rep_2_120120_SPADE_00132_FC63A5M_L7_TGCT.bedgraph.gz GSM1138402 Embryo NA GSE46779 NHR-12 EMB ChIPRep1 embryo OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW ) NHR-12 GFP EMB C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 NHR-12 GFP EMB C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138402_Snyder_NHR-12_GFP_EMB_GFP_rep_1_120120_SPADE_00132_FC63A5M_L7_ACGT.bedgraph.gz GSM1138395 Embryo NA GSE46777 ELT-3 EMB ChIPRep2 embryo OP75(official name : OP75 genotype : unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. made_by : R Waterston ) ELT-3 GFP EMB C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 ELT-3 GFP EMB C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138395_Snyder_ELT-3_GFP_EMB_GFP_rep_2_120106_ROCKFORD_00116_FC64YG3_L6_TGCT.bedgraph.gz GSM1138394 Embryo NA GSE46777 ELT-3 EMB ChIPRep1 embryo OP75(official name : OP75 genotype : unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. made_by : R Waterston ) ELT-3 GFP EMB C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. Peak Calling protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 ELT-3 GFP EMB C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138394_Snyder_ELT-3_GFP_EMB_GFP_rep_1_120106_ROCKFORD_00116_FC64YG3_L6_ACGT.bedgraph.gz GSM1138387 Embryo NA GSE46775 UNC-39 EMB ChIPRep2 embryo OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ) UNC-39 GFP EMB C.elegans ChIP Rep2 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 UNC-39 GFP EMB C.elegans ChIP Rep2 bg_0_1_2_4_ce10 GSM1138387_Snyder_UNC-39_GFP_EMB_GFP_rep_2_111129_COLUMBO_00128_FC6376J_L3_CATT.bedgraph.gz GSM1138386 Embryo NA GSE46775 UNC-39 EMB ChIPRep1 embryo OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ) UNC-39 GFP EMB C.elegans ChIP Rep1 ChIP-Seq WS220 Illumina Data Analysis protocol. We used the recommended Illumina Data Analysis pipeline to process raw image files produced by the Genome Analyzer and generate aligned sequence reads. Illumina Data Merging protocol. This data analysis step effectively merges the processed data from each biological replicate (i.e., all of the high quality, unique, control ChIP-seq reads end up in one file, and all of the high quality, unique, experimental ChIP-seq reads end up in another file.These two files will become the input for the PeakSeq base calling algorithm. ChIP-seq replicate verification protocol. The PeakSeq method treats each aligned sequence read as a 200 nt fragment. The number of reads at each genomic site is counted, and compared to both a randomized model of the worm genome, and the number of parallel reads obtained from sequencing the input (non-ChIP) DNA. These calculations result in an enrichment ratio and a corresponding P-value. Processed data are obtained using following parameters: genome version is WS220 UNC-39 GFP EMB C.elegans ChIP Rep1 bg_0_1_2_4_ce10 GSM1138386_Snyder_UNC-39_GFP_EMB_GFP_rep_1_111129_COLUMBO_00128_FC6376J_L3_GTAT.bedgraph.gz GSM391297 Embryo NA GSE15628 pha-4 transgenic worm OP37 embryo OP37 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. Pha-4 emb replicate 2 POL II bd_0_1_2_6_ce10 UsingSRR GSM391296 Embryo NA GSE15628 pha-4 transgenic worm OP37 embryo OP37 POLR2A ChIP-Seq Sequence reads were aligned to the reference genome, and the fragment count at any given position was estimated as the number of uniquely aligned reads oriented towards it and within 200?bp. Pha-4 emb replicate 1 POL II bd_0_1_2_6_ce10 UsingSRR