GSE23537, ChIP-seq of TFs on larva's developmental stages

Description

This SuperSeries is composed of the following subset Series:
GSE23122: modENCODE_White Lab: genome-wide ChIP data of Sin3A from E0-12h on Illumina Genome Analyzer.
GSE23123: modENCODE_White Lab: genome-wide ChIP data of hkb from E8-16h on Illumina Genome Analyzer.
GSE23124: modENCODE_White Lab: genome-wide ChIP data of GFP from 10T-W3L on Illumina Genome Analyzer.
GSE23126: modENCODE_White Lab: genome-wide ChIP data of GFP from 10T-E16-24h on Illumina Genome Analyzer.
GSE23127: modENCODE_White Lab: genome-wide ChIP data of Pcl from E0-8h on Illumina Genome Analyzer.
GSE23144: modENCODE_White Lab: genome-wide ChIP data of disco from E0-8h on Illumina Genome Analyzer.
GSE23145: modENCODE_White Lab: genome-wide ChIP data of 3dFemale from 7T on Illumina Genome Analyzer.
GSE23146: modENCODE_White Lab: genome-wide ChIP data of Trl from E16-24h on Illumina Genome Analyzer.
GSE23147: modENCODE_White Lab: genome-wide ChIP data of kni from E8-16h on Illumina Genome Analyzer.
GSE23148: modENCODE_White Lab: genome-wide ChIP data of CBP from E0-4h on Illumina Genome Analyzer.
GSE23149: modENCODE_White Lab: genome-wide ChIP data of K4me3 from Kc on Illumina Genome Analyzer.
GSE23150: modENCODE_White Lab: genome-wide ChIP data of Trl-D2 from Kc on Illumina Genome Analyzer.
GSE23237: modENCODE_White Lab: genome-wide ChIP data of disco from E8-16h on Illumina Genome Analyzer.
GSE24136: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[tll] from E0-4h on Illumina Genome Analyzer.
GSE24137: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[Dfd] from E0-8h on Illumina Genome Analyzer.
GSE24139: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[eve] from E1-6h on Illumina Genome Analyzer.
GSE24140: modENCODE_White Lab: genome-wide ChIP data of KW4-CG8478-D1 from E8-16h on Illumina Genome Analyzer.
GSE24143: modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[eve] from E8-16h on Illumina Genome Analyzer.
GSE25026: modENCODE_White Lab: genome-wide ChIP data of Trl from E0-8h on Illumina Genome Analyzer.
GSE25027: modENCODE_White Lab: genome-wide ChIP data of CG8478 from E16-24h on Illumina Genome Analyzer.
GSE25239: modENCODE_White Lab: genome-wide ChIP data of GFP from 5T-0-6 on Illumina Genome Analyzer.
GSE25240: modENCODE_White Lab: genome-wide ChIP data of GFP from E16-24h on Illumina Genome Analyzer.
GSE25241: modENCODE_White Lab: genome-wide ChIP data of GFP from ECR-WPP+12 on Illumina Genome Analyzer.
GSE25242: modENCODE_White Lab: genome-wide ChIP data of GFP from ECR-WPP+90 on Illumina Genome Analyzer.
GSE25259: modENCODE_White Lab: genome-wide ChIP-chip data
GSE25559: modENCODE_White Lab: genome-wide ChIP data of KW4-Hr39-D1 from E16-24h on Illumina Genome Analyzer.
GSE25560: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from E8-16h on Illumina Genome Analyzer.
GSE25562: modENCODE_White Lab: genome-wide ChIP data of HP1-Covance from E16-24h on Illumina Genome Analyzer.
GSE25563: modENCODE_White Lab: genome-wide ChIP data of HP1-Abcam from E16-24h on Illumina Genome Analyzer.
GSE25565: modENCODE_White Lab: genome-wide ChIP data of GFP from 15T_8-16_NW on Illumina Genome Analyzer.
GSE25566: modENCODE_White Lab: genome-wide ChIP data of Trem from Adult-Female on Illumina Genome Analyzer.
GSE25567: modENCODE_White Lab: genome-wide ChIP data of KW3-D-D2 from E0-8h_D on Illumina Genome Analyzer.
GSE25568: modENCODE_White Lab: genome-wide ChIP data of GFP from 7T_W3L on Illumina Genome Analyzer.
GSE25569: modENCODE_White Lab: genome-wide ChIP data of GFP from EcR_WPP-4-5h on Illumina Genome Analyzer.
GSE25917: modENCODE_White Lab: genome-wide ChIP data of GFP from 5T-8-16h on Illumina Genome Analyzer.
GSE25918: modENCODE_White Lab: genome-wide ChIP data of GFP from R13-E1-6h-Set2 on Illumina Genome Analyzer.
GSE25919: modENCODE_White Lab: genome-wide ChIP data of KW3-Kr-D2 from E16-24h on Illumina Genome Analyzer.
GSE25920: modENCODE_White Lab: genome-wide ChIP data of Su[var]3-9 from E0-12h on Illumina Genome Analyzer.
GSE25921: modENCODE_White Lab: genome-wide ChIP data of anti-Bonus-[GP37] from E16-24h on Illumina Genome Analyzer.
GSE25646: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.yak_E0-4h on Illumina Genome Analyzer.
GSE25650: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.yak_WPP on Illumina Genome Analyzer.
GSE25654: modENCODE_White Lab: genome-wide ChIP data of KW3-Kr-D2 from D.yak_E0-4h on Illumina Genome Analyzer.
GSE25655: modENCODE_White Lab: genome-wide ChIP data of KW3-Psq-D2 from D.yak_E0-4h on Illumina Genome Analyzer.
GSE25657: modENCODE_White Lab: genome-wide ChIP data of KW3-Pcl-D2 from D.yak_E0-4h on Illumina Genome Analyzer.
GSE25658: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.sim_E0-4h on Illumina Genome Analyzer.
GSE25659: modENCODE_White Lab: genome-wide ChIP data of KW3-Kr-D2 from D.sim_E0-4h on Illumina Genome Analyzer.
GSE25660: modENCODE_White Lab: genome-wide ChIP data of KW3-Pcl-D2 from D.sim_E0-4h on Illumina Genome Analyzer.
GSE25662: modENCODE_White Lab: genome-wide ChIP data of KW3-Pcl-D2 from D.sim_WPP on Illumina Genome Analyzer.
GSE25663: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.sim_WPP on Illumina Genome Analyzer.
GSE25664: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.sim_E0-4h on Illumina Genome Analyzer.
GSE25665: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.pse_E0-4h on Illumina Genome Analyzer.
GSE25666: modENCODE_White Lab: genome-wide ChIP data of KW3-Psq-D2 from D.pse_E0-4h on Illumina Genome Analyzer.
GSE25667: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from D.pse_E0-4h on Illumina Genome Analyzer.
GSE25668: modENCODE_White Lab: genome-wide ChIP data of H3K27me3 from D.pse_WPP on Illumina Genome Analyzer.
GSE26793: Genome-wide binding of Ubx and Hth in 3rd thoracic imaginal discs
GSE27102: modENCODE_White Lab: genome-wide ChIP data of KW3-h-D1 from E8-16h on Illumina Genome Analyzer.
GSE27103: modENCODE_White Lab: genome-wide ChIP data of GFP from EcR_mF3d on Illumina Genome Analyzer.
GSE27104: modENCODE_White Lab: genome-wide ChIP data of KW4-Fer3-D1 from E16-24h on Illumina Genome Analyzer.
GSE27106: modENCODE_White Lab: genome-wide ChIP data of anti-cbt from E16-24h on Illumina Genome Analyzer.
GSE27107: modENCODE_White Lab: genome-wide ChIP data of Yki-91 from E0-4 on Illumina Genome Analyzer.
GSE27108: modENCODE_White Lab: genome-wide ChIP data of exd-GFP from E16-24h_13T on Illumina Genome Analyzer.
GSE27109: modENCODE_White Lab: genome-wide ChIP data of KW3-Trl-D2 from WPP on Illumina Genome Analyzer.
GSE27110: modENCODE_White Lab: genome-wide ChIP data of Hr4_GFP from E0-12 on Illumina Genome Analyzer.
GSE27111: modENCODE_White Lab: genome-wide ChIP data of K27me3 from WPP on Illumina Genome Analyzer.
GSE27118: modENCODE_White Lab: genome-wide ChIP data of core from BRC on Illumina Genome Analyzer.
GSE32661: modENCODE_White Lab: genome-wide ChIP data of CNC from WPP on Illumina Genome Analyzer.
GSE34182: modENCODE_White Lab: genome-wide ChIP data of CNC from AdultFemale on Illumina Genome Analyzer.
GSE34342: modENCODE_White Lab: genome-wide ChIP data of CNC from AdultMale on Illumina Genome Analyzer.
GSE34343: modENCODE_White Lab: genome-wide ChIP data of Ash2 from E0-12 on Illumina Genome Analyzer.
GSE34345: modENCODE_White Lab: genome-wide ChIP data of Prd from E0-12 on Illumina Genome Analyzer.
GSE34347: modENCODE_White Lab: genome-wide ChIP data of sc from E0-12 on Illumina Genome Analyzer.
GSE34348: modENCODE_White Lab: genome-wide ChIP data of br-core from E0-8 on Illumina Genome Analyzer.
GSE34350: modENCODE_White Lab: genome-wide ChIP data of dm from E0-8 on Illumina Genome Analyzer.
GSE34352: modENCODE_White Lab: genome-wide ChIP data of CG16778 from E16-24 on Illumina Genome Analyzer.
GSE34354: modENCODE_White Lab: genome-wide ChIP data of CNC from E16-24 on Illumina Genome Analyzer.
GSE34357: modENCODE_White Lab: genome-wide ChIP data of Fru from E16-24 on Illumina Genome Analyzer.
GSE34358: modENCODE_White Lab: genome-wide ChIP data of sr from E16-24 on Illumina Genome Analyzer.
GSE34359: modENCODE_White Lab: genome-wide ChIP data of SuH from E16-24 on Illumina Genome Analyzer.
GSE34360: modENCODE_White Lab: genome-wide ChIP data of HP1 from E8-16 on Illumina Genome Analyzer.
GSE34361: modENCODE_White Lab: genome-wide ChIP data of Hth from E8-16 on Illumina Genome Analyzer.
GSE34362: modENCODE_White Lab: genome-wide ChIP data of jim from E8-16 on Illumina Genome Analyzer.
GSE34367: modENCODE_White Lab: genome-wide ChIP data of sr from E8-16 on Illumina Genome Analyzer.
GSE34371: modENCODE_White Lab: genome-wide ChIP data of SuH from E8-16 on Illumina Genome Analyzer.
GSE34372: modENCODE_White Lab: genome-wide ChIP data of dCTBP from Kc167 on Illumina Genome Analyzer.
GSE34373: modENCODE_White Lab: genome-wide ChIP data of Kr from Kc167 on Illumina Genome Analyzer.
GSE34374: modENCODE_White Lab: genome-wide ChIP data of psq from Kc167 on Illumina Genome Analyzer.
GSE34376: modENCODE_White Lab: genome-wide ChIP data of Sin3A from Kc167 on Illumina Genome Analyzer.
GSE34377: modENCODE_White Lab: genome-wide ChIP data of en from W3L on Illumina Genome Analyzer.
GSE34385: modENCODE_White Lab: genome-wide ChIP data of psq from WPP on Illumina Genome Analyzer.
GSE34386: modENCODE_White Lab: genome-wide ChIP data of Stat92E from WPP on Illumina Genome Analyzer.
GSE34431: modENCODE_White Lab: genome-wide ChIP data of CG8478 from WPP on Illumina Genome Analyzer.
GSE34597: modENCODE_White Lab: genome-wide ChIP data of FAIRE from CNS on Illumina Genome Analyzer.
GSE34598: modENCODE_White Lab: genome-wide ChIP data of USP from E0-12 on Illumina Genome Analyzer.
GSE34601: modENCODE_White Lab: genome-wide ChIP data of CG16778 from E0-8 on Illumina Genome Analyzer.
GSE34604: modENCODE_White Lab: genome-wide ChIP data of Hth from E0-8 on Illumina Genome Analyzer.
GSE34609: modENCODE_White Lab: genome-wide ChIP data of TCF from E0-8 on Illumina Genome Analyzer.
GSE34610: modENCODE_White Lab: genome-wide ChIP data of Hnf4 from E16-24 on Illumina Genome Analyzer.
GSE34611: modENCODE_White Lab: genome-wide ChIP data of SuHw from E16-24 on Illumina Genome Analyzer.
GSE34613: modENCODE_White Lab: genome-wide ChIP data of Dfd from E0-8 on Illumina Genome Analyzer.
GSE34693: modENCODE_White Lab: genome-wide ChIP data of TCF from E16-24 on Illumina Genome Analyzer.
GSE34694: modENCODE_White Lab: genome-wide ChIP data of Ttk from E16-24 on Illumina Genome Analyzer.
GSE34695: modENCODE_White Lab: genome-wide ChIP data of Bcd from E8-16 on Illumina Genome Analyzer.
GSE34696: modENCODE_White Lab: genome-wide ChIP data of Tango from Kc167 on Illumina Genome Analyzer.
GSE34698: modENCODE_White Lab: genome-wide ChIP data of Ttk from Kc167 on Illumina Genome Analyzer.
GSE34699: modENCODE_White Lab: genome-wide ChIP data of Yki from Kc167 on Illumina Genome Analyzer.
GSE34700: modENCODE_White Lab: genome-wide ChIP data of Zfh1 from Kc167 on Illumina Genome Analyzer.
GSE34701: modENCODE_White Lab: genome-wide ChIP data of modmdg4 from W3L on Illumina Genome Analyzer.
GSE34703: modENCODE_White Lab: genome-wide ChIP data of USP from WPP+12 on Illumina Genome Analyzer.
GSE34704: modENCODE_White Lab: genome-wide ChIP data of H3K4me3 from WPP on Illumina Genome Analyzer.
GSE34706: modENCODE_White Lab: genome-wide ChIP data of SuHw from WPP on Illumina Genome Analyzer.
GSE34707: modENCODE_White Lab: genome-wide ChIP data of Usp from W3L on Illumina Genome Analyzer.
GSE34708: modENCODE_White Lab: genome-wide ChIP data of Ubx from E0-12 on Illumina Genome Analyzer.
GSE34710: modENCODE_White Lab: genome-wide ChIP data of Fru from E0-8 on Illumina Genome Analyzer.
GSE34712: modENCODE_White Lab: genome-wide ChIP data of sc from E0-8 on Illumina Genome Analyzer.
GSE34713: modENCODE_White Lab: genome-wide ChIP data of sim from E0-8 on Illumina Genome Analyzer.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Source

Files downloaded from FTP site: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP003/SRP003255
Input file format: SRA

Samples

From Fruit Fly Apr. 2006 (R5/dm3) Assembly

Filename Description Feature GEO-ID
1 GSM570049.sga E0-4h rbCBP rbCBP GSM570049
2 GSM570050.sga E0-4h rbCBP Input Input GSM570050
3 GSM594213.sga E0-4h NW-GFP-Goat[tll] NW-GFP-Goat[tll] GSM594213
4 GSM594214.sga E0-4h NW-GFP-Goat[tll] Input rep1 Input GSM594214
5 GSM594215.sga E0-4h NW-GFP-Goat[tll] Input rep2 Input GSM594215
6 GSM669539.sga E0-4 Yki-91 Yki-91 GSM669539
7 GSM669540.sga E0-4 Yki-91 Input Input GSM669540
8 GSM594216.sga E0-8h NW-GFP-Goat[Dfd] NW-GFP-Goat[Dfd] GSM594216
9 GSM594217.sga E0-8h NW-GFP-Goat[Dfd] Input rep1 Input GSM594217
10 GSM594218.sga E0-8h NW-GFP-Goat[Dfd] Input rep2 Input GSM594218
11 GSM569800.sga E0-8h KW4-Pcl-D2 KW4-Pcl-D2 GSM569800
12 GSM569801.sga E0-8h KW4-Pcl-D2 Input Input GSM569801
13 GSM570038.sga E0-8h KW3-disco-D2 KW3-disco-D2 GSM570038
14 GSM570039.sga E0-8h KW3-disco-D2 Input Input GSM570039
15 GSM628262.sga E0-8h_D KW3-D-D2 KW3-D-D2 GSM628262
16 GSM614652.sga E0-8h Trl Trl GSM614652
17 GSM614653.sga E0-8h Trl Input rep1 Input GSM614653
18 GSM614654.sga E0-8h Trl Input rep2 Input GSM614654
19 GSM847657.sga E0-8 br-core br-core GSM847657
20 GSM847658.sga E0-8 br-core Input Input GSM847658
21 GSM847659.sga E0-8 dm dm GSM847659
22 GSM847660.sga E0-8 dm Input Input GSM847660
23 GSM851729.sga E0-8 CG16778 CG16778 GSM851729
24 GSM851730.sga E0-8 CG16778 Input Input GSM851730
25 GSM851743.sga E0-8 Hth Hth GSM851743
26 GSM851744.sga E0-8 Hth Input Input GSM851744
27 GSM851817.sga E0-8 TCF TCF GSM851817
28 GSM851818.sga E0-8 TCF Input Input GSM851818
29 GSM851848.sga E0-8 Dfd Dfd GSM851848
30 GSM851849.sga E0-8 Dfd Input Input GSM851849
31 GSM853488.sga E0-8 Fru Fru GSM853488
32 GSM853489.sga E0-8 Fru Input Input GSM853489
33 GSM853490.sga E0-8 sc sc GSM853490
34 GSM853491.sga E0-8 sim sim GSM853491
35 GSM636838.sga E0-12h Su[var]3-9 Su[var]3-9 GSM636838
36 GSM636839.sga E0-12h Su[var]3-9 Input Input GSM636839
37 GSM847577.sga E0-12 Ash2 Ash2 GSM847577
38 GSM847578.sga E0-12 Ash2 Input Input GSM847578
39 GSM847619.sga E0-12 Prd Prd GSM847619
40 GSM847656.sga E0-12 sc sc GSM847656
41 GSM851706.sga E0-12 USP USP GSM851706
42 GSM851707.sga E0-12 USP Input Input GSM851707
43 GSM853486.sga E0-12 Ubx Ubx GSM853486
44 GSM669545.sga E0-12 Hr4_GFP Hr4_GFP GSM669545
45 GSM669546.sga E0-12 Hr4_GFP Input Input GSM669546
46 GSM569791.sga E0-12h Sin3A Sin3A GSM569791
47 GSM569792.sga E0-12h SIn3A Input Input GSM569792
48 GSM594222.sga E1-6h NW-GFP-Goat[eve] NW-GFP-Goat[eve] GSM594222
49 GSM594223.sga E1-6h NW-GFP-Goat[eve] Input rep1 Input GSM594223
50 GSM594224.sga E1-6h NW-GFP-Goat[eve] Input rep2 Input GSM594224
51 GSM569793.sga E8-16h KW3-hkb-D1 KW3-hkb-D1 GSM569793
52 GSM569794.sga E8-16h KW3-hkb-D1 Input Input GSM569794
53 GSM570045.sga E8-16h KW3-kni-D2 KW3-kni-D2 GSM570045
54 GSM570046.sga E8-16h Kni Input rep1 Input GSM570046
55 GSM570047.sga E8-16h Kni Input rep2 Input GSM570047
56 GSM570048.sga E8-16h Kni Input rep3 Input GSM570048
57 GSM628226.sga E8-16h KW3-Trl-D2 KW3-Trl-D2 GSM628226
58 GSM628227.sga E8-16h KW3-Trl-D2 Input Input GSM628227
59 GSM570043.sga E16-24h KW3-Trl-D2 KW3-Trl-D2 GSM570043
60 GSM570044.sga E16-24h Trl Input Input GSM570044
61 GSM571141.sga E8-16h KW3-disco-D2 KW3-disco-D2 GSM571141
62 GSM571140.sga E8-16h disco Input Input GSM571140
63 GSM594225.sga E8-16h KW4-CG8478-D1 KW4-CG8478-D1 GSM594225
64 GSM594226.sga E8-16h CG8478 Input Input GSM594226
65 GSM594245.sga E8-16h NW-GFP-Goat[eve] NW-GFP-Goat[eve] GSM594245
66 GSM594246.sga E8-16h NW-GFP-Goat[eve] Input Input GSM594246
67 GSM669472.sga E8-16h KW3-h-D1 KW3-h-D1 GSM669472
68 GSM847702.sga E8-16 HP1 HP1 GSM847702
69 GSM847703.sga E8-16 Input Input GSM847703
70 GSM847704.sga E8-16 Hth Hth GSM847704
71 GSM847705.sga E8-16 Hth Input Input GSM847705
72 GSM847706.sga E8-16 jim jim GSM847706
73 GSM847707.sga E8-16 jim Input Input GSM847707
74 GSM847752.sga E8-16 sr sr GSM847752
75 GSM847753.sga E8-16 sr Input Input GSM847753
76 GSM847767.sga E8-16 SuH SuH GSM847767
77 GSM853471.sga E8-16 Bcd Bcd GSM853471
78 GSM853472.sga E8-16 Bcd Input Input GSM853472
79 GSM614655.sga E16-24h CG8478 CG8478 GSM614655
80 GSM614657.sga E16-24h CG8478 Input Input GSM614657
81 GSM847673.sga E16-24 CG16778 CG16778 GSM847673
82 GSM847675.sga E16-24 CNC CNC GSM847675
83 GSM621130.sga E16-24h GFP GFP GSM621130
84 GSM621131.sga E16-24h GFP Input Input GSM621131
85 GSM628224.sga E16-24h KW4-Hr39-D1 KW4-Hr39-D1 GSM628224
86 GSM628225.sga E16-24h KW4-Hr39-D1 Input Input GSM628225
87 GSM636835.sga E16-24h KW3-Kr-D2 KW3-Kr-D2 GSM636835
88 GSM636836.sga E16-24h KW3-Kr Input rep1 Input GSM636836
89 GSM636837.sga E16-24h KW3-Kr Input rep2 Input GSM636837
90 GSM669477.sga E16-24h KW4-Fer3-D1 KW4-Fer3-D1 GSM669477
91 GSM669478.sga E16-24h KW4-Fer3 Input Input GSM669478
92 GSM628251.sga E16-24h HP1-Covance HP1-Covance GSM628251
93 GSM628252.sga E16-24h HP1-Abcam HP1-Abcam GSM628252
94 GSM628253.sga E16-24h HP1-Abcam-Covance Input Input GSM628253
95 GSM669537.sga E16-24h anti-cbt anti-cbt GSM669537
96 GSM669538.sga E16-24h anti-cbt Input Input GSM669538
97 GSM669541.sga E16-24h_13T exd-GFP exd-GFP GSM669541
98 GSM669542.sga E16-24h_13T exd-GFP Input Input GSM669542
99 GSM851839.sga E16-24 Hnf4 Hnf4 GSM851839
100 GSM851840.sga E16-24 Hnf4 Input Input GSM851840
101 GSM851841.sga E16-24 SuHw SuHw GSM851841
102 GSM851842.sga E16-24 SuHw Input Input GSM851842
103 GSM853468.sga E16-24 TCF TCF GSM853468
104 GSM853469.sga E16-24 TCF Input Input GSM853469
105 GSM853470.sga E16-24 Ttk Ttk GSM853470
106 GSM636840.sga E16-24h anti-Bonus-[GP37] anti-Bonus-[GP37] GSM636840
107 GSM636841.sga E16-24h Input Input GSM636841
108 GSM847676.sga E16-24 Input Input GSM847676
109 GSM847696.sga E16-24 Fru Fru GSM847696
110 GSM847697.sga E16-24 Input Input GSM847697
111 GSM847698.sga E16-24 sr sr GSM847698
112 GSM847699.sga E16-24 Input Input GSM847699
113 GSM847700.sga E16-24 SuH SuH GSM847700
114 GSM847701.sga E16-24 Input Input GSM847701
115 GSM621132.sga ECR-WPP+12 GFP GFP GSM621132
116 GSM621133.sga ECR-WPP+12 Input Input GSM621133
117 GSM621134.sga ECR-WPP+90 GFP GFP GSM621134
118 GSM621135.sga ECR-WPP+90 Input Input GSM621135
119 GSM628268.sga EcR_WPP-4-5h GFP GFP GSM628268
120 GSM628269.sga EcR_WPP-4-5h Input rep1 Input GSM628269
121 GSM628270.sga EcR_WPP-4-5h Input rep2 Input GSM628270
122 GSM669474.sga EcR_mF3d GFP GFP GSM669474
123 GSM669475.sga EcR_mF3d Input rep1 Input GSM669475
124 GSM669476.sga EcR_mF3d Input rep2 Input GSM669476
125 GSM628259.sga Adult-Female Trem Trem GSM628259
126 GSM628260.sga Adult-Female Input Input GSM628260
127 GSM843544.sga AdultFemale CNC CNC GSM843544
128 GSM843545.sga AdultFemale Input Input GSM843545
129 GSM847575.sga AdultMale CNC CNC GSM847575
130 GSM847576.sga AdultMale Input Input GSM847576
131 GSM570040.sga 3dFemale NWG-GFP NWG-GFP GSM570040
132 GSM570041.sga 3dFemale Input rep1 Input GSM570041
133 GSM570042.sga 3dFemale Input rep2 Input GSM570042
134 GSM621128.sga 5T-0-6 GFP GFP GSM621128
135 GSM621129.sga 5T-0-6 GFP Input Input GSM621129
136 GSM636830.sga 5T-8-16h GFP GFP GSM636830
137 GSM636831.sga 5T-8-16h GFP Input Input GSM636831
138 GSM628264.sga 7T_W3L GFP GFP GSM628264
139 GSM628265.sga 7T_W3L GFP Input rep1 Input GSM628265
140 GSM628266.sga 7T_W3L GFP Input rep2 Input GSM628266
141 GSM628267.sga 7T_W3L GFP Input rep3 Input GSM628267
142 GSM569795.sga 10T-W3L NWG-GFP NWG-GFP GSM569795
143 GSM569796.sga 10T-W3L Input rep1 Input GSM569796
144 GSM569797.sga 10T-W3L Input rep2 Input GSM569797
145 GSM569798.sga 10T-E16-24h NWG-GFP NWG-GFP GSM569798
146 GSM569799.sga 10T-E16-24h Input Input GSM569799
147 GSM628255.sga 15T_8-16_NW GFP GFP GSM628255
148 GSM628256.sga 15T_8-16_NW Input Input GSM628256
149 GSM570051.sga Kc H3K4me3-LP H3K4me3-LP GSM570051
150 GSM570052.sga Kc H3K4me3-LP Input rep1 Input GSM570052
151 GSM570053.sga Kc H3K4me3-LP Input rep2 Input GSM570053
152 GSM570054.sga Kc KW3-Trl-D2 KW3-Trl-D2 GSM570054
153 GSM847768.sga Kc167 dCTBP dCTBP GSM847768
154 GSM847769.sga Kc167 dCTBP Input Input GSM847769
155 GSM847770.sga Kc167 Kr Kr GSM847770
156 GSM847771.sga Kc167 Kr Input Input GSM847771
157 GSM847772.sga Kc167 psq psq GSM847772
158 GSM847773.sga Kc167 psq Input Input GSM847773
159 GSM847774.sga Kc167 Sin3A Sin3A GSM847774
160 GSM853473.sga Kc167 Tango Tango GSM853473
161 GSM853474.sga Kc167 Ttk Ttk GSM853474
162 GSM853475.sga Kc167 Yki Yki GSM853475
163 GSM853476.sga Kc167 Zfh1 Zfh1 GSM853476
164 GSM636832.sga R13-E1-6h-Set2 GFP GFP GSM636832
165 GSM636833.sga R13-E1-6h-Set2 GFP Input rep1 Input GSM636833
166 GSM636834.sga R13-E1-6h-Set2 GFP Input rep2 Input GSM636834
167 GSM847775.sga W3L en en GSM847775
168 GSM847776.sga W3L en Input Input GSM847776
169 GSM853484.sga W3L Usp Usp GSM853484
170 GSM853485.sga W3L Usp Input Input GSM853485
171 GSM853477.sga W3L modmdg4 modmdg4 GSM853477
172 GSM853478.sga W3L modmdg4 Input Input GSM853478
173 GSM669543.sga WPP KW3-Trl-D2 KW3-Trl-D2 GSM669543
174 GSM669544.sga WPP KW3-Trl-D2 Input Input GSM669544
175 GSM810644.sga WPP CNC CNC GSM810644
176 GSM810645.sga WPP CNC Input Input GSM810645
177 GSM669547.sga WPP K27me3 K27me3 GSM669547
178 GSM669548.sga WPP K27me3 Input Input GSM669548
179 GSM847952.sga WPP psq psq GSM847952
180 GSM847953.sga WPP psq Input Input GSM847953
181 GSM847954.sga WPP Stat92E Stat92E GSM847954
182 GSM847955.sga WPP Stat92E Input Input GSM847955
183 GSM848956.sga WPP CG8478 CG8478 GSM848956
184 GSM853481.sga WPP H3K4me3 H3K4me3 GSM853481
185 GSM853482.sga WPP H3K4me3 Input Input GSM853482
186 GSM853483.sga WPP SuHw SuHw GSM853483
187 GSM853479.sga WPP+12 USP USP GSM853479
188 GSM853480.sga WPP+12 USP Input Input GSM853480
189 GSM669694.sga BRC core core GSM669694
190 GSM669695.sga BRC core Input Input GSM669695
191 GSM851705.sga CNS FAIRE FAIRE GSM851705

Technical Notes

SRA files were downloaded from GEO and processed using the following bash commands:

  1. Extract FASTQ from SRA file:
    fastq-dump SAMPLE.sra
    
  2. Map reads to genome using Bowtie:
    bowtie --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -q SAMPLE.fastq > SAMPLE.sam
    
  3. Clean the results from unmapped reads:
    awk 'BEGIN {FS="\t"} $3 != "\*" {print $0}' SAMPLE.sam > SAMPLE_clean.sam
    
  4. Make BAM file:
    samtools view -bS -o SAMPLE.bam SAMPLE_clean.sam
    
  5. Sort it:
    samtools sort SAMPLE.bam SAMPLE_sorted
    
  6. Make BED file:
    bamToBed -i SAMPLE_sorted.bam > SAMPLE.bed
    
  7. Make SGA file:
    bed2sga.pl -s hg18 -f FEATURE < SAMPLE.bed | sort -s -k1,1 -k3,3n -k4,4 | compactsga > SAMPLE.sga
    

References

  1. Nègre N, Brown CD, et al.
    A cis-regulatory map of the Drosophila genome Nature 471, 527-531 (24 March 2011). PMID: 21430782

  2. GEO series GSE23537 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data.