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

Transcription factors genomic maps in D. melanogaster whole animals from the following developmental stages: embryonic stages 0-4h, 4-8h, 12-16h, 16-20h, 20-24h, larval stages L1, L2, and L3, pupal stage and adult male and female.

• Raw data was downloaded from: Provide the website and link to raw data
• Input file format: SRA, TXT, BED, ...
• Download date: 12-10-2017

From D. melanogaster (Apr 2006 BDGP R5/dm3).

ChIP-seq data:

	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

Notes on samples nomenclature:

• E0-4, embryos 0-4 hours (h) after egg lay (AEL);
• E4-8, embryos 4-8h AEL;
• E8-12, embryos 8-12h AEL;
• E12-16, embryos 12-16h AEL;
• E16-20, embryos 16-20h AEL;
• E20-24, embryos 20-24h AEL;
• L1, first larval instar;
• L2, second larval instar;
• L3, third larval instar.

For many samples it was not possible to determine at which stage they were collected. For example: WPP, 5T, 7t, 10T, 15T.

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Morrison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP
  A cis-regulatory map of the Drosophila genome. Nature. 2011 Mar 24;471(7339):527-31. doi: 10.1038/nature09990. 21430782
• GEO series GSE23537: modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data