Kranz 2013, Genome-wide analysis of condensin binding.

ChIP-seq experiments on several subunits of condensine I (DPY26, DPY28), II (KLE2, HCP6, CAPG2) and IDC (CAPG1, DPY27) complexis along with condensine loader SCC-2 (PQN85) in WT embryos of mixed stages (WT), wild type embryos in L3 stage (WT L3) and mutants of the sdc-2 (TY1072) protein, a condensine recruter.

• Raw data was downloaded from: Provide the website and link to raw data
• Input file format: SRA, TXT, BED, ...
• Download date: 19-9-2017

From C. elegans (Oct 2010 WBcel215/ce10).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	N2_L3_KLE2.sga	WT L3|KLE2|All	KLE2	-
2	GSM1200339.sga	WT L3|KLE2|Rep1	KLE2	GSM1200339
3	GSM1200340.sga	WT L3|KLE2|Rep2	KLE2	GSM1200340
4	GSM1200341.sga	WT L3|KLE2|Rep3	KLE2	GSM1200341
5	GSM1200342.sga	WT L3|KLE2|Rep4	KLE2	GSM1200342
6	N2_L3_Input.sga	WT L3|Input|All	Input	-
7	GSM1200343.sga	WT L3|Input|Rep1	Input	GSM1200343
8	GSM1200344.sga	WT L3|Input|Rep2	Input	GSM1200344
9	TY1072_DPY26.sga	TY1072|DPY26|All	DPY26	-
10	GSM1111775.sga	TY1072|DPY26|Rep1	DPY26	GSM1111775
11	GSM1111776.sga	TY1072|DPY26|Rep2	DPY26	GSM1111776
12	TY1072_HCP6.sga	TY1072|HCP6|All	HCP6	-
13	GSM1111789.sga	TY1072|HCP6|Rep1	HCP6	GSM1111789
14	GSM1111790.sga	TY1072|HCP6|Rep2	HCP6	GSM1111790
15	TY1072_KLE2.sga	TY1072|KLE2|All	KLE2	-
16	GSM1171491.sga	TY1072|KLE2|Rep1	KLE2	GSM1171491
17	GSM1171492.sga	TY1072|KLE2|Rep2	KLE2	GSM1171492
18	TY1072_PQN85.sga	TY1072|PQN85|All	PQN85	-
19	GSM1111804.sga	TY1072|PQN85|Rep1	PQN85	GSM1111804
20	GSM1111805.sga	TY1072|PQN85|Rep2	PQN85	GSM1111805
21	GSM1171493.sga	TY1072|PQN85|Rep3	PQN85	GSM1171493
22	WT_AMA1.sga	WT|AMA1|All	AMA1	-
23	GSM1111760.sga	WT|AMA1|Rep1	AMA1	GSM1111760
24	GSM1111761.sga	WT|AMA1|Rep2	AMA1	GSM1111761
25	WT_CAPG1.sga	WT|CAPG1|All	CAPG1	-
26	GSM1111762.sga	WT|CAPG1|Rep1	CAPG1	GSM1111762
27	GSM1111763.sga	WT|CAPG1|Rep2	CAPG1	GSM1111763
28	GSM1111764.sga	WT|CAPG1|Rep3	CAPG1	GSM1111764
29	WT_CAPG2.sga	WT|CAPG2|All	CAPG2	-
30	GSM1111765.sga	WT|CAPG2|Rep1	CAPG2	GSM1111765
31	GSM1111766.sga	WT|CAPG2|Rep2	CAPG2	GSM1111766
32	GSM1111767.sga	WT|CAPG2|Rep3	CAPG2	GSM1111767
33	GSM1111768.sga	WT|CAPG2|Rep4	CAPG2	GSM1111768
34	GSM1111769.sga	WT|CAPG2|Rep5	CAPG2	GSM1111769
35	WT_DPY26.sga	WT|DPY26|All	DPY26	-
36	GSM1111770.sga	WT|DPY26|Rep1	DPY26	GSM1111770
37	GSM1111771.sga	WT|DPY26|Rep2	DPY26	GSM1111771
38	GSM1111772.sga	WT|DPY26|Rep3	DPY26	GSM1111772
39	GSM1111773.sga	WT|DPY26|Rep4	DPY26	GSM1111773
40	GSM1111774.sga	WT|DPY26|Rep5	DPY26	GSM1111774
41	WT_DPY27.sga	WT|DPY27|All	DPY27	-
42	GSM1111777.sga	WT|DPY27|Rep1	DPY27	GSM1111777
43	GSM1111778.sga	WT|DPY27|Rep2	DPY27	GSM1111778
44	GSM1111779.sga	WT|DPY27|Rep3	DPY27	GSM1111779
45	GSM1111780.sga	WT|DPY27|Rep4	DPY27	GSM1111780
46	WT_DPY28.sga	WT|DPY28|All	DPY28	-
47	GSM1111781.sga	WT|DPY28|Rep1	DPY28	GSM1111781
48	GSM1111782.sga	WT|DPY28|Rep2	DPY28	GSM1111782
49	GSM1111783.sga	WT|DPY28|Rep3	DPY28	GSM1111783
50	GSM1111784.sga	WT|DPY28|Rep4	DPY28	GSM1111784
51	WT_HCP6.sga	WT|HCP6|All	HCP6	-
52	GSM1111785.sga	WT|HCP6|Rep1	HCP6	GSM1111785
53	GSM1111786.sga	WT|HCP6|Rep2	HCP6	GSM1111786
54	GSM1111787.sga	WT|HCP6|Rep3	HCP6	GSM1111787
55	GSM1111788.sga	WT|HCP6|Rep4	HCP6	GSM1111788
56	WT_HTZ.sga	WT|HTZ|All	HTZ	-
57	GSM1111791.sga	WT|HTZ|Rep1	HTZ	GSM1111791
58	GSM1111792.sga	WT|HTZ|Rep2	HTZ	GSM1111792
59	WT_IgG.sga	WT|IgG|All	IgG	-
60	GSM1111809.sga	WT|IgG|Rep1	IgG	GSM1111809
61	GSM1111810.sga	WT|IgG|Rep2	IgG	GSM1111810
62	GSM1111811.sga	WT|IgG|Rep3	IgG	GSM1111811
63	WT_Input.sga	WT|Input|All	Input	-
64	GSM1111812.sga	WT|Input|Rep1	Input	GSM1111812
65	GSM1111821.sga	WT|Input|Rep10	Input	GSM1111821
66	GSM1111822.sga	WT|Input|Rep11	Input	GSM1111822
67	GSM1111823.sga	WT|Input|Rep12	Input	GSM1111823
68	GSM1111824.sga	WT|Input|Rep13	Input	GSM1111824
69	GSM1111825.sga	WT|Input|Rep14	Input	GSM1111825
70	GSM1111826.sga	WT|Input|Rep15	Input	GSM1111826
71	GSM1111827.sga	WT|Input|Rep16	Input	GSM1111827
72	GSM1111828.sga	WT|Input|Rep17	Input	GSM1111828
73	GSM1111829.sga	WT|Input|Rep18	Input	GSM1111829
74	GSM1171494.sga	WT|Input|Rep19	Input	GSM1171494
75	GSM1111813.sga	WT|Input|Rep2	Input	GSM1111813
76	GSM1171495.sga	WT|Input|Rep20	Input	GSM1171495
77	GSM1111814.sga	WT|Input|Rep3	Input	GSM1111814
78	GSM1111815.sga	WT|Input|Rep4	Input	GSM1111815
79	GSM1111816.sga	WT|Input|Rep5	Input	GSM1111816
80	GSM1111817.sga	WT|Input|Rep6	Input	GSM1111817
81	GSM1111818.sga	WT|Input|Rep7	Input	GSM1111818
82	GSM1111819.sga	WT|Input|Rep8	Input	GSM1111819
83	GSM1111820.sga	WT|Input|Rep9	Input	GSM1111820
84	WT_KLE2.sga	WT|KLE2|All	KLE2	-
85	GSM1111793.sga	WT|KLE2|Rep1	KLE2	GSM1111793
86	GSM1111794.sga	WT|KLE2|Rep2	KLE2	GSM1111794
87	GSM1111795.sga	WT|KLE2|Rep3	KLE2	GSM1111795
88	WT_MIX1.sga	WT|MIX1|All	MIX1	-
89	GSM1111796.sga	WT|MIX1|Rep1	MIX1	GSM1111796
90	GSM1111797.sga	WT|MIX1|Rep2	MIX1	GSM1111797
91	GSM1111798.sga	WT|MIX1|Rep3	MIX1	GSM1111798
92	GSM1111799.sga	WT|MIX1|Rep4	MIX1	GSM1111799
93	GSM1111800.sga	WT|MIX1|Rep5	MIX1	GSM1111800
94	WT_PQN85.sga	WT|PQN85|All	PQN85	-
95	GSM1111801.sga	WT|PQN85|Rep1	PQN85	GSM1111801
96	GSM1111802.sga	WT|PQN85|Rep2	PQN85	GSM1111802
97	GSM1111803.sga	WT|PQN85|Rep3	PQN85	GSM1111803
98	WT_SMC4.sga	WT|SMC4|All	SMC4	-
99	GSM1111806.sga	WT|SMC4|Rep1	SMC4	GSM1111806
100	GSM1111807.sga	WT|SMC4|Rep2	SMC4	GSM1111807
101	GSM1111808.sga	WT|SMC4|Rep3	SMC4	GSM1111808

Merged samples:

Biological replicates were merged into one single file and annotated as 'All'.

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).

• Kranz AL, Jiao CY, Winterkorn LH, Albritton SE, Kramer M, Ercan S
  Genome-wide analysis of condensin binding in Caenorhabditis elegans. Genome Biol. 2013;14(10):R112. 24125077
• GEO series GSE45678: Genome-wide distribution of the three condensin complexes in C. elegans