Kranz13,Genome-wide analysis of condensin binding.

Description

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.

Source

Samples

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'.

Technical Notes

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).

References

Last update: 19 Sep 2017