Yu 2010, TFs and histone modifications in prostate cancer cells and tissue

Description

ChIP-seq against 6 histone methylations, H3, AR (androgen receptor), ERG (oncogenic ETS transcription factor), RNA Polymerase II (Pol II) and FoxA1 in LNCaP (Lymph Node Carcinoma) and VcaP prostate cancer cell lines, un-treated or treated with synthetic androgen R1881 or ethanol control, as well as in prostate cancer tissues.
ChIP-seq against ERG in stable RWPE+ERG cells (RWPE cells expressing ERG).
ChIP-seq against ERG in stable RWPE+GUS cells (RWPE cells expressing GUS, control of ERG).
ChIP-seq against AR in 22RV1 prostate carcinoma cells.

Source

Samples

From Human Mar. 2006 (GRCh36/hg18) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM353601_VCaP_Ethl_H3K9me3.sga VCaP|H3K9me3|Ethl H3K9me3 GSM353601
2 GSM353602_VCaP_R1881_H3K9me3.sga VCaP|H3K9me3|R1881 H3K9me3 GSM353602
3 GSM353603_VCaP_Ethl_H3K4me3.sga VCaP|H3K4me3|Ethl H3K4me3 GSM353603
4 GSM353604_VCaP_R1881_H3K4me3.sga VCaP|H3K4me3|R1881 H3K4me3 GSM353604
5 GSM353605_VCaP_Ethl_H3K27me3.sga VCaP|H3K27me3|Ethl H3K27me3 GSM353605
6 GSM353606_VCaP_R1881_H3K27me3.sga VCaP|H3K27me3|R1881 H3K27me3 GSM353606
7 GSM353607_VCaP_Ethl_Polll.sga VCaP|PolII|Ethl PolII GSM353607
8 GSM353608_VCaP_R1881_Polll.sga VCaP|PolII|R1881 PolII GSM353608
9 GSM353609_LnCaP_Ethl_H3K9me3.sga LnCaP|H3K9me3|Ethl H3K9me3 GSM353609
10 GSM353610_LnCaP_R1881_H3K9me3.sga LnCaP|H3K9me3|R1881 H3K9me3 GSM353610
11 GSM353611_LnCaP_Ethl_H3K27me3.sga LnCaP|H3K27me3|Ethl H3K27me3 GSM353611
12 GSM353612_LnCaP_R1881_H3K27me3.sga LnCaP|H3K27me3|R1881 H3K27me3 GSM353612
13 GSM353613_LnCaP_Ethl_H3K4me3.sga LnCaP|H3K4me3|Ethl H3K4me3 GSM353613
14 GSM353614_CS57.LnCaP_Ethl_H3K4me3.sga CS57.LnCaP|H3K4me3|Ethl H3K4me3 GSM353614
15 GSM353615_LnCaP_R1881_H3K4me3.sga LnCaP|H3K4me3|R1881 H3K4me3 GSM353615
16 GSM353616_CS58.LnCaP_R1881_H3K4me3.sga CS58.LnCaP|H3K4me3|R1881 H3K4me3 GSM353616
17 GSM353617_LnCaP_Ethl_Polll.sga LnCaP|PolII|Ethl PolII GSM353617
18 GSM353618_LnCaP_R1881_Polll.sga LnCaP|PolII|R1881 PolII GSM353618
19 GSM353619_VCaP_regular_medium_H3K9me3.sga VCaP|H3K9me3 H3K9me3 GSM353619
20 GSM353620_VCaP_regular_medium_H3K4me3.sga VCaP|H3K4me3 H3K4me3 GSM353620
21 GSM353621_VCaP_regular_medium_H3K27me3.sga VCaP|H3K27me3 H3K27me3 GSM353621
22 GSM353622_VCaP_regular_medium_Pan_H3.sga VCaP|Pan-H3 H3 GSM353622
23 GSM353623_VCaP_regular_medium_Polll.sga VCaP|PolII PolII GSM353623
24 GSM353624_VCaP_regular_medium_H3K36me3.sga VCaP|H3K36me3 H3K36me3 GSM353624
25 GSM353625_LnCaP_regular_medium_H3K9me3.sga LnCaP|H3K9me3 H3K9me3 GSM353625
26 GSM353626_LnCaP_regular_medium_H3K4me3.sga LnCaP|H3K4me3 H3K4me3 GSM353626
27 GSM353627_LnCaP_regular_medium_H3K36me3.sga LnCaP|H3K36me3 H3K36me3 GSM353627
28 GSM353628_LnCaP_regular_medium_Ace_H3.sga LnCaP|Ace-H3 Ace_H3 GSM353628
29 GSM353629_VCaP_regular_medium_Ace_H3.sga VCaP|Ace-H3 Ace_H3 GSM353629
30 GSM353630_VCaP_regular_medium_FoxA1.sga VCaP|FoxA1 FoxA1 GSM353630
31 GSM353631_VCaP_regular_medium_H3K4me1.sga VCaP|H3K4me1 H3K4me1 GSM353631
32 GSM353632_VCaP_regular_medium_H3K4me2.sga VCaP|H3K4me2 H3K4me2 GSM353632
33 GSM353633_LnCaP_regular_medium_FoxA1.sga LnCaP|FoxA1 FoxA1 GSM353633
34 GSM353634_LnCaP_regular_medium_H3K4me1.sga LnCaP|H3K4me1 H3K4me1 GSM353634
35 GSM353635_LnCaP_regular_medium_H3K4me2.sga LnCaP|H3K4me2 H3K4me2 GSM353635
36 GSM353636_VCaP_NT_AR.sga VCaP|AR|NTarget.siRNA AR GSM353636
37 GSM353637_VCaP_NT_ERG.sga VCaP|ERG|NTarget.siRNA ERG GSM353637
38 GSM353638_VCaP_siERG_AR.sga VCaP|AR|siERG AR GSM353638
39 GSM353639_VCaP_siERG_ERG.sga VCaP|ERG|siERG ERG GSM353639
40 GSM353640_22RV1_no_treat_AR.sga 22RV1|AR|no treated AR GSM353640
41 GSM353641_LnCaP_10nmR_AR.sga LnCaP|AR|10nm R1881 AR GSM353641
42 GSM353642_LnCaP_1nmR_AR.sga LnCaP|AR|1nm R1881 AR GSM353642
43 GSM353643_LNCaP_ethl_AR_jy9.sga LNCaP|AR|Ethl AR_jy9 GSM353643
44 GSM353644_LNCaP_R1881_AR_jy10.sga LNCaP|AR|R1881 AR_jy10 GSM353644
45 GSM353645_VCaP_ethl_AR_jy11.sga VCaP|AR|Ethl AR_jy11 GSM353645
46 GSM353646_VCaP_R1881_AR_jy12.sga VCaP|AR|R1881 AR_jy12 GSM353646
47 GSM353647_VCaP_ERG_jy13.sga VCaP|ERG ERG_jy13 GSM353647
48 GSM353648_LNCaP_ERG_jy14.sga LNCaP|ERG ERG_jy14 GSM353648
49 GSM353649_RWPE+ERG_ERG_jy15.sga RWPE+ERG|ERG ERG_jy15 GSM353649
50 GSM353650_RWPE+GUS_ERG_jy16.sga RWPE+GUS|ERG ERG_jy16 GSM353650
51 GSM353651_tissue_AR.sga tissue|AR AR GSM353651
52 GSM353652_tissue_ERG.sga tissue|ERG ERG GSM353652
53 GSM353653_tissue_H3K4me3.sga tissue|H3K4me3 H3K4me3 GSM353653
54 GSM353654_tissue_H3K9me3.sga tissue|H3K9me3 H3K9me3 GSM353654
55 GSM353655_tissue_H3K27me3.sga tissue|H3K27me3 H3K27me3 GSM353655
56 GSM353656_tissue_PolII.sga tissue|PolII PolII GSM353656
57 GSM356767_ERG_AR_re_ChIP.sga VCaP|ERG_re-ChIP AR ChIP GSM356767

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg18 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. 1.5.2).

References

Last update: 24 Mar 2016