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| Status |
Public on Dec 14, 2018 |
| Title |
DHTtreated_ERG_ChIAPET |
| Sample type |
SRA |
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| Source name |
VCaP cells, DHT 2hr, ERG ChIP
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| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP
cell type: prostate cancer cell line
treatment: DHT for 2hrs
chip antibody: anti-ERG (vendor: Santa Cruz; catalog number: sc-353; lot#: I2509)
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| Treatment protocol |
Hormone-deprived VCaP cells were treated with 100nM DHT for 2 hours.
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| Growth protocol |
VCaP cells were seeded in DMEM supplemented with 10% fetal bovine serum (FBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution for 3 days. Prior to ETOH/DHT stimulation, VCaP cells were washed and the medium was replaced with phenol red-free DMEM supplemented with 10% charcoal stripped fetal bovine serum (CDFBS), sodium pyruvate, sodium bicarbonate and penicillin:streptomycin solution to starve the cells for 24 hours.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIA-PET: ChIP Chromatin was divided into two aliquots and each aliquot was ligated with two different barcoded biotinylated half-linkers (linker A or linker B) that contain a flanking MmeI site using T4 DNA ligase. These chromatins ligated with different linkers were pooled and molecular circularization/ligation was carried out in extremely dilute condition. After ligation, DNA was purified and digested with MmeI.
The biotinylated PETs purified on Streptavidin Dynabeads were ligated with a sequencing adapter by T4 DNA ligase (RT for 16h with rotation). The nick on one strand of the DNA at the ligation site was subsequently repaired by incubation with E. coli DNA polymerase I at RT for 2h, followed by 18-20 rounds of PCR. This PCR product was used as the template for Illumina GAIIx 2x36 bp pair end sequencing.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
ERG ChIA-PET after DHT treatment. CHV031M_L1.cluster.pet2+.txt is a file storing all the AR mediated chromatin interaction with PET count>=2. And CHV031M_L1.peak.bed is a bed file storing the AR binding site locations estimated from self-ligation pet.
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| Data processing |
Alignment: For ChIA-PET, GRO-seq, we use program called BATMIS - Basic Alignment Tool for Mismatches http://code.google.com/p/batmis/. For G-PET, sequence tags were uniquely mapped to the human reference sequence (NCBI Build 37) allowing 2 mismatches. For RNA-PET, we use the RNA alignment program TopHat. For G-PET, sequence tags were mapped to the human reference sequence (NCBI Build 37) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems).
Interaction cluster calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Peak calling: ChIA-PET data was processed with ChIA-PET Tool software: Li, G., Fullwood, M.J., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.S., Tennakoon, C., Wei, C.L., Ruan, Y. and Sung, W.K. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol, 11 (2). R22
Coverage data: use bedtool "genomeCoverageBed" with the alignment data
SV calling: Detect all Structural Variations (deletions, inversions, insertions, tandem and translocations) for each library using SVGenModule program.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bed.gz: peak
Supplementary_files_format_and_content: bedpe.gz: chromatin interaction
Supplementary_files_format_and_content: bedgraph.gz: RNA-seq coverage
Supplementary_files_format_and_content: pet2+.txt: chromatin interaction
Supplementary_files_format_and_content: xls: structure variation
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| Submission date |
Feb 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Edwin Cheung |
| E-mail(s) |
rnapolii@outlook.com
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| Organization name |
Genome Institute of Singapore
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| Department |
Cancer Biology and Pharmacology
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| Street address |
Genome Institute of Singapore 60 Biopolis Street, Genome, #02-01
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| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE54946 |
An AR-ERG co-mediated chromatin interactome defines the transcriptional network in prostate cancer cells |
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| Relations |
| BioSample |
SAMN02640984 |
| SRA |
SRX470040 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1327094_CHV031M_L1.cluster.pet2+.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSM1327094_ERG_peak.bed.gz |
331.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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