|
| Status |
Public on Oct 28, 2016 |
| Title |
ERG-ChIP_RWPE1-ERG(P436A) |
| Sample type |
SRA |
| |
|
| Source name |
RWPE1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RWPE1
cell type: normal prostate
antibody: Anti-ERG Clone 9FY Biocare # CM421 C
|
| Growth protocol |
VCaP cells were grown in DMEM media (Mediatech-cellgro) with 10%FBS and 1% penicillin/streptomycin. RWPE1 cells stably expressing either wild type (WT) or point mutant (P436A) of ERG were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract, human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA was extracted as described in Hollenhorst et al., Genes and Dev. 2011
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol. ChIP DNA's were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Casava1.8.2 software was used for basecalling
Reads were aligned to Homo sapiens Genome (UCSC Hg19) using Bowtie2 (v0.12.8)
Peaks were called using Useq program (v8.4.0)
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab delimited text files with chromosome:start-end
|
| |
|
| Submission date |
Jun 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vivekananda Kedage |
| E-mail(s) |
vkedage@indiana.edu
|
| Organization name |
Indiana University
|
| Street address |
1001 E. third Street
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE73616 |
An interaction with Ewing's sarcoma breakpoint protein EWS defines the subset of ETS factors rearranged in prostate cancer |
|
| Relations |
| BioSample |
SAMN05219969 |
| SRA |
SRX1835124 |
