|
| Status |
Public on Jul 15, 2014 |
| Title |
RI-muEIP1 |
| Sample type |
SRA |
| |
|
| Source name |
Prosate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: vertebral metastatic lesion derived prostate cancer cells
cell line: VCaP
chip antibody: ERG (Epitomics, 2805-1)
treatment: mutational form of the peptide (*ERG inhibitory peptidomimetics*)
|
| Treatment protocol |
VCaP cells were treated with 50 µM peptide inhibitors for 12hrs.
|
| Growth protocol |
Cells were grown in DMEM containing 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode). ChIP DNA was isolated (IPure Kit, Diagenode) from samples by incubation with the antibody at 4°C overnight followed by wash and reversal of cross-linking.
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
EIP1
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Reads were aligned to HG19 using Bowtie2
Coverage files were generated using Bedtools
BigWig files were generated using bedGraphToBigWig
Genome_build: hg19
|
| |
|
| Submission date |
Jun 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaoju Wang |
| E-mail(s) |
xiaojuw@umich.edu
|
| Phone |
734-763-6056
|
| Organization name |
University of Michigan
|
| Street address |
1500 E. Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE58939 |
Development of peptidomimetic inhibitors of the ERG transcription factor in prostate cancer (ChIP-seq) |
| GSE58975 |
Development of peptidomimetic inhibitors of the ERG gene fusion product in prostate cancer |
|
| Relations |
| BioSample |
SAMN02898982 |
| SRA |
SRX643471 |
