|
| Status |
Public on Jun 22, 2010 |
| Title |
GM10861_vitaminD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblastoid, GM10861, vitamin D
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM10861
cell type: lymphoblastoid
treatment: calcitriol
antibody: anti-VDR
antibody name: VDR (C-20)
antibody vendor: Santa Cruz Biotechnology
antibody catalog number: sc-1008
antibody lot number: B1809
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM10861
|
| Treatment protocol |
Cell lines were either stimulated for 36 hours with calcitriol or unstimulated.
|
| Growth protocol |
Cells were grown in RPMI-1640 medium supplemented with 10% FBS, 0.2 mM L-glutamine at 37 degrees Celsius in 5% humidified CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from formaldehyde-crosslinked cells and ChIP-ed using anti-VDR antibody sc-1008 (Santa Cruz Biotech; lot# B1809). ChIP DNA was processed into library by following the Illumina ChIP-Seq library construction protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ChIP against VDR.
08_861_D3_R2
|
| Data processing |
Sequences: Standard Illumina software base-calling and quality-control filtering was applied.
Alignment: Reads were aligned to human genome hg18 (NCBI Build 36) using Eland software (Illumina pipeline).
Peaks: MACS peak-calling algorithm was used with a cut-off of pvalue = 1.00e-09 (http://liulab.dfci.harvard.edu/MACS/). MACS peaks were filtered by removing a small number of peaks in locations where the Input sample had peaks with >12 overlapping reads.
|
| |
|
| Submission date |
Jun 21, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Sreeram Ramagopalan |
| E-mail(s) |
[email protected]
|
| Phone |
00441865287659
|
| Fax |
00441865287501
|
| Organization name |
University of Oxford
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE22484 |
Genome-wide Analysis of Vitamin D Receptor Binding By ChIP-Seq |
|
| Relations |
| Reanalyzed by |
GSE53041 |
| SRA |
SRX022397 |
| BioSample |
SAMN00016445 |
