|
| Status |
Public on Oct 07, 2011 |
| Title |
WCE_K562bmp4_r1_100608_1 |
| Sample type |
SRA |
| |
|
| Source name |
Input ChIP-Seq K562 BIO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
chip antibody: WCE
antibody catalog number: None WCE
|
| Treatment protocol |
Cells were stimulated with 5µM BIO dissolved in DMSO for 4hrs.
|
| Growth protocol |
K562 cells were maintained in IMDM medium (Invitrogen 12440) with 10% Fetal Bovine serum, 2µM Glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin (1% P/S). Cells were split 1:10 every 2-3 days. Prior to stimulation, cells were serum starved in IMDM medium with 2µM Glutamine, 1% P/S for 24hrs at a concentration of 106cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Input ChIP-Seq in K562 cells treated with BMP
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build (hg18) using Eland.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 10bp bins. Counts were normalized to reads per million, and bins with at least 0.5-1 reads per million are shown.
|
| |
|
| Submission date |
May 10, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Teresa Venezia Bowman |
| Organization name |
Children's Hospital Boston
|
| Lab |
Zon Laboratory
|
| Street address |
One Blackfan Circle, 7th floor
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE29195 |
Genome-wide location analysis of WNT (Tcf7l2) and BMP (SMAD1) in human hematopoeitic cell lines co-occupied with lineage specific regulators (GATA1, GATA2, CEBPA) |
| GSE29196 |
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration |
|
| Relations |
| SRA |
SRX097094 |
| BioSample |
SAMN00717426 |
