|
| Status |
Public on Oct 07, 2011 |
| Title |
WCE_U937dmso_r1_100505_3 |
| Sample type |
SRA |
| |
|
| Source name |
Input ChIP-Seq U937 DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U937
chip antibody: WCE
antibody catalog number: None WCE
|
| Growth protocol |
U937 cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI-1640 media with 10% Fetal Bovine Serum by the National Cell Culture Center(NCCC). For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.
|
| 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 U937 treated with DMSO
|
| 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 |
SRX097104 |
| BioSample |
SAMN00717436 |
