|
| Status |
Public on Oct 07, 2011 |
| Title |
SMAD1_CD34prog_bmp_r1_100901_1 |
| Sample type |
SRA |
| |
|
| Source name |
SMAD1 ChIP-seq CD34+ progenitors BMP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hematopoietic Stem & Progenitor Cells
chip antibody: SMAD1
antibody catalog number: Santa Cruz SC-7965
|
| Treatment protocol |
At day 6 cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/µl and harvested for performing chromatin immunoprecipitation.
|
| Growth protocol |
CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were obtained from the Yale Center of Excellence in Molecular Hematology. The cells were maintained and differentiated as previously described (Sankaran et al., 2008). Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with 1X CC100 cytokine mix (Stem Cell Technologies Inc.) and 2% P/S for a total of 6 days.
|
| 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 |
SMAD1 ChIP-seq in CD34+ progenitors 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) |
| GSE29194 |
Genome-wide location analysis of WNT (Tcf7l2) and BMP (SMAD1) in human hematopoeitic progenitors co-occupied with lineage specific regulators (GATA1, GATA2) |
| GSE29196 |
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration |
|
| Relations |
| SRA |
SRX097072 |
| BioSample |
SAMN00717404 |
