|
| Status |
Public on Oct 07, 2011 |
| Title |
Smad1_G1Ebmp_r1_100914_6 |
| Sample type |
SRA |
| |
|
| Source name |
Smad1 ChIP-Seq in mouse G1E treated with BMP
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Erthyroid Progenitor (G1E)
chip antibody: Smad1
antibody catalog number: Santa Cruz SC-7965
|
| Treatment protocol |
During the last two hours of estradiol treatment, cells were serum-starved for 24 hrs and stimulated for 2hrs with 25ng/ml recombinant human BMP4 (R&D 314-BP-010).
|
| Growth protocol |
G1E cells were maintained in IMDM medium plus 15% heat-inactivated fetal calf serum (Hyclone SH30071.01) in the presence of 2% P/S, 2 U/mL Epo, 50ng/ml mouse SCF (R&D 455-MC-010), and 124 X 10-4 monothioglycerol (Sigma M6145) as previously described (Tsang et al., Cell 1997). Erythroid differentiation was induced with 10-7 M β-estradiol for 24hrs both in G1ER and in G1E cells as a control.
|
| 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 |
Chromatin IP against G1E BMP SMAD1
|
| 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 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 |
GPL9250 |
| Series (2) |
| GSE29193 |
Genome-wide location analysis of BMP (SMAD1) in mouse erythroid progenitors co-occupted with lineage specific regulators (GATA1, GATA2) |
| GSE29196 |
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration |
|
| Relations |
| SRA |
SRX100314 |
| BioSample |
SAMN00738262 |
