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Sample GSM722407 Query DataSets for GSM722407
Status Public on Oct 07, 2011
Title WCE_CD34eryth_bmp_r2_101105_2
Sample type SRA
 
Source name Input ChIP-Seq CD34 erythroid BMP
Organism Homo sapiens
Characteristics cell type: Pro-erythroblasts
chip antibody: WCE
antibody catalog number: None WCE
Treatment protocol At day 5 of differentiation cells reached the proerythroblast 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. For studying the binding in differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM β-estradiol), at a density of 0.5–1 X 106 cells/ml till harvesting. At day 5 of differentiation cells reached the proerythroblast cells were stimulated for 2hrs with rhBMP4 at a final concentration of 25ng/µl and harvested for performing chromatin immunoprecipitation.
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 CD34 erythroid 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 SRX097080
BioSample SAMN00717412

Supplementary file Size Download File type/resource
GSM722407_WCE_CD34eryth_bmp_r2_101105_2_HG18_eland.ylf.gz 50.9 Mb (ftp)(http) YLF
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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