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Sample GSM722389 Query DataSets for GSM722389
Status Public on Oct 07, 2011
Title WCE_G1ERbio_r1_100914_1
Sample type SRA
 
Source name Input ChIP-Seq in mouse G1ER treated with BIO
Organism Mus musculus
Characteristics cell type: Erthyroid Progenitor (G1ER)
chip antibody: None
antibody catalog number: None WCE
Treatment protocol During the last two hours of estradiol treatment, cells were stimulated for 4hrs with 5μM BIO dissolved in DMSO and were harvested for chromatin immunoprecipitation.
Growth protocol G1ER 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 BIO G1ER INPUT
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 SRX100315
BioSample SAMN00738263

Supplementary file Size Download File type/resource
GSM722389_WCE_G1Ebio_r1_100914_4_LNL_MM8_eland.ylf.gz 52.5 Mb (ftp)(http) YLF
SRA Run SelectorHelp
Raw data not provided for this record
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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