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Sample GSM788367 Query DataSets for GSM788367
Status Public on Oct 07, 2011
Title GATA1 ChIP-seq K562
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics cell line: K562
chip antibody: GATA1
chip antibody vendor: Santa Cruz
chip antibody cat. #: SC-265
cell type: K562
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 GATA1 ChIP-seq in K562 cells
Data processing Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build 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 Aug 31, 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 SRX097108
BioSample SAMN00717440

Supplementary file Size Download File type/resource
GSM788367_GATA1_K562_HG18.WIG.gz 5.3 Mb (ftp)(http) WIG
GSM788367_GATA1_K562_r1_110722_6_HG18_eland.ylf.gz 28.3 Mb (ftp)(http) YLF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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