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Sample GSM802477 Query DataSets for GSM802477
Status Public on Jan 30, 2012
Title H3K27ac_ChIPSeq
Sample type SRA
Source name sorted erythroid cells (Ter119+)
Organism Mus musculus
Characteristics tissue: erythroid cells
strain: C57BL/6/CBA
chip antibody: antiH3K27ac [Abcam ChIP grade ab 4729 lot730178]
Treatment protocol Mouse primary erythroid cells were sorted from the spleens of acetylphenylhydrazine-treated mice based on the expression of Ter119 (Spivak et al., 1973; Vernimmen et al., 2009).
Extracted molecule genomic DNA
Extraction protocol ChIPs were performed according to the Millipore ChIP protocol, as described previously (De Gobbi et al., 2007). For ChIP-Seq experiments, Ter119+ cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Immunoprecipitations were performed, after an overnight incubation with the appropriate antibody, with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Immunoprecipitations were performed after an overnight incubation with the appropriate antibody with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Input and immunoprecipitated DNA were purified by phenol and chloroform extraction followed by ethanol precipitation. Subsequently the material was analysed by real time PCR (ABI Prism 7000 Sequence Detection System, Applied Biosystems) using a series of PCR amplicons and 5'FAM-3'TAMRA probes across the alpha-globin locus.
The library was constructed using Illumina protocol. The library was amplified prior to size selection (150-200bp).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Chromatin IP against H3K27ac
Data processing The reads were aligned to the mm9 mouse genome build using bowtie (version 0.12.3) with indices on m2 (map twice to the genome). Before downstream analysis duplicate reads of the same chromosome and start position were collapsed to a single representative read to exclude overrepresented PCR products. All aligned reads starts were summed in sliding windows of 300 bp to create summary windows.
Submission date Sep 27, 2011
Last update date Jun 11, 2013
Contact name Monika S Kowalczyk
Organization name Weatherall Institute of Molecular Medicine, University of Oxford
Department MRC Molecular Haematology Unit
Lab Higgs Group
Street address Headley Way
City Oxford
State/province Oxfordshire
ZIP/Postal code OX3 9DS
Country United Kingdom
Platform ID GPL13112
Series (2)
GSE27918 Genome-wide maps of chromatin state in mouse erythroid cells.
GSE27921 Intragenic enhancers act as alternative promoters
BioSample SAMN02198038

Supplementary file Size Download File type/resource
GSM802477_ChIPSeq_Ter119_H3K27ac.sam.gz 3.0 Gb (ftp)(http) SAM
Processed data provided as supplementary file
Raw data not provided for this record

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