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Sample GSM751037 Query DataSets for GSM751037
Status Public on Jun 30, 2011
Title MafA_ChIPSeq
Sample type SRA
Source name Pancreatic islets_MafA
Organism Mus musculus
Characteristics strain: CD-1
age: 8-10 week old
tissue/cell type: hand-picked pancreatic islets
chip antibody: MafA (Abcam ab17976 lot 950583)
Growth protocol Islets were purified by collagenase digestion, filtration through a 70um filter with subsequent hand picking, livers were perfused and homogenized.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in 1% formaldehyde and incubated at room temperature (RT) for 10min, prior to the addition of glycine to 0.125M followed by incubation at RT for 5min. Cells were pelleted, washed and resuspended in 500ul ChIP cell lysis buffer (10mM Tris-Cl, pH 8.0, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) containing 1x protease inhibitor cocktail (Thermo Scientific, Waltham, MA, USA). Cells were then rehomogenized, incubated on ice for 5min and repelleted. The pellet was resuspended in 400ul ChIP nuclear lysis buffer (1% SDS, 5mM EDTA, 50mM Tris-Cl, pH 8.1) supplemented with protease inhibitor cocktail tablets (Thermo Scientific). Cells were sonicated in ice-water bath (Sonicator 3000, Misonix, Farmingdale, NY, USA) for 24 cycles of 30s on, 30s off. Samples were pelleted to remove cellular debris and transferred to fresh tubes.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Description Chromatin IP against MafA
Data processing Alignment: Sequence reads were mapped to mm9 (NCBI 37) using BWA (v 0.5.7) and default parameters.
Submission date Jun 29, 2011
Last update date May 15, 2019
Contact name Patrick Plettner
Organization name BC Cancer Agency GSC
Street address 100-570 West 7th Avenue
City Vancouver
State/province BC
ZIP/Postal code V5Z 4S6
Country Canada
Platform ID GPL9250
Series (1)
GSE30298 Identification and analysis of pancreatic islet specific enhancers
SRA SRX081539
BioSample SAMN00631867

Supplementary file Size Download File type/resource
GSM751037_MM0555_7_lanes_dupsFlagged.bam 6.2 Gb (ftp)(http) BAM
GSM751037_MafA_MM0555_7L_bwa_mm9_xset200_dupsN_ht6.wig.gz 172.0 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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