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Sample GSM691596 Query DataSets for GSM691596
Status Public on Mar 21, 2011
Title G1ME_WCE
Sample type SRA
 
Source name G1ME Cells
Organism Mus musculus
Characteristics strain: C58BL/6 Bruce 4 (B4)
cell type: G1ME cells
chip antibody: none
Growth protocol Mouse C57BL/6 Bruce 4 (B4) ES cells were adapted to culture without helper fibroblasts and expanded using standard techniques. mESCs were cultured in DMEM (Invitrogen) with 15% (v/v) FCS (batch tested for ES cell culture), 100 ug/ml streptomycin, 100 IU/ml penicillin, beta-mercaptoethanol (Sigma), non-essential amino acids, Glutamax (Gibco) and recombinant mLIF 103 IU/ml (Millipore). To prepare chromatin for ChIP, mESCs were grown to ~80% confluence and fixed with buffered formaldehyde (1%) for 10 minutes at room temperature. G1ME cells were grown in alpha-MEM (Invitrogen) supplemented with 20% (v/v) FCS, 100 ug/ml streptomycin, 100 IU/ml penicillin and 70 ng/ml recombinant thrombopoietin (Stachura, 2006). For ChIP studies G1ME cells were grown at 5x105 cells/ml and were fixed with 1% formaldehyde for 20 minutes at room temperature.
Extracted molecule genomic DNA
Extraction protocol Chromatin was prepared from fixed mouse ES cells and G1ME cells and was sonicated with a Bandelin sonicator (30% amplitude, 15-25 30 second bursts with a 2 minute reprieve) to produce fragments from 200-1000 bp, with peak signal between 200-500 bp. Approximately 2 x107 cell equivalents were used for each immunoprecipitation. 1.7% of the sample was removed for use as an input control. ChIP was performed as described previously (Lee, 2006), using antibodies towards H3K27Me3 (07-449, Millipore) or phosphorylated RNA polymerase C-terminal domain (ab5131, Abcam).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing All reads were mapped to version 9 of the mouse reference genome (mm9) using bowtie version 0.11.3 with the default settings and output to SAM format. Any reads that appeared on the same strand at the same location more than 5 times was discarded to remove PCR artifacts (i.e. at most five reads were allowed to start at any one location).
 
Submission date Mar 15, 2011
Last update date Jun 11, 2013
Contact name Matthew Daniel Young
E-mail(s) myoung@wehi.edu.au
Organization name Walter & Eliza Hall Institute of Medical Research
Department Bioinformatics
Street address 1G Royal Parade
City Parkville
State/province Victoria
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL9250
Series (2)
GSE27967 ChIP-seq analysis reveals distinct H3K27me3 profiles associated with gene regulation [ChIP-seq]
GSE27970 ChIP-seq analysis reveals distinct H3K27me3 profiles associated with gene regulation
Relations
BioSample SAMN02196916

Supplementary file Size Download File type/resource
GSM691596_G1ME.WCE.sorted.bam 411.7 Mb (ftp)(http) BAM
Processed data provided as supplementary file

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