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Sample GSM440256 Query DataSets for GSM440256
Status Public on Nov 04, 2009
Title Eset_ChIPseq
Sample type SRA
Source name embryonic stem cells, unperturbed
Organism Mus musculus
Characteristics cell line: E14
cell type: embryonic stem cells
knockdown: unperturbed
antibody: rabbit polyclonal anti-Eset antibody
Treatment protocol The ES cells were fixed in 1% formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.
Growth protocol E14 mouse ES cells, cultured under feeder-free conditions, were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15 % heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon). Control shRNA and Eset shRNA knockdown samples were obtained by transfecting ES cells with the respective shRNAs using lipofectamine-2000(invitrogen). The transfected ES cells were maintained in the ES medium with 0.8ug/ml puromycin.
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 500 bp were immunoprecipitated using different antibodies. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Custom-made rabbit polyclonal antibody was used for ChIP.
A pool of 20 ChIP samples was used.
Data processing The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.

The following supplementary files contain alignments:

The supplementary file 'GSM440256_Eset_peaks.bed' contains the peak calls for the Eset enzyme ChIP-seq library (CME039). Peaks were called using MACS.
Submission date Aug 13, 2009
Last update date May 15, 2019
Contact name Mikael Huss
Phone +6564788042
Organization name Genome Institute of Singapore
Street address 60 Biopolis Street
City Singapore
ZIP/Postal code 138672
Country Singapore
Platform ID GPL9185
Series (1)
GSE17642 Genome-wide mapping of Eset-binding sites and H3K9me3 state in mouse embryonic stem cells
SRA SRX014433
BioSample SAMN00006248
Named Annotation GSM440256_Eset_peaks.bed.gz

Supplementary file Size Download File type/resource
GSM440256_CME039_R00087_lane7_s_7_sorted.txt.gz 264.6 Mb (ftp)(http) TXT
GSM440256_CME039_R00087_lane8_s_8_sorted.txt.gz 275.0 Mb (ftp)(http) TXT
GSM440256_Eset_peaks.bed.gz 40.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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