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Sample GSM867826 Query DataSets for GSM867826
Status Public on Aug 12, 2015
Title Rbp2 WT_H3K4me3_ChIPSeq
Sample type SRA
 
Source name Rbp2 f/f ES cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: Rbp2 f/f wild type
cell type: embryonic stem cells
chip antibody: Anti-trimethyl-Histone H3 (Lys4)
chip antibody vendor: Upstate Tech
chip antibody cat. #: 07-473
Treatment protocol None
Growth protocol Wild-type (Rbp2 f/f) and Rbp2-/- (Rbp2 KO) ES cells were maintained on irradiated mouse embryonic fibroblast (IEF) feeders in standard ES medium (DMEM; Dulbecco's modified Eagle's medium) supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 1000U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and antibiotics. For ChIP assays, the cells were seeded on gelatin-coated plates.
Extracted molecule genomic DNA
Extraction protocol ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101). After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~320 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against H3K4me3
Data processing Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak/significant island detection was performed with the program SICER (http://home.gwu.edu/~wpeng/Software.htm)
Genome Build:
H3K4me3_mmuES_ff_map-mm9.bed: mm9
H3K4me3_ff_mm9_ES.wig: mm9
H3K4me3_mmuES_ff_island.bed: mm9
 
Submission date Jan 30, 2012
Last update date May 15, 2019
Contact name Elizaveta V Benevolenskaya
E-mail(s) evb@uic.edu
Phone 312-413-8947
Organization name University of Illinois at Chicago
Department Biochemistry and Molecular Genetics
Street address 900 S. Ashland Ave.
City Chicago
State/province IL
ZIP/Postal code 60607
Country USA
 
Platform ID GPL9185
Series (1)
GSE28348 Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells.
Relations
SRA SRX118195
BioSample SAMN00779770

Supplementary file Size Download File type/resource
GSM867826_H3K4me3_ff_mm9_ES.wig.gz 279.2 Mb (ftp)(http) WIG
GSM867826_H3K4me3_mmuES_ff_island.bed.gz 319.2 Kb (ftp)(http) BED
GSM867826_H3K4me3_mmuES_ff_map-mm9.bed.gz 228.9 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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