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Sample GSM850470 Query DataSets for GSM850470
Status Public on Feb 01, 2012
Title RNAPII S2P ChIPSeq
Sample type SRA
 
Source name Undifferentiated ES cells
Organism Mus musculus
Characteristics modification: RNAPII S2P
cell line: OS25 ES cells
chip antibody: H5 (MMS-129R, Covance)
chip antibody manufacturer: Covance
chip antibody catalog #: MMS-129R
chromatin: Fixed
beads: Magnetic beads
Growth protocol Mouse ES-OS25 cells were grown on 0.1% gelatin-coated surfaces in GMEM-BHK21 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 1% MEM non-essential amino acids, 1 mM sodium pyruvate (all from Gibco), 50 μM 2-mercaptoethanol, 1000 U/ml of human recombinant leukaemia inhibitory factor (Chemicon) and 0.1 mg/ml Hygromycin (Roche).
Extracted molecule genomic DNA
Extraction protocol ChIP-seq libraries were prepared from 10 ng DNA (quantified by Qubit) according to Illumina protocols (Part #11257047 Rev A), with some modifications. Samples were PCR amplified prior to size selection on an agarose gel. Libraries were quantified by Qubit (Invitrogen) and qPCR, and library size was assessed by Bioanalyzer (Agilent).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing RNAPII_S2P.bw; genome build: mm9
Wig and Bw files: Reads were aligned against the UCSC mouse mm9 genome (July 2007) using Illumina Eland extended software allowing 2 mismatches and unique reads only. Multiple sequencing runs were merged and used to create bedgraph and bigwig (bw) summary files.

**Correction (Mar 14, 2012):
Due to curation error, runs for SRX112177 and SRX112179 switched, specifically,
Run SRR391034.1 was removed from experiment SRX112177 (GSM850468) and added to experiment SRX112179 (GSM850470) as SRR391034.3
Run SRR391040.1 was removed from experiment SRX112179 (GSM850470) and added to experiment SRX112177 (GSM850468) as SRR391040.3
 
Submission date Dec 17, 2011
Last update date May 15, 2019
Contact name Ines de Santiago
E-mail(s) desantiago.ines07@imperial.ac.uk
Phone +44 (0) 2083838526
Organization name MRC Clinical Sciences Centre
Department Epigenetics
Lab Genome Function
Street address Hammersmith Hospital Campus
City London
ZIP/Postal code W12 0NN
Country United Kingdom
 
Platform ID GPL9250
Series (2)
GSE34518 Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ES cells (ChIP-Seq)
GSE34520 Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ES cells
Relations
SRA SRX112179
BioSample SAMN00766452
Named Annotation GSM850470_RNAPII_S2P.bw

Supplementary file Size Download File type/resource
GSM850470_RNAPII_S2P.bw 943.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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