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Sample GSM698699 Query DataSets for GSM698699
Status Public on Apr 01, 2011
Title RCOR3 ChIP-Seq
Sample type SRA
 
Source name E14
Organism Mus musculus
Characteristics cell line: E14
passages: 15-18
transgene: V5 tagged RCOR3
chip antibody: V5
chip antibody manufacturer: Invitrogen
chip antibody catalog #: R96125
Growth protocol E14 cell were maintained under normal condition for mouse ES cell culture.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and REST and its cofactors DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 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 RCOR3
Data processing Alignment: Sequence reads were obtained and mapped to the mouse (Build 36, Feb, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (SCISSRS) algorithm
 
Submission date Mar 29, 2011
Last update date Jun 11, 2013
Contact name hongbing yu
E-mail(s) yuhb@gis.a-star.edu.sg
Phone 65 68088488
Fax 65 68088306
Organization name genome institute of singapore
Department stem cell and development
Lab stem cell 3
Street address 60 biopolis street, #02-01, genome
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL9185
Series (2)
GSE28233 Genome-wide maps of REST and its cofactors in mouse E14 cells
GSE28289 REST ChIP-chip and knockdown expression profiling
Relations
BioSample SAMN02198585

Supplementary file Size Download File type/resource
GSM698699_RCOR3_ChIP-seqpeaks_mm8.bed.gz 31.4 Kb (ftp)(http) BED
Processed data provided as supplementary file
Raw data not provided for this record

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