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Sample GSM480163 Query DataSets for GSM480163
Status Public on Dec 24, 2009
Title Jarid1a_ChIPSeq
Sample type SRA
 
Source name Embryonic stem cells (chromatin IP fraction)
Organism Mus musculus
Characteristics cell line: LF2
chip antibody: Jarid1a
Treatment protocol none
Growth protocol standard passaging
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and ChIP-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 Jarid1a
Data processing Enrichment analysis was performed using QuEST software (http://mendel.stanford.edu/sidowlab/downloads/quest/)
 
Submission date Dec 04, 2009
Last update date May 15, 2019
Contact name Anton Valouev
Organization name Stanford University
Department Pathology
Lab Sidow Lab
Street address 300 Pasteur Dr.
City Stanford
State/province CA
ZIP/Postal code 94035
Country USA
 
Platform ID GPL9185
Series (1)
GSE18776 Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells
Relations
SRA SRX015832
BioSample SAMN00007545

Supplementary file Size Download File type/resource
GSM480163_Jarid1a.bed.gz 96.6 Mb (ftp)(http) BED
GSM480163_Jarid1a_calls.bed.gz 61.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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