|
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 |