|
Status |
Public on Jan 22, 2010 |
Title |
Mock ChIP using anti-HA antibody |
Sample type |
SRA |
|
|
Source name |
embryonic stem cells
|
Organism |
Mus musculus |
Characteristics |
cell type: embryonic stem cells dev stage: E14 antibody: anti-HA
|
Treatment protocol |
The ES cells were fixed in 1 % formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.
|
Growth protocol |
E14 mouse ES cells, cultured under feeder-free conditions were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15 % heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon). Control shRNA and Eset shRNA knockdown samples were obtained by transfecting ES cells with the respective shRNAs using lipofectamine-2000(invitrogen). The transfected ES cells were maintained in the ES medium with 0.8ug/ml puromycin.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
|
|
Description |
Anti-HA ChIP was performed for ES cells
|
Data processing |
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches.
|
|
|
Submission date |
Nov 13, 2009 |
Last update date |
May 15, 2019 |
Contact name |
Mikael Huss |
E-mail(s) |
hussem@gis.a-star.edu.sg
|
Phone |
+6564788042
|
Organization name |
Genome Institute of Singapore
|
Street address |
60 Biopolis Street
|
City |
Singapore |
ZIP/Postal code |
138672 |
Country |
Singapore |
|
|
Platform ID |
GPL9185 |
Series (1) |
GSE19019 |
Genome-wide mapping of Nr5a2 in mouse embryonic stem cells |
|
Relations |
SRA |
SRX016208 |
BioSample |
SAMN00008304 |