|
| Status |
Public on Nov 04, 2009 |
| Title |
Eset_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells, unperturbed
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14
cell type: embryonic stem cells
knockdown: unperturbed
antibody: rabbit polyclonal anti-Eset antibody
|
| 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 |
Custom-made rabbit polyclonal antibody was used for ChIP.
A pool of 20 ChIP samples was used.
|
| 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.
The following supplementary files contain alignments:
GSM440256_CME039_R00087_lane7_s_7_sorted.txt
GSM440256_CME039_R00087_lane8_s_8_sorted.txt
The supplementary file 'GSM440256_Eset_peaks.bed' contains the peak calls for the Eset enzyme ChIP-seq library (CME039). Peaks were called using MACS.
|
| |
|
| Submission date |
Aug 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) |
| GSE17642 |
Genome-wide mapping of Eset-binding sites and H3K9me3 state in mouse embryonic stem cells |
|
| Relations |
| SRA |
SRX014433 |
| BioSample |
SAMN00006248 |
| Named Annotation |
GSM440256_Eset_peaks.bed.gz |
