 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 31, 2019 |
| Title |
LEO1 WT Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
treatment: Wild-type
passages: Passage 21
strain: Mouse strain:129 SvJae F1
chip antibody: LEO1 (Bethyl Laboratories. Inc, cat# A300-175A)
|
| Growth protocol |
ESCs were grown under standard conditions in DMEM supplemented with 10% fetal bovine serum, LIF, glutamine, pen-strep, and beta-mercaptoethanol.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For H3K36me3, H3K79me2 and Pol II ChIP-seq experiments: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed with IP-Star (Diagenode) buffer. Chromatin was sonicated on the Bioruptor (Diagenode) to an average size of 0.2-1 kb. ChIP was performed on chromatin from approximately 5 million cells with 3 μg of antibody (above) using the IP-Star Automated System (Diagenode), and 2.5% of chromatin was used for each whole cell extract (WCE). Following reversal of crosslinks, sample and WCE DNA was purified. ChIP DNA was dissolved in water and placed on the SPRI-TE (Beckman Coulter) for Illumina sample preparation. For H3K9ac, H3K56ac and LEO1 ChIP-seq experiements: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed and prepared for ChIP-seq according to the protocol described by Black et al., (2013) (PMID: 23871696).
For H3K9ac, H3K56ac and LEO1 ChIP-seq experiments: libraries were constructued according to the protocol described by TruSeq ChIP Sample ptreparation from Illumina Part# 15023092 Rev.B, Cat# IP-202-9001DOC.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to mm9 using BWA 0.7.4, and PCR duplicates were removed by samtools.
bigWig files were generated by bamCoverage in Deeptools.
Genome_build: mm9
|
| |
|
| Submission date |
May 03, 2019 |
| Last update date |
Nov 01, 2019 |
| Contact name |
Jean-Pierre Etchegaray |
| E-mail(s) |
[email protected]
|
| Phone |
9733530825
|
| Organization name |
Rutgers University
|
| Department |
Biological Sciences
|
| Street address |
225 University Ave
|
| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07102 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE130689 |
The histone deacetylase SIRT6 controls transcription elongation via promoter- proximal pausing (ChIP-Seq) |
| GSE130692 |
The histone deacetylase SIRT6 restrains transcription elongation via promoter-proximal pausing |
|
| Relations |
| BioSample |
SAMN11569995 |
| SRA |
SRX5785865 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3747810_Leo1.WT.rep2.bw |
100.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
