|
| Status |
Public on Apr 21, 2011 |
| Title |
GLIB_5hmC-BGT biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
V6.5 ES cells
|
| Organism |
Mus musculus |
| Characteristics |
biological replicate: First
sample prep: neg control for GLIB method
instrument model: Helicos HeliScope
|
| Treatment protocol |
Samples were treated with 0ng BGT per 1ug DNA (negative control) at 30C for 3hr (50mM HEPES pH 8.0, 25 mM MgCl2, 50 uM UDPG for 3 hr at 30C), then oxidized with 23mM Sodium periodate 16hr at 22C in 0.1M Sodium Phosphate pH 7.0. Periodate was quenched by the addition of 46mM Sodium Sulfite at room temperature for 10 minutes, then exchanged into 1xPBS and incubated with 2mM Aldehyde Reactive Probe (Invitrogen) for 1hr at 37C. DNA was then precipitated with M280 Streptavidin Dynabeads (Invitrogen) and eluted by incubation with 95% Formamide 10mM EDTA for 5 minutes. The eluted DNA was chilled, diluted with an equal volume of water, and ethanol precipitated.
|
| Growth protocol |
ES cells cultured in presence of LIF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted by cell lysis and phenol chloroforme extraction. Sonicated with Covaris S2 to target size 200-400bp
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
neg control for GLIB method
instrument: Helicos HeliScope
|
| Data processing |
alignment: Quality filtered reads were aligned to the mouse genome (mm9) using Helicos open source aligner IndexDP Genomic available at the Open Source HeliSphere
peaks: After balancing the number of reads between treatment and control (+BGT and âBGT) by random sampling, enriched regions were calculated by enrichment of treatment reads using a local background model estimated from control reads employing the statistical software MACS. Enriched regions with a false discovery rate of less than 5% were defined as peaks. Data from both biological replicates were pooled for the analysis shown in this spreadsheets.
|
| |
|
| Submission date |
Apr 20, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
William Abraham Pastor |
| E-mail(s) |
william.pastor@mcgill.ca
|
| Phone |
514-618-3348
|
| Organization name |
McGill University
|
| Department |
Biochemistry
|
| Lab |
Pastor
|
| Street address |
3655 Promenade Sir William Osler
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
USA |
| |
|
| Platform ID |
GPL14759 |
| Series (1) |
| GSE28682 |
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells |
|
| Relations |
| SRA |
SRX101497 |
| BioSample |
SAMN00739495 |
