NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM711883 Query DataSets for GSM711883
Status Public on Apr 21, 2011
Title GLIB_5hmC+BGT biol rep2
Sample type SRA
 
Source name V6.5 ES cells
Organism Mus musculus
Characteristics biological replicate: Second
sample prep: hmC-pulldown by GLIB method
instrument model: Helicos HeliScope
Treatment protocol Samples were treated with 20ng BGT per 1ug DNA 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 hmC-pulldown by 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 –BGT) 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 SRX101496
BioSample SAMN00739494

Supplementary file Size Download File type/resource
GSM711883_glib_d_1.bed.gz 110.5 Mb (ftp)(http) BED
GSM711883_glib_e_1.bed.gz 118.3 Mb (ftp)(http) BED
GSM711883_glib_e_2.bed.gz 113.6 Mb (ftp)(http) BED
GSM711883_glib_e_3.bed.gz 111.5 Mb (ftp)(http) BED
GSM711883_glib_e_4.bed.gz 105.8 Mb (ftp)(http) BED
GSM711883_glib_e_5.bed.gz 103.8 Mb (ftp)(http) BED
GSM711883_glib_e_6.bed.gz 97.3 Mb (ftp)(http) BED
GSM711883_glib_e_7.bed.gz 93.4 Mb (ftp)(http) BED
GSM711883_glib_e_8.bed.gz 86.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap