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Sample GSM777317 Query DataSets for GSM777317
Status Public on Nov 24, 2011
Title Input_ES
Sample type SRA
Source name E14 stem cells (TNG-A)
Organism Mus musculus
Characteristics sample type: Embryonic stem cells carrying the EGFP reporter at the Nanog locus (TNG) from Austin Smith
antibody: none
Growth protocol Embryonic stem cells were cultured without feeders in the presence of leukaemia inhibitory factor (LIF) in DMEM containing 10% fetal calf serum.
Extracted molecule genomic DNA
Extraction protocol MeDIP-/hMeDIP-seq: ESC genomic DNA was purified and sonicated. Illumina adapters were ligated before MeDIP/hMeDIP. Adaptor-ligated DNA was denatured and incubated with 2µg of anti-5mC or 2µg of anti-5hmC antibody at 4°C overnight. Antibody-DNA complexes were captured by magnetic beads and the immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols. MethylCap-seq: ESC genomic DNA was purified and sonicated. Capturing of methylated DNA was done by incubating 2 ug of His6-GST-MBD (Diagenode) with 1 ug of fragmented DNA. GST-MBD-DNA complexs were captured by magnetic GST-beads. Beads-GST-MBD-DNA complexes were washed and eluted using different concentrations of NaCl. The collected eluates were purified using QIAquick PCR purification spin columns (Qiagen), eluted with 100ul elution buffer and prepared following standard Illumina protocols.
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina Genome Analyzer IIx
Description genomic DNA derived from the chromatin input
Data processing Reads (36bp) were aligned to the NCBI build 37 (mm9) with BWA v0.5.8 allowing 0/1 mismatches and unique mapped reads were converted to BED format. The aligned reads for MethylCap-seq_medium and MethylCap-seq_high were merged in an unique bed file.
Submission date Aug 11, 2011
Last update date May 15, 2019
Contact name H.G. Stunnenberg
Phone +31-24-3610520
Organization name Radboud University
Department Department of Molecular Biology (274)
Street address Geert Grooteplein 28
City Nijmegen
ZIP/Postal code 6525 GA
Country USA
Platform ID GPL11002
Series (1)
GSE31343 5-hydroxymethylcytosine: the sixth DNA base
SRA SRX091985
BioSample SAMN00709483

Supplementary file Size Download File type/resource
GSM777317_61WNUAAXX_1_customTrack.bed.gz 123.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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