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Sample GSM278891 Query DataSets for GSM278891
Status Public on Jul 06, 2008
Title Astro_primary_p2_RRBS_MspI
Sample type genomic
Source name Astrocytes
Organism Mus musculus
Characteristics Strain: 129SvJae/C57/B6
Extracted molecule genomic DNA
Extraction protocol Full details can be found in Meissner et al. (2008). Briefly, 1-10ug of genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EpiTect Bisulfite Kit (QIAGEN) with 3 extra cycles, PCR amplified with 18-24 cycles and sequenced.
Description Bisulfite treated, MspI digestion
Data processing Full details can be found in Meissner et al. (2008). Briefly, 36bp reads were aligned to a fully bisulfite converted reference sequence database containing all predicted MspI fragments in the 40-220bp range. An alignment was kept if the second best alignment at >= 2 additional mismatches. Methylated CpGs were identified by comparison of the aligned reads to the original reference sequence, and only positions with quality scores >= 20 were kept for analysis.
Submission date Apr 02, 2008
Last update date May 15, 2019
Contact name Tarjei S Mikkelsen
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platform ID GPL6677
Series (1)
GSE11034 Genome-scale DNA methylation maps of pluripotent and differentiated cells
SRA SRX000298

Supplementary file Size Download File type/resource
GSM278891.Astro.primary.p2.cpgs.txt.gz 5.8 Mb (ftp)(http) TXT
GSM278891.Astro.primary.p2.processed.2017W.1.txt.gz 197.9 Mb (ftp)(http) TXT
GSM278891.Astro.primary.p2.processed.2032R.1.txt.gz 234.3 Mb (ftp)(http) TXT
GSM278891.Astro.primary.p2.processed.2032R.2.txt.gz 136.3 Mb (ftp)(http) TXT
GSM278891.Astro.primary.p2.processed.2032R.3.txt.gz 137.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file

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