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Sample GSM278893 Query DataSets for GSM278893
Status Public on Jul 06, 2008
Title NPC_p9_RRBS_MspI
Sample type genomic
Source name Neural progenitor cells (ES-derived)
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 SRX000300

Supplementary file Size Download File type/resource
GSM278893.NPC.p9.cpgs.txt.gz 5.7 Mb (ftp)(http) TXT
GSM278893.NPC.p9.processed.14088.3.txt.gz 167.0 Mb (ftp)(http) TXT
GSM278893.NPC.p9.processed.14092.6.txt.gz 117.9 Mb (ftp)(http) TXT
GSM278893.NPC.p9.processed.14094.6.txt.gz 190.8 Mb (ftp)(http) TXT
GSM278893.NPC.p9.processed.14098.3.txt.gz 287.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file

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