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Status |
Public on Jul 06, 2008 |
Title |
MEF_RRBS_MspI |
Sample type |
genomic |
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Source name |
Mouse embryonic fibroblasts (E14.5)
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Organism |
Mus musculus |
Characteristics |
Strain: 129SvJae/C57/B6
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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.
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Description |
Bisulfite treated, MspI digestion
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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.
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Submission date |
Apr 02, 2008 |
Last update date |
May 15, 2019 |
Contact name |
Tarjei S Mikkelsen |
Organization name |
Broad Institute
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Street address |
7 Cambridge Center
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
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Platform ID |
GPL6677 |
Series (1) |
GSE11034 |
Genome-scale DNA methylation maps of pluripotent and differentiated cells |
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Relations |
SRA |
SRX000295 |
Supplementary file |
Size |
Download |
File type/resource |
GSM278888.MEF.cpgs.txt.gz |
5.6 Mb |
(ftp)(http) |
TXT |
GSM278888.MEF.processed.6515.6.txt.gz |
76.3 Mb |
(ftp)(http) |
TXT |
GSM278888.MEF.processed.7665.6.txt.gz |
137.0 Mb |
(ftp)(http) |
TXT |
GSM278888.MEF.processed.7735.7.txt.gz |
67.4 Mb |
(ftp)(http) |
TXT |
GSM278888.MEF.processed.7740.5.txt.gz |
71.0 Mb |
(ftp)(http) |
TXT |
GSM278888.MEF.processed.7740.8.txt.gz |
85.5 Mb |
(ftp)(http) |
TXT |
GSM278888.MEF.processed.7873.1.txt.gz |
107.9 Mb |
(ftp)(http) |
TXT |
GSM278888.MEF.processed.7873.2.txt.gz |
108.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Processed data provided as supplementary file |
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