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| Status |
Public on Jul 06, 2008 |
| Title |
NPC_p9_RRBS_MspI |
| Sample type |
genomic |
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| Source name |
Neural progenitor cells (ES-derived)
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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 |
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 Selector |
| Processed data provided as supplementary file |
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