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Status |
Public on Feb 14, 2013 |
Title |
HSC_young_2x5FU_1 |
Sample type |
SRA |
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Source name |
bone marrow
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Organism |
Mus musculus |
Characteristics |
cell type: hematopoietic stem cell strain: C57Bl/6 age: 3.5 months + 6 months treatment: 2 doses of 5-FU replicate: Rep 1
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Extracted molecule |
genomic DNA |
Extraction protocol |
Please see Gu et al., 2011 (PMID: 21412275) and Smith et al., 2012 (PMID: 22456710) RRBS was performed according to a previously published protocol (Smith et al., 2009 PMID: 19442738) with some optimizations for small cell numbers (Gu et al., 2010, PMID: 20062050)
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
Reduced Representation |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using MAQ bisulfite alignment mode. Aligned bam files were processed using custom software (PMID: 20852634). Genome_build: mm9 Supplementary_files_format_and_content: bed file columns: chrom, chromstart, chromend,'number methylated cytosines/number total cytosines',score,strand
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Submission date |
Feb 08, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Isabel Beerman |
Organization name |
Boston Childrens Hospital
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Street address |
200 Longwood Ave, WAB 156
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City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE44117 |
DNA methylation of hematopoietic stem cells during ontogeny and after enforced proliferative history |
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Relations |
SRA |
SRX230371 |
BioSample |
SAMN01915480 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1079940_RRBS_cpgMethylation_Mouse_blood_HSC_young_2x5FU_1.RRBS.bed.gz |
13.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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