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| Status |
Public on Feb 14, 2013 |
| Title |
HSC_old_500_reconst_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
treatment: 500 old HSCs transplanted
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 |
SRX230359 |
| BioSample |
SAMN01915468 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1079928_RRBS_cpgMethylation_Mouse_blood_HSC_old_500_reconst_1.RRBS.bed.gz |
13.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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