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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 30, 2014 |
| Title |
m24_b3 |
| Sample type |
SRA |
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| Source name |
24 month Hematopoietic Stem Cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow derived primary HSCs
cell surface marker: SP-KSL-CD150+
strain: C57BL/6
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| Treatment protocol |
Adapter-ligated fragments were treated with sodium bisulfite (Qiagen)
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| Growth protocol |
Freshly forted 4 month and 24 month-old mouse HSCs (SP-KSL-CD150+)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extract genomic DNA using Invitrogen PureLink Genomic DNA kits
Tru-Seq DNA sample prep kit
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
technical replicate of old biological replicate 10
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| Data processing |
The bisulfite sequencing data is processed by a newly developed program MOABS: MOdel based Analysis of Bisulfite Sequencing (Sun et al.
http://code.google.com/p/MOABS/). It seamlessly integrates alignment, methylation calling, identification of hypomethylation for one sample and differential methylation for multiple samples, and other downstream analysis integrating histone modification ChIP-Seq data and gene expression RNA-Seq data.
Genome_build: mm9
Supplementary_files_format_and_content: text; chromosome, start, end, methylation ratio, total reads, methylated reads, strand, next nucletide of cytosine, plus_strand, total reads from plus strand, methylated reads from plus strand, minus strand, total reads from minus strand, methylated reads from minus strand
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| Submission date |
Jun 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
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| Phone |
(713) 677-7439
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| Organization name |
Texas A&M University
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| Street address |
2121 W Holcombe Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE47815 |
Epigenetic and genetic changes during mouse hematopoietic stem cell aging [Bisulfite-Seq] |
| GSE47819 |
Epigenetic and genetic changes during mouse hematopoietic stem cell aging |
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| Relations |
| BioSample |
SAMN02194747 |
| SRA |
SRX299557 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1160019_m24_b3.bsmapv260R.bam.G.bed.gz |
157.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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