|
| Status |
Public on Nov 16, 2013 |
| Title |
m12_b4l1 Bisulfite-Seq |
| Sample type |
SRA |
| |
|
| Source name |
12 month Hematopoietic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Mx1-cre-;Dnmt3afl/fl
cell type: Murine bone marrow derived primary HSCs
cell surface marker: SP-KSL-CD150+
|
| Treatment protocol |
Adapter-ligated fragments were treated with sodium bisulfite (Qiagen)
|
| Growth protocol |
Freshly sorted 12 month wild type (Mx1-cre-;Dnmt3afl/fl) and knockout (Mx1-cre+;Dnmt3a-/-) mouse HSCs (SP-KSL-CD150+)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extract genomic DNA using Invitrogen PureLink Genomic DNA kits
Tru-Seq DNA sample prep kit
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
technical replicate of biological replicate 2
|
| Data processing |
use moabs to process bisulfite treated 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
|
| |
|
| Submission date |
Aug 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Margaret Goodell |
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza, N1030
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE49191 |
Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a |
| GSE49714 |
Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a [Bisulfite-Seq] |
|
| Relations |
| BioSample |
SAMN02315120 |
| SRA |
SRX333393 |
