|
| Status |
Public on May 20, 2016 |
| Title |
Tet2_Dnmt3aDKO r1 Bisulfite-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cells (HSC)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Tet2 and Dnmt3a double knockout Hematopoietic stem cell
cell surface marker: Lin- ckit+Sca1+ CD48- CD150+
strain: C57/B6
|
| Treatment protocol |
Tet2 KO and Tet2_3a DKO whole bone marrow are transplanted into lethally irradiated recipient mouse, LSK CD48- CD150+ HSCs are isolated from secondary transplanted mouse
|
| Growth protocol |
secondary transplanted mouse HSCs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction by Purelink extraction kit
bisulfite treated DNA was made into library with Illumina TruSeq DNA sample preparation kit
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
technical replicate of biological replicate 1
|
| Data processing |
use BSMAP-2.87 to align bisulfite-treated sequencing reads to the mouse genome mm9 of bisulfite treated data
use moabs to compute the methylation ratio of single base level
Genome_build: mm9
Supplementary_files_format_and_content: 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 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianzhong Su |
| E-mail(s) |
jianzhongsu82@gmail.com
|
| Phone |
8322902241
|
| Organization name |
Baylor college of Medicine
|
| Street address |
1 Baylor Plaza
|
| City |
HOUSTON |
| State/province |
TEXAS |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE72148 |
DNMT3A and TET2 Compete and Cooperate to Repress Differentiation Lineage-Specific Factors in Hematopoietic Stem Cells |
|
| Relations |
| BioSample |
SAMN03998614 |
| SRA |
SRX1156650 |
