|
| Status |
Public on Aug 19, 2014 |
| Title |
ko3ab_hsc_l4 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Dnmt-KO Hematopoietic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow derived primary HSCs
cell surface marker: SP-KSL-CD150+
strain: C57BL/6
|
| Treatment protocol |
PolyA selection
|
| Growth protocol |
Freshly sorted wild type and Dnmt3a-KO mouse HSCs (SP-KSL-CD150+)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extract RNA using Qiagen Rneasy Micro kit.
Tru-Seq RNA sample prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
technical replicate of biological replicate 2
|
| Data processing |
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample; XLS file for two sample comparison testing if a gene is differentially expressed;
|
| |
|
| Submission date |
Sep 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
|
| Phone |
(713) 677-7439
|
| Organization name |
Texas A&M University
|
| Street address |
2121 W Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE50775 |
Role of de novo DNA methyltransferases in hematopoietic stem cells (RNA-seq) |
| GSE50793 |
Role of de novo DNA methyltransferases in hematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN02354083 |
| SRA |
SRX348825 |
