|
| Status |
Public on Nov 16, 2013 |
| Title |
wt_hsc_l2 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
wild type Hematopoietic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: wild type
cell type: Murine bone marrow derived primary HSCs
cell surface marker: SP-KSL-CD150+
|
| 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 1
|
| 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; TXT file for two sample comparison testing if a gene is differentially expressed;
|
| |
|
| 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 |
| GSE49715 |
Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN02315129 |
| SRA |
SRX333407 |
