|
| Status |
Public on Jan 31, 2020 |
| Title |
RNA-seq DKO1 |
| Sample type |
SRA |
| |
|
| Source name |
Naïve T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: naive T cells
surface marker: TCRb+CD4+CD25-CD62LhiCD44low
genotype: BTG1/2 double KO, Btg1f/f Btg2f/f-CD4-Cre
|
| Treatment protocol |
n/a
|
| Growth protocol |
Naive CD4 T cells (TCRb+CD4+CD25-CD62LhiCD44low) from two pairs of WT and DKO mice were isolated by FACS sorting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated by RNeasy Micro Kit (QIAGEN, 74004).
RNA-seq libraries were constructed by Yale Center for Genome Analysis (YCGA) using SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
rRNA-depleted RNA-seq
|
| Data processing |
The sequences were basecalled by Illumina RTA embedded in HiSeq X Control Software by the standard workflow.
Reads were mapped to the mouse transcriptome (ensembl release 89; cDNA and ncRNA) and quantified by Kallisto with a k-mer index 31 and 60 bootstrapping.
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including transcript identifiers, length, expected count, and TPM
|
| |
|
| Submission date |
Jan 29, 2019 |
| Last update date |
Jan 31, 2020 |
| Contact name |
Jaechul Lim |
| E-mail(s) |
jaechul.lim@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Street address |
1 Gwanak-ro, 1 Gwanak-gu
|
| City |
Seoul |
| State/province |
CT |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE125865 |
mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence [RNA-seq] |
| GSE125890 |
mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence |
|
| Relations |
| BioSample |
SAMN10842033 |
| SRA |
SRX5307519 |
