|
| Status |
Public on Jan 01, 2020 |
| Title |
RNA-seq Control 2 naïve |
| Sample type |
SRA |
| |
|
| Source name |
Naïve CD8 T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Naive CD8 T cells
surface marker: CD8+CD25-CD62LhiCD44low
treatment: Control
|
| Growth protocol |
Naïve OT-I (CD45+, CD8+, CD62L+, CD44-) or stimulated (CD4-, CD8+) CD8 T cells were sorted from spleen and/or LNs. T cells were enriched before FACS by utilizing Pan T cell MACS kit (Miltenyi Biotec) and sorted with BD FACS Aria (BD Bioscience).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was purified from T cells using QIAGEN RNeasy columns (74106) with on-column DNase digestion according to the manufacturer’s instructions.
RNA-seq libraries were constructed following Illumina Tru-seq stranded mRNA protocol (20020594).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq
Naive_processed.txt
|
| Data processing |
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software by the standard workflow.
Reads were aligned to the mouse genome (mm10) using STAR (v2.5.3a) and annotated with Ensembl Transcripts release 91 in Partek® Genomics Suite® software, version 7.0 (2018).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including Gene symbol, Gene type and CPM (counts per million).
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Jan 01, 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 |
GPL19057 |
| Series (2) |
| GSE136978 |
Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone [RNA-seq] |
| GSE136980 |
Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone |
|
| Relations |
| BioSample |
SAMN12703294 |
| SRA |
SRX6809359 |
