|
| Status |
Public on Aug 19, 2022 |
| Title |
CD62L-_Ly108+_P14_spleen_LCMV_Armstrong_d28pi_1 |
| Sample type |
SRA |
| |
|
| Source name |
splenic CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cells
strain: C57BL/6
tissue: spleen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10000 cells were sorted of each population. Rneasy Plus Mini Kit (Quiagen) was used for RNA isolation according to the manufacturer's protocol.
SMART-Seq V4 Ultra Low Input RNA Kit (Takara) was used according to the manufacturer's protocol for library contruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
bulkRNA-Seq of 10000 cells
|
| Data processing |
RNA-seq reads were aligned to the mouse reference genome GRCm38/mm10 using STAR (Version 2.5.4). Read counts per gene locus were obtained using htseq-count (Version 0.11.4).
R package DESeq2 (version 1.26.0) was used to perform size factor normalization and differential expression analysis. Batch effects were identified using sva (Version 3.34.0) and subsequently modelled in the design formula of DESeq2.
Assembly: mm10
Supplementary files format and content: Matrix table, in txt format, with raw read counts per gene locus from htseq-count.
|
| |
|
| Submission date |
May 23, 2022 |
| Last update date |
Aug 19, 2022 |
| Contact name |
Lorenz Kretschmer |
| E-mail(s) |
lorenz.kretschmer@tum.de
|
| Organization name |
TU Munich
|
| Department |
Institute for Medical Microbiology, Immunology and Hygiene
|
| Lab |
Dr. Veit R. Buchholz
|
| Street address |
Trogerstr. 30
|
| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
81675 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE203575 |
c-Myb instructs both stemness and functional exhaustion of CD8+ T cells during chronic infection [bulkRNA-seq] |
| GSE205608 |
c-Myb instructs both stemness and functional exhaustion of CD8+ T cells during chronic infection |
|
| Relations |
| BioSample |
SAMN28596943 |
| SRA |
SRX15413933 |
