|
| Status |
Public on Aug 09, 2024 |
| Title |
KLR_2 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: CD8+ T cell
genotype: C57BL/6
treatment: Exhausted_KLR
|
| Treatment protocol |
CD8+ T cells were isolated and enriched using the Miltenyi CD8+ T cell isolation kit and prepared for FACs as described above.
|
| Growth protocol |
Spleens from 4 mice bearing KP.SIY flank tumors were harvested 14 days after tumor inoculation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
CXCR3+CX3CR1+ and CXCR3+CX3CR1- SIY-reactive CD8+ T cells were FACS-sorted directly into TRIzol reagent and RNA was isolated using a TRIzol-cholorform extraction.
The RNA-containing aqueous layer was collected and purified using the RNeasy MinElute Cleanup Kit (QIAGEN) following manufacturer’s instructions and submitted to the KI Genomics Core / MIT BioMicro Center for RNA library preparation (Clonetech ZapR) and sequencing (Illumina NextSeq500).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
KLR.6
|
| Data processing |
Reads were aligned to the mm10 genome with salmon v1.10.0, and differential gene expression analysis was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: txImport_processed.txt: raw and tpm counts of gene/sample
|
| |
|
| Submission date |
Aug 07, 2024 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Duncan Matthew Morgan |
| E-mail(s) |
dmmorgan@mit.edu
|
| Organization name |
MIT
|
| Department |
Koch Institute
|
| Lab |
Love lab
|
| Street address |
500 Main St
|
| City |
CAMBRIDGE |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE270050 |
Expansion of Tumor-Infiltrating CD8+ T Cell Clonotypes Occurs in the Spleen in Response to Immune Checkpoint Blockade |
|
| Relations |
| BioSample |
SAMN43072428 |
| SRA |
SRX25634636 |
