|
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 |