|
| Status |
Public on Dec 02, 2018 |
| Title |
LCMV_Cp2_Slamf6_C10_TechRep1 |
| Sample type |
SRA |
| |
|
| Source name |
LCMV_Cp2_Slamf6
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD8+ T-cells
cell subtype: GP33-Tetramer+CD44+CD8+Slamf6+Tim-3- T cells isolated from biologic replicate #2 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #1
isolation of cd8+ t cells: CD8+ MACS negative selection (Miltenyi) followed by FACS
|
| Treatment protocol |
LCMV-infected mice were not treated. Tumor inoculated mice were treated with 100mcg anti-PD-1 or isotype control antibody on days 9 and 12 after implantation
|
| Growth protocol |
For LCMV experiments, C57BL/6 mice were infected with 2 x 10^6 pfu LCMV Clone 13 via IV injection. On day 30 after infection, mice were sacrificed and spleens removed for CD8+ T cell isolation. For tumor experiments, C57BL/6 mice were injected subcutaneously with 3 x 10^5 B16-ova cells. Tumors were harvested on day 22 after implantation for CD8+ T cell isolation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD8+ T cells were isolated from LCMV-infected mice by CD8+ MACS negative selection performed on single-cell suspensions of splenocytes, followed by FACS. CD8+ T cells were isolated from B16-ova tumors by dissecting tumors from the surrounding fascia, mechanically mincing and treating with collagenase P and DNAse I for 10 minutes at 37C. Tumor-infiltrating leukocytes were enriched by CD8+ MACS positive selection (Miltenyi) and FACS isolation. In both contexts, cells were sorted directly into RLT buffer + 1% BME in 96 well plates.
Library construction was performed according to a modified Smart-Seq2 protocol as described in Yates et al., PNAS, 2018.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
LCMV_Cp2_Slamf6_C10_S75
|
| Data processing |
Quality trimming of Fastqs was performed using Trimmomatic
Trimmed reads were aligned to the mm10 mouse genome using Bowtie2
HTSeq was used to map aligned reads to genes and quanitfy gene counts for each technical replicate
Counts for technical replicates were averaged and rounded to the nearest integer to obtain a raw counts matrix (rawCount_cleaned_merged.txtt)
Library size normalization was performed using DESeq2 to obtain a final normalized counts matrix (normalizedCount_cleaned_merged.txt)
Genome_build: mm10
|
| |
|
| Submission date |
Dec 01, 2018 |
| Last update date |
Dec 03, 2018 |
| Contact name |
Kevin Bi |
| E-mail(s) |
kevin_bi@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Haining Lab
|
| Street address |
450 Brookline Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215-5450 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE122713 |
scRNA-seq, bulk RNA-seq, and ATAC-seq data from progenitor exhausted and terminally exhausted CD8+ T cells from tumors and chronic viral infection |
| GSE123235 |
Bulk RNA-Seq profiling of progenitor exhausted (Slamf6+Tim-3-) and terminally exhausted (Slamf6-Tim-3+) CD8+ T-cells from tumors and chronic viral infection |
|
| Relations |
| BioSample |
SAMN10510033 |
| SRA |
SRX5086755 |
