|
| Status |
Public on Jul 17, 2019 |
| Title |
Sample1_PTPN2N1_Slam_3 |
| Sample type |
SRA |
| |
|
| Source name |
cells isolated from the mouse after infection or tumor extraction.
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: CD8+ T cells
strain: C57BL/6
sgrna: PTPN2
phenotype: Slamf6+
|
| Growth protocol |
Antigen specific T cells (OT-1 specific for SIINFEKL peptide within OVA) were transferred to MC38-OVA tumors and allowed to respond and proliferate in response to the tumor for 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted in pools of 500 cells into 25uL Qiagen RLT + 1%beta-mercaptoethanol (v/v) and frozen at -80C
Lysates were converted to cDNA following capture with Agencourt RNA Clean beads using the SmartSeq2 protocol as previously described (Trombetta et al, Curr Protoc Mol Biol, 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file:
GSE119270_lcmv_raw_count_matrix.txt.gz
|
| Data processing |
Basecalls performed using Illumina NextSeq500 and converted to fastq files using Bcl2fastq
Fastq files trimmed for poor quality reads using Trimmomatic with the parameters LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:16
Trimmed Fastq files were aligned to the mouse genome mm10 using Bowtie2
Aligned reads aggregated to a gene count matrix using HTSeq
Count normalization and differential expression analysis performed using DESeq2 (quality filter: gene expression threshold of 100,000)
Genome_build: mm10
Supplementary_files_format_and_content: normalized count matrix, tab-delimited text
|
| |
|
| Submission date |
Jul 10, 2019 |
| Last update date |
Jul 17, 2019 |
| Contact name |
Brian Christopher Miller |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard Medical School
|
| Department |
Immunology
|
| Lab |
Sharpe Lab
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE119270 |
Ptpn2 regulates the generation of cytotoxic Tim-3+ CD8+ T cells and restrains anti-tumor immunity |
| GSE134413 |
PTPN2 regulates the generation of exhausted CD8+ T cell subpopulations and restrains tumor immunity |
|
| Relations |
| BioSample |
SAMN12249598 |
| SRA |
SRX6427855 |
