|
| Status |
Public on Aug 08, 2023 |
| Title |
133_isotype_C1_CD4_TREG |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
cell type: TREG
treatment: isotype control
|
| Treatment protocol |
B16F10-OVA tumor-bearing mice were treated with 200ug of either isotype control antibody, anti-PD-1 antibody or anti-JAML antibody. 1 day later, the tumors were harvested and the tumor-infiltrating cells were purified, FACS stained and sorted into lysis buffer
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
CD4+FOXP3+ or CD8+ T cells from different treatment conditions were sorted into PCR tubes containing 8ul lysis buffer
Bulk RNA-seq libraries were prepared for sequencing using the Smart-seq2 protocol adapted for samples with small cell numbers (Rosales et al, 2018) and following standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
<400 cells bulk, full-transcriptome (Smart-seq2)
|
| Data processing |
FASTQ was merged and filtered using fastp (v0.20.1)
Reads were aligned with the STAR aligner (v2.7.3a)
samtools (v0.1.19-44428cd) was used to index and sort the BAM files from STAR
QC reports was performed with bamCoverage (v3.3.1) and Qualimap (vv.2.2.2-dev)
Raw and transcripts per million reads (TPM) counts were taken from STAR's BAM aligned output
Genome_build: mm10
Supplementary_files_format_and_content: bulk_counts.txt.gz raw counts for 202 samples in TAB delimited TXT
Supplementary_files_format_and_content: bulk_metadata.txt.gz metadata for 202 samples in TAB delimited TXT
Supplementary_files_format_and_content: bulk_tpm.txt.gz transcripts per million reads (TPM) for 202 samples in TAB delimited TXT
|
| |
|
| Submission date |
Oct 01, 2021 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Pandurangan Vijayanand |
| E-mail(s) |
vijay@lji.org
|
| Organization name |
La Jolla Institute for Immunology
|
| Department |
Vaccine Discovery
|
| Lab |
Vijayanand Lab
|
| Street address |
9420 Athena Circle
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE185160 |
JAML is a novel immunotherapy target for tissue-resident memory T cells [bulk RNA-seq] |
| GSE185162 |
JAML is a novel immunotherapy target for tissue-resident memory T cells |
|
| Relations |
| BioSample |
SAMN21973486 |
| SRA |
SRX12435208 |
