|
Status |
Public on May 14, 2024 |
Title |
scRNA_OT-I_rep2 |
Sample type |
SRA |
|
|
Source name |
primary CD8 T cell
|
Organism |
Mus musculus |
Characteristics |
cell type: primary CD8 T cell genotype: OT-I CD45.1-CD45.2+ treatment: MC38-OVA bearing
|
Treatment protocol |
For subcutaneous tumor models, MC38-OVA (1 × 10^6) tumor cells were injected subcutaneously into the flanks of WT recipient mice (CD45.1+). Tumor-engrafted recipient mice were first intraperitoneally injected with 200 mg kg-1 cyclophosphamide (CTX, Aladdin) when the tumor is palpable, then OT-I naive T (1x10^6) cells were adoptively transferred by tail-vein injection into recipient mice.
|
Growth protocol |
CD8+ T cells were enriched from the spleens and peripheral lymph nodes of donor mice using a naïve CD8+ T cell isolation kit.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Two weeks after adoptive transfer, WT (OT-I CD45.1-CD45.2+) T cells were flow-sorted. OT-I T cells from two mice were pooled for one library preparation. Cells were counted and loaded onto the Chromium Controller (10 × Genomics) for a target recovery of 1 × 10^4 single cells. Samples were processed per the manufacturer’s protocol and sequenced on an Illumina NovaSeq6000 sequencer using a 150-bp kit with paired-end reads.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
scRNA_OTI_2
|
Data processing |
Basecalls were performed using CASAVA version 1.8 All following steps were performed using the CellRanger analysis pipeline (v.7.0.1). Sample demultiplexing, barcode processing alignment, filtering UMI counting and aggregation of sequencing runs Assembly: mm10 Supplementary files format and content: Raw features, barcodes, and matrices (raw_feature_bc_matrix) for each library.
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|
|
Submission date |
Jan 18, 2023 |
Last update date |
May 14, 2024 |
Contact name |
Dawang Zhou |
E-mail(s) |
dwzhou@xmu.edu.cn
|
Organization name |
Xiamen University
|
Department |
Life Science
|
Lab |
Dawang Zhou Lab
|
Street address |
Xiang'an south rd, Xiang'an district
|
City |
Xiamen |
State/province |
Fujian |
ZIP/Postal code |
361102 |
Country |
China |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE223160 |
Osr2 functions as a mechanical checkpoint to augment CD8+ T cell exhaustion [TIL_scRNA_CD8] |
GSE223164 |
Osr2 functions as a biomechanical checkpoint to aggravate CD8+ T cell exhaustion in tumor |
|
Relations |
BioSample |
SAMN32782538 |
SRA |
SRX19062543 |