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Sample GSM6940461 Query DataSets for GSM6940461
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.
 
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.
 
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

Supplementary file Size Download File type/resource
GSM6940461_scRNA_OTI_2.tar.gz 235.1 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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