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Sample GSM6213279 Query DataSets for GSM6213279
Status Public on Jan 14, 2023
Title Drug_Control, scRNA-seq
Sample type SRA
 
Source name tissue
Organism Mus musculus
Characteristics treatment: phosphate-buffered solution (PBS) on days 5, 8, and 11 after tumor inoculation. Mice were sacrificed 13 days after tumor inoculation. Tissue specimens were analyzed by immunofluorescence tissue staining, scRNAseq(10x genemics).
tissue: tissue
strain: balb/c
age: 6 weeks old
Treatment protocol For the anti-CTLA-4 treatment group, 100 μg of anti-CTLA-4(9H10) was intraperitoneally injected on days 5, 8, and 11 after tumor inoculation.
Extracted molecule total RNA
Extraction protocol Single cell suspension was generated from the tissue following the manufacturer's recommentations (Tumor Dissociation Kit, mouse, Miltenyi). Total RNA capture and cDNA amplification were performed according to the manufacter’s protocol (Single Cell 5' Immune Profiling v1.1 protocol, 10x Genomics). Briefly, Single-cell suspensions were loaded onto the 10x Chromium system targeting 5,000 cells. For each single cell, total RNA from the cell lysate contained in gel bead-in-emulsion (GEM) was captured with UMI and 10x barcoded gel bead and then reverse transcribed to cDNA. The barcoded cDNAs were pooled and amplified.
Library was constructed according to the manufacter’s instructions (Single Cell 5' Immune Profiling v1.1 protocol, 10x Genomics).
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing The barcoded processing and gene counting were performed using the Cell Ranger software v5.0.0 multi pipeline with mm10-2020-A and vdj-GRCm38-alts-ensembl-5.0.0 reference genomes.
Assembly: mm10
Supplementary files format and content: Output files of 10x Cell Ranger software: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv
 
Submission date Jun 03, 2022
Last update date Jan 14, 2023
Contact name AREUM JO
E-mail(s) areum15.jo@gmail.com
Phone +82 1045262367
Organization name The Catholic University of KOREA
Street address 222, Banpo-daero, Seocho-gu
City Seoul
ZIP/Postal code 06591
Country South Korea
 
Platform ID GPL24247
Series (1)
GSE205470 CTLA-4 inhibition facilitates follicular T-B cell interaction and the production of tumor-specific antibodies
Relations
BioSample SAMN28861585
SRA SRX15592643

Supplementary file Size Download File type/resource
GSM6213279_Control_barcodes.tsv.gz 28.0 Kb (ftp)(http) TSV
GSM6213279_Control_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM6213279_Control_matrix.mtx.gz 54.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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