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Status |
Public on Jan 14, 2023 |
Title |
Drug_aCTLA4, scRNA-seq |
Sample type |
SRA |
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Source name |
tissue
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Organism |
Mus musculus |
Characteristics |
treatment: 100ug anti-CTLA-4(9H10) tissue: tissue strain: balb/c age: 6 weeks old
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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.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
10x Genomics
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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
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Submission date |
Jun 03, 2022 |
Last update date |
Jan 14, 2023 |
Contact name |
AREUM JO |
E-mail(s) |
areum15.jo@gmail.com
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Phone |
+82 1045262367
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Organization name |
The Catholic University of KOREA
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Street address |
222, Banpo-daero, Seocho-gu
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City |
Seoul |
ZIP/Postal code |
06591 |
Country |
South Korea |
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Platform ID |
GPL24247 |
Series (1) |
GSE205470 |
CTLA-4 inhibition facilitates follicular T-B cell interaction and the production of tumor-specific antibodies |
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Relations |
BioSample |
SAMN28861583 |
SRA |
SRX15592645 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6213281_aCTLA4_barcodes.tsv.gz |
21.2 Kb |
(ftp)(http) |
TSV |
GSM6213281_aCTLA4_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
GSM6213281_aCTLA4_matrix.mtx.gz |
21.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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