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| Status |
Public on Aug 29, 2023 |
| Title |
Day26, scRNAseq |
| Sample type |
SRA |
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| Source name |
E7-TCR T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: E7-TCR T cells
age: 28-year-old
treatment: E7-TCR T cells were continuously exposed to tumor cells and harvested after 14 challenges
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| Extracted molecule |
total RNA |
| Extraction protocol |
E7-TCR T cells were challenged with CaSki tumor cells and collected at days 0, 12, and 26 after the challenge. In each sample, we labeled the IL15 cells with TotalSeq-C0251, cat. no. 394661, barcode seq. GTCAACTCTTTAGCG; - IL15/21 cells TotalSeq-C0252, cat. no. 394663, barcode seq. TGATGGCCTATTGGG
The cellular samples were loaded in the lanes according to the 10x Genomics 5’v2 Single Cell Chromium User Guide (Dual Index), with a single capture lane consisting of two samples. The target recovery was 8,000 cells per lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
10x Genomics
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| Data processing |
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v6.1.2 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.2 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided human reference sequence (refdata-gex-GRCh38-2020-A). HTOs used for the analysis are human HTO01 and HTO02, TotalSeqC from BioLegend.
Supplementary files format and content: hg38
Supplementary files format and content: h5 files
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| Submission date |
Apr 13, 2023 |
| Last update date |
Sep 11, 2024 |
| Contact name |
Xiyuan Zhang |
| E-mail(s) |
xiyuan.zhang.phd@rutgers.edu
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| Organization name |
Rutgers Cancer Institute
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| Department |
Pediatric Hematology/Oncology
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| Street address |
195 Little Albany St.
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| City |
New Brunswick |
| State/province |
NJ |
| ZIP/Postal code |
08901 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE229651 |
Cooperative armoring of CAR and TCR T-cells by T cell-restricted IL-15 and IL-21 universally enhances solid tumor efficacy |
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| Relations |
| SRA |
SRX19959424 |
| BioSample |
SAMN34170731 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7169811_SCAF3069_RUT_SC001_day26_filtered_feature_bc_matrix.h5 |
32.5 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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