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| Status |
Public on Aug 12, 2024 |
| Title |
SStim day 10 CD8+ T cells, StimR, donor3 |
| Sample type |
SRA |
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| Source name |
Live CD45+EGFR+CD8+ CAR-T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Live CD45+EGFR+CD8+ CAR-T cells
treatment: CAR-T cells produced using StimR
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected and cryopreserved at the end of the third stimulation (Day 10) for transcriptomic analyses. Cryopreserved samples were thawed and cells were aliquoted for flow staining, followed by Fc receptor blocking using Human TruStain FcX™ blocking reagent (BioLegend) for 10 minutes at 4 °C, prior to staining with a cocktail of fluorochrome-conjugated antibodies specific for human CD45, CD8, CD4, EGFR and fixable viability dye eFluor™ 506 for 30 minutes at 4 °C. Approximately 3 x 104 live CD45+EGFR+CD8+ T cells were flow sorted into 100 μL of Lysis Binding Mix (Thermo Fisher Scientific) using the BD FACSAria™ Fusion cell sorter (BD Biosciences) and stored at −80 °C until processing. Total RNA was extracted from sorted CD45+EGFR+CD8+ T cells using the MagMAX™ mirVana™ Total RNA Isolation kit (Thermo Fisher Scientific) and stored at −80 °C.
Libraries for mRNA sequencing were prepared with 5 ng of total RNA for cDNA generation using the SMART-Seq v4 Ultra Low Input RNA kit (Takara) following the manufacturer’s protocol. Next,150 pg of cDNA was used to prepare barcoded libraries using the Nextera XT DNA Library Preparation Kit (Illumina) following the manufacturer’s protocol. Barcoded libraries from multiple samples were then pooled in an equimolar ratio, purified, and sequenced together using the NovaSeq 6000 system (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Trim_galore (v0.6.5) was used for adaptor trimming and STAR (v2.7.2c) was used for alignment to the human GRCh38 reference genome. Gene expression quantification was performed by RSEM (v1.3.1) with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes transcript lengths, counts, TPM and FPKM for each sample (RSEM output)
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| Submission date |
Jun 05, 2024 |
| Last update date |
Aug 12, 2024 |
| Contact name |
Jia Lu |
| E-mail(s) |
jlu@lyell.com
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| Organization name |
Lyell Immunopharma
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| Street address |
201 Haskins Way, Suite 101
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE269134 |
Engineering potent chimeric antigen receptor T cells by programming signaling during T-cell activation [RNA-seq] |
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| Relations |
| BioSample |
SAMN41689742 |
| SRA |
SRX24811266 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8306881_SSday10-CD8-StimR-donor3.genes.results.gz |
1.6 Mb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
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