|
| Status |
Public on Jul 29, 2024 |
| Title |
TCR-T-TIL-4 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
cell line: primary cells
cell type: TCR-engineered human T cells
genotype: NY-ESO-1 TCR expression
treatment: PBS
|
| Treatment protocol |
i.p. injection of PBS or orthogonal human IL-2
|
| Growth protocol |
Tumor infiltrating T cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NSG mice were inoculated s.c. with A375 cells (1 × 106) and received i.v. adoptive cell transfer of 3 × 106 NY-ESO-1 TCR-T cells (WT NY-ESO-1 TCR-T cells, or ho22R, or hoGCSFR expressing NY-ESO-1 TCR-T cells) on day 10 post-tumor inoculation followed by i.p. administration of MSA-hoIL-2 (2.5 × 104 unit × 3 doses, 2.5 × 104 unit × 3 doses) or PBS control every other day until day 20. On day 21, mice were sacrificed, tumors were minced and dissociated using a human tumor dissociation kit (Miltenyi Biotec) and a gentleMACS Octo Dissociator (Miltenyi Biotec). Tumor-infiltrating lymphocytes (TILs) were first enriched by density gradient centrifugation against Percoll (GE healthcare), and then stained with surface markers and DAPI (Sigma-Aldrich). CD3+ EGFR+ or CD3+ EGFR+YFP+ T cells were sorted using an Aria II sorter (BD Biosciences) at the Stanford Share FACS Facility for ATAC sequencing
ATAC-seq library was generateded using Active Motif ATAC-Seq Kit
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Description |
Omni-ATAC-seq
|
| Data processing |
ATAC-seq reads were mapped onto the reference genome (hg19) using RSubread (version 2.18.0) in the “DNA” mode
The aligned reads were then subjected to peak calling with MACS3
Assembly: hg19
Supplementary files format and content: ATACSeq_DESeq2_rsubread.rds, summarized peak count data
|
| |
|
| Submission date |
Jul 16, 2024 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Yang Zhao |
| E-mail(s) |
yannzhao@stanford.edu
|
| Phone |
6505058145
|
| Organization name |
Stanford University
|
| Department |
MCP
|
| Lab |
Garcia lab
|
| Street address |
Beckman B169B, 279 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE272385 |
Natural and non-natural cytokine receptors generate diverse cell states to enhance T cell therapy |
|
| Relations |
| BioSample |
SAMN42537153 |
| SRA |
SRX25346685 |
