Need Help?

RNA-sequencing of ex vivo exhausted human antigen-specific T cells

Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. To explore new pathways for reinvigoration of anti-tumor immune functions, we developed a human ex vivo exhaustion model by repetitive antigenic stimulation of primary CD8 T cells. This results in T cells that resemble patient-derived T cells in tumors on a phenotypic and transcriptional level. Four human healhy donor CD8+ T cells were isolated, transduced with an NY-ESO-1 TCR lentivirus construct, stimulated in four different conditions (Trested, Ttumor, Tex, Teff) with T2 tumor cells and specific peptides over 12 days. Cells were then sorted for TCR Vbeta 13.1+ (NY-ESO-1 TCR) CD8+ CD3+ CD56- CD4- DAPI- cells. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode (2x51bp) on 2 lanes of an Illumina NovaSeq 6000 flow-cell. FASTQ sequence files were generated with the Illumina RTA version 3.4.4 and Base-calling Version bcl2fastq-2.20.0.422.

Request Access

Data Access Policy of Datasets controlled by MF-DAC

ATTENTION: Please check the following policy and the documents/information to provide in order to get access to the requested datasets. You can find the governing policy on Zenodo under the link: https://zenodo.org/records/12517622 Please provide all information as requested in the document to the MF-DAC. Additionally, you can find more information about the Data Access Committee of the Medical Faculty of the University of Basel (MF-DAC) under the following link on Zenodo: https://zenodo.org/records/10137776

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001006794 RNASeq
  • Updated a data type to RNASeq
  • Updated policy to match request of MF-DAC.
  • Set back the correct policy number.
  • Dataset Released

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00007774187 fastq.gz 655.3 MB
EGAF00007774188 fastq.gz 690.6 MB
EGAF00007774189 fastq.gz 648.1 MB
EGAF00007774190 fastq.gz 682.7 MB
EGAF00007774191 fastq.gz 638.1 MB
EGAF00007774192 fastq.gz 664.5 MB
EGAF00007774193 fastq.gz 629.9 MB
EGAF00007774194 fastq.gz 655.8 MB
EGAF00007774195 fastq.gz 875.5 MB
EGAF00007774196 fastq.gz 914.6 MB
EGAF00007774197 fastq.gz 864.6 MB
EGAF00007774198 fastq.gz 902.5 MB
EGAF00007774199 fastq.gz 771.2 MB
EGAF00007774200 fastq.gz 805.2 MB
EGAF00007774201 fastq.gz 760.9 MB
EGAF00007774202 fastq.gz 794.1 MB
EGAF00007774203 fastq.gz 817.0 MB
EGAF00007774204 fastq.gz 852.2 MB
EGAF00007774205 fastq.gz 808.1 MB
EGAF00007774206 fastq.gz 842.5 MB
EGAF00007774207 fastq.gz 788.0 MB
EGAF00007774208 fastq.gz 818.2 MB
EGAF00007774209 fastq.gz 777.9 MB
EGAF00007774210 fastq.gz 807.5 MB
EGAF00007774211 fastq.gz 761.8 MB
EGAF00007774212 fastq.gz 801.2 MB
EGAF00007774213 fastq.gz 753.5 MB
EGAF00007774214 fastq.gz 792.1 MB
EGAF00007774215 fastq.gz 779.6 MB
EGAF00007774216 fastq.gz 811.4 MB
EGAF00007774217 fastq.gz 769.3 MB
EGAF00007774218 fastq.gz 800.3 MB
EGAF00007774219 fastq.gz 662.1 MB
EGAF00007774220 fastq.gz 704.0 MB
EGAF00007774221 fastq.gz 655.5 MB
EGAF00007774222 fastq.gz 696.5 MB
EGAF00007774223 fastq.gz 675.8 MB
EGAF00007774224 fastq.gz 706.5 MB
EGAF00007774225 fastq.gz 667.2 MB
EGAF00007774226 fastq.gz 697.2 MB
EGAF00007774227 fastq.gz 603.5 MB
EGAF00007774228 fastq.gz 634.7 MB
EGAF00007774229 fastq.gz 596.2 MB
EGAF00007774230 fastq.gz 626.6 MB
EGAF00007774231 fastq.gz 606.0 MB
EGAF00007774232 fastq.gz 637.9 MB
EGAF00007774233 fastq.gz 598.1 MB
EGAF00007774234 fastq.gz 629.1 MB
EGAF00007774235 fastq.gz 681.3 MB
EGAF00007774236 fastq.gz 713.8 MB
EGAF00007774237 fastq.gz 671.7 MB
EGAF00007774238 fastq.gz 703.4 MB
EGAF00007774239 fastq.gz 769.1 MB
EGAF00007774240 fastq.gz 802.4 MB
EGAF00007774241 fastq.gz 759.7 MB
EGAF00007774242 fastq.gz 792.1 MB
EGAF00007774243 fastq.gz 793.0 MB
EGAF00007774244 fastq.gz 830.2 MB
EGAF00007774245 fastq.gz 785.3 MB
EGAF00007774246 fastq.gz 821.8 MB
EGAF00007774247 fastq.gz 699.0 MB
EGAF00007774248 fastq.gz 724.5 MB
EGAF00007774249 fastq.gz 689.6 MB
EGAF00007774250 fastq.gz 714.6 MB
64 Files (47.1 GB)