|
| Status |
Public on Sep 28, 2022 |
| Title |
2nd restim GBBz rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Healthy donor-derived T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD3+CAR+ T cells
genotype: CAR expressing T cell with GFP downregulation
|
| Treatment protocol |
6 days after ΔLNGFR+ cell isolation, CAR T cells were co-cultured with γ-irradiated Nalm-6-PD-L1-CD80 for 6 day. Subsequently, CAR T cells were restimulated under the same condition. 1st or 2nd restimulated CAR-T cells were collected at 48 hr after each stimulation, followed by magnetic selection of ΔLNGFR+ T cells. .
|
| Growth protocol |
CD19-specific CAR+ΔLNGFR+ T cells are sorted by LNGFR microbeads (Miltenyi), and cultured for 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of isolated CAR T cells was isolated using NucleoSpin RNA XS kit (MACHEREY-NAGEL, Germany). The RNA quality was determined with the Agilent 4200 Tapestation (RIN value > 9).
RNA sequencing libraries were constructed using Illumina Truseq Stranded mRNA LP kit. Briefly, mRNA was purified by oligo-dT beads and fragmented through an enzymatic reaction. After fragmentation, cDNA was generated through reverse transcription. The cDNA libraries were constructed and followed by 100 bp paired-end mode on DNBSEQ-400 platform. External RNA controls consortium (ERCC) RNA spike-in mixes (Thermo Fisher, 4456740) were included for quality assurance. The quality of all paired-end reads was analyzed using FastQC software, and the per base sequence quality of all sample was above Q30.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
RNA-seq analysis carried out via Galaxy platform (https://usegalaxy.org/).
The FASTQ data was mapped to the reference genome hg19 using HISAT2 v2.1.0.
The number of reads per annotated gene was then computed from the mapped reads using featurecounts v1.6.4.
The R package limma with voom method v3.38.3 was used to both normalized all dataset and analyzed differential expression between all groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts
|
| |
|
| Submission date |
Sep 28, 2020 |
| Last update date |
Sep 28, 2022 |
| Contact name |
YoungHo Lee |
| E-mail(s) |
yhlee@curocellbtx.com
|
| Organization name |
Curocell
|
| Street address |
48, Yuseong-daero 1184beon-gil, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
34109 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE158676 |
Simultaneous, cell-intrinsic downregulation of PD-1 and TIGIT can enhance effector function of CD19-targeting CAR T cells and promote early memory phenotype |
|
| Relations |
| BioSample |
SAMN16282610 |
| SRA |
SRX9204287 |
