|
| Status |
Public on May 08, 2024 |
| Title |
control_stimulated_2 |
| Sample type |
SRA |
| |
|
| Source name |
T cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T cell
donor: Healthy donor
genetic modification: α-Lewis-Y-CAR
genotype: control
treatment: 24 h activation with plate bound anti-idiotype LeY
|
| Treatment protocol |
Cultured without stimulation (non-stimulated), activated with plate bound anti-idiotype-LeY (anti-CAR) antibody for 24 h (stimulated) or activated with plate bound anti-idiotype-LeY (anti-CAR) antibody for 24 h followed by 7 days recovery.
|
| Growth protocol |
Human peripheral blood mononuclear cells (PBMCs) were isolated from normal buffy coats using Ficoll centrifugation and PBMCs were cultured in RPMI supplemented with 10% FCS, sodium pyruvate, glutamax, NEAA, HEPES and penicillin/streptomycin. PBMCs were activated with antihuman CD3 (30ng/ ml) and IL-2 (600 IU/ml) for 48 hours before transduction with a lentvirus encoding a second generation scFv–anti–Lewis-Y CAR (41BBz and CD3ζ). Cells were cultured at a density of 1x106/ml following the transduction process.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
control_stimulated_2
1.8_sorted.bam
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: hg19
Supplementary files format and content: count file generated by featureCounts. Processed data include raw and normalized counts CPM.
|
| |
|
| Submission date |
Apr 04, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Kevin C sek |
| E-mail(s) |
[email protected]
|
| Phone |
0432960331
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Cancer Immunology
|
| Lab |
Beavis Lab
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE263257 |
FOXO1 enhances CAR T cell stemness, metabolic fitness and efficacy [human_FOXO1OE_stimulation/rest_RNAseq] |
|
| Relations |
| BioSample |
SAMN40753314 |
| SRA |
SRX24159810 |
