|
| Status |
Public on Nov 10, 2023 |
| Title |
OTI_Ctrl_TG_Rest_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse T-cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: OT-I/Cas9 CD8 T cells
genotype: Ctrl
activation?: Resting
treatment: Thapsigargin
|
| Treatment protocol |
For drug treatment, DMSO or thapsigargin (50ng/mL) was added to the culture where indicated. For activation, a 24-well non-tissue-culture-treated plate was coated with anti-CD3 antibodies overnight and on the day of the experiment, cells were seeded on this plate at a density of 1*10^6/mL where indicated.
|
| Growth protocol |
B16F10 were maintained in DMEM/10%FCS/Penicillin (100U/mL)/Streptomycin (100ug/mL)/Puromycin (1ug/mL) and passaged 1:10 every two days. T cells were maintained in RPMI/10%FCS/Penicillin (100U/mL)/Streptomycin (100ug/mL) with IL-2 (10ng/mL), IL-7 (0.5ng/mL), IL-15 (1ng/mL), betamercaptoethanol (50uM) and puromycin (4ug/mL) and passaged every day at a density of 1*10^6/mL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
replicate 2
5894_12_OT-I_Ctrl-1_TG_Rest_rep2_GTGAAAC_S24_R1_001
|
| Data processing |
Sequence samples were mapped to the mouse genome (GRCm38) using STAR(2.6.0c) using 2-pass mapping with default settings. Sequence reads were counted using HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: Un-processed read count data
|
| |
|
| Submission date |
Nov 10, 2020 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Oscar Krijgsman |
| E-mail(s) |
o.krijgsman@nki.nl, oscarkrijgsman@gmail.com
|
| Phone |
31205122028
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Molecular Oncology and Immunology
|
| Lab |
Peeper
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| State/province |
Outside the US or Canada |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE161209 |
Serca2b inhibition aids T cell activation and selectively promotes tumor cell death |
|
| Relations |
| BioSample |
SAMN16728073 |
| SRA |
SRX9470989 |
