|
Status |
Public on Nov 10, 2023 |
Title |
B16_Ctrl_Veh_rep1 |
Sample type |
SRA |
|
|
Source name |
murine melanoma
|
Organism |
Mus musculus |
Characteristics |
cell type: B16F10 genotype: Ctrl activation?: NA treatment: DMSO
|
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 1 5894_1_B16_Ctrl_Veh_rep1_CGATGTA_S14_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 |
SAMN16728085 |
SRA |
SRX9470978 |