|
| Status |
Public on Jul 18, 2024 |
| Title |
06__T15smarcb1A3 |
| Sample type |
SRA |
| |
|
| Source name |
T15 cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: T15
treatment group: Smarcb1-reexpression
|
| Treatment protocol |
For T15-Smarcb1 re-expression, T15 cells were lentivirally transduced with a control (Smarcb1-) or Smarcb1 expression plasmid pInd20. After antibiotic selection (G418) and Doxycyclin induction (0.5 µg/µl) (72 h) total RNA was extracted and sequenced. For T15-SAHA: T15 cells were treated with SAHA (1 µM final concentration) or vehicle twice in 72 h. Afterwards, RNA was isolated and sequenced.
|
| Growth protocol |
All cells were maintained at 37°C and 5% CO2 in RPMI 1640 medium with 10% FBS, 1% HEPES 1M, 1% penicillin/streptomycin (10,000 U/ml), sodium pyruvate (100 nM), l-glutamine (200 nM) and 0.1% β-mercaptoethanol (50 nM; all from Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini Kit (Qiagen) as specified by the manufacturer.
Sequencing libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's guidelines.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw FASTQ files were obtained and, after explorative quality control with FastQC (v0.11.8) and MultiQC (v1.7), we used Salmon (v0.14.1) for pseudo-alignment and quantification of the samples to the mouse transcriptome (downloaded from Ensembl, release 94). Default parameters were used.
Further analyses were performed in R. We employed the Bioconductor package tximport (v1.10.1) to summarize transcript-level estimates computed by Salmon for a gene-level analysis.
To find differentially expressed genes, we used the package DESeq2 (v1.22.2) and tested for SMARCB1 re-expression versus control conditions.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_gene_counts_matrix.txt contains tab-separated raw counts for each gene and each sample
|
| |
|
| Submission date |
Dec 06, 2021 |
| Last update date |
Jul 18, 2024 |
| Contact name |
Carolin Walter |
| E-mail(s) |
c_walt03@uni-muenster.de
|
| Organization name |
Westfälische Wilhelms-Universität Münster
|
| Department |
Medical Faculty of the WWU Münster
|
| Lab |
Institute of Medical Informatics
|
| Street address |
Domagkstraße 9
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE190273 |
SMARCB1 loss defines a novel PTCL-NOS subtype displaying an immunosuppressive TME susceptible to HDAC inhibitors [bulk RNA-seq] |
| GSE190276 |
SMARCB1 loss defines a novel PTCL-NOS subtype displaying an immunosuppressive TME susceptible to HDAC inhibitors |
|
| Relations |
| BioSample |
SAMN23703968 |
| SRA |
SRX13326143 |
