|
| Status |
Public on Apr 01, 2018 |
| Title |
mc38 treated with co colture sup (2) |
| Sample type |
SRA |
| |
|
| Source name |
MC38
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MC38
treatment: treatedwithcocolturesup
|
| Growth protocol |
10 percent FCS in DMEM + Pen/Strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Nucleospin® RNA extraction kit (Macherey-Nagel, Bethlehem, PA) as per the manufacturer's instructions.
cDNA libraries were prepared using the QuantSeq 3' mRNA seq kit, Lexogen.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
170605_NB501056_0018_AH2FYTBGX3_MC38_invitro_normalizedcounts.csv
Sup2
10-ck-260517-Sup-2
|
| Data processing |
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package
The Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression. Genes with read counts under 10 were filtered before Limma analysis.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts
|
| |
|
| Submission date |
Mar 23, 2018 |
| Last update date |
Apr 01, 2018 |
| Contact name |
Stephin J Vervoort |
| E-mail(s) |
stephin.vervoort@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE112252 |
Tumor immune evasion arises through loss of TNF sensitivity [MC38] |
| GSE112253 |
Tumor immune evasion arises through loss of TNF sensitivity |
|
| Relations |
| BioSample |
SAMN08783594 |
| SRA |
SRX3837169 |
