|
| Status |
Public on Feb 06, 2020 |
| Title |
1.B 72h.2 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Panc-215
cell type: Pancreatic cancer cell line
treatment: Taxol
time-point: 72 hours
|
| Treatment protocol |
Taxol was added during 24 hours and then washed out.
Palbociclib treatment started 24 hours later and was maintained until the indicated time points.
Combination: Taxol 24 hours followed by Palbociclib maintained until the indicated time points.
DMSO was added during 24 hours.
|
| Growth protocol |
Panc-163 and Panc-410 cell lines were grown in DMEM 10% pen/strep 10% FBS.
Panc-215 cell line was grown in RPMI 10% pen/strep 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Life Technologies) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
1.B 72h.2
processed data file: ALLsamples.normalizedCounts.xls
|
| Data processing |
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Fastq files were quality-checked using FastQC v0.10.1.
Reads were aligned to the human genome (GRCh38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.1.9 allowing two mismatches and five multihits.
Transcript quantification was calculated with htseq and differential expression was calculated with DEseq2 using the human GRCh38 transcript annotations.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: ALLsamples.normalizedCounts.xls: Excel file includes normalized counts for each sample.
|
| |
|
| Submission date |
Jul 31, 2019 |
| Last update date |
Mar 19, 2020 |
| Contact name |
Elena Piñeiro-Yáñez |
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Street address |
Calle de Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE135215 |
RNAseq analysis of taxol and palbociclib combination in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN12418682 |
| SRA |
SRX6631479 |
