|
| Status |
Public on Apr 17, 2024 |
| Title |
RSEM_siCYP3A5_1 |
| Sample type |
SRA |
| |
|
| Source name |
RSEM_siCYP3A5
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AsPC-1
cell type: pancreatic cancer cell line
disease: cancer
tissue: Pancreas
genotype/variation: CYP3A5 knockdown
|
| Treatment protocol |
Cells were not drug treated
|
| Growth protocol |
All cells were maintained according to respective ATCC recommended culture conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each cell line using the Maxwell 16 LEV automation system and simplyRNA purification kit (Promega, Cat. No. 1280) according to the manufacturer’s protocol. The extracted RNA was quantified by spectrophotometry using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA) to ensure a reading of OD260/OD280 between 1.8 and 2.0.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Preparation Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequence files were merged across lanes according to sample and subjected to a first round of quality control using the FastQC tool (www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina universal adapters were trimmed from all samples using Trim Galore ([www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and samples were then subjected to a second round of quality control
Reads were mapped to the human Hg38 reference genome using Bowtie2
The edgeR package with Limma/Voom was used for linear modeling, empirical Bayes smoothing, TMM normalization, generation of Log2(CPM), and statistical analysis
Genome_build: Hg38
Supplementary_files_format_and_content: Log2(Normalized Counts per Million + 1)
|
| |
|
| Submission date |
Apr 21, 2020 |
| Last update date |
Apr 17, 2024 |
| Contact name |
William C. Wright |
| E-mail(s) |
charlie.wright@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Computational Biology
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE149000 |
Sequencing of AsPC-1 cells with CYP3A5 expression modulation |
|
| Relations |
| BioSample |
SAMN14651438 |
| SRA |
SRX8147033 |
