|
| Status |
Public on May 31, 2018 |
| Title |
LNCaP parental PD treated replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
human prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: immortalized cell line
developmental stage: derived from lymph node metastasis
concentration: 0.5uM PD
|
| Treatment protocol |
Cells were seeded (without drugs) in standard culture media and treated for 24 hours with 0.5uM PD or vehicle control before harvesting RNA
|
| Growth protocol |
Palbociclib (PD) resistant cells (PDR) were generated from LAPC4 and LNCaP cells via sustained treatment with 0.5uM PD and kept under PD-selection to maintain the cells. Parental cells were cultured in parallel in standard growth media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with a RNeasy Mini Kit by Qiagen
RNA-seq from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
LN-PDR1-PD_vs_LN-WT-PD.txt
LN-PDR2-PD_vs_LN-WT-PD.txt
LNWTPD_vs_LNWTCntrl.txt
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRampē“ advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...
|
| |
|
| Submission date |
Jun 05, 2017 |
| Last update date |
Mar 26, 2021 |
| Contact name |
Gary Hardiman |
| E-mail(s) |
[email protected], [email protected], [email protected]
|
| Organization name |
Medical University of South Carolina
|
| Department |
Medicine
|
| Street address |
135 Cannon Street
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
SC |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE99675 |
CDK4/6 inhibitor resistance in prostate cancer |
|
| Relations |
| BioSample |
SAMN07194389 |
| SRA |
SRX2883858 |
