|
| Status |
Public on Aug 01, 2023 |
| Title |
16D_CRPC_CSS_ENZ10days_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
16D Prostate cancer cell line generated from mouse xenograft of LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Castration Resistant Prostate Cancer (CRPC)
treatment: Enzalutamide for 10days
disease state: Castration resistant
|
| Treatment protocol |
16D cells in RPMI-1640 media containing CSS were treated with 10mM ENZ for 10 days and sample for RNA-seq was prepared. 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum and ROR2 was knock down using short-hairpin (sh) RNA strategy and then treated with 10mM ENZ for 10 days and samples were prepared for RNA-seq. 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum and ROR2 was overexpressed. The ROR2 was knock down using short-hairpin (sh) RNA strategy in 42D-ENZR to generate 42D-ENZR-shROR2 cell line before being used for RNA-seq sample preparation.
|
| Growth protocol |
16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum, 42D ENZ-resistant (ENZR) cells were cultured in RPMI-1640 media containing 5% fetal bovine serum supplemented with 10mM ENZ.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from cell lines using TRIazol method (Rio et al., 2010).
Library constructions were performed using the NEBnext Ultra II Directional RNA Library Prep Kit (Cat E7760L) and NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat E7490L). Sequencing was performed on an Illumina NextSeq 500 (43x43 or 59 x 59 or 61 x 61 bp paired-end reads)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
AZLab_RNAseq1
|
| Data processing |
Base calling and de-multiplexing were performed using either bcl2fastq2 Conversion Software (v2.20) or bcl-convert (v3.8.4) with default parameters as per Illumina recommendation.
RNA-seq data processing was performed by sequencing facilty using Illumina RNA-Seq Alignment (BaseSpace Workflow) v1.1.0
Briefly, Read sequences were aligned to the hg19 human reference genome using STAR aligner v2.5.0b. Assembly and differential expression was estimated using Cufflinks software (version 2.2.1).
Assembly: hg19
|
| |
|
| Submission date |
Feb 02, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Amina Zoubeidi |
| E-mail(s) |
azoubeidi@prostatecentre.com
|
| Organization name |
Vancouver Prostate Centre
|
| Street address |
2660 Oak Street
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6H 3Z6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE224420 |
ASCL1 is activated downsrteam of ROR2/CREB signaling pathway to support lineage plasticity [RNA-seq] |
| GSE224422 |
ASCL1 is activated downsrteam of ROR2/CREB signaling pathway to support lineage plasticity. |
|
| Relations |
| BioSample |
SAMN33031163 |
| SRA |
SRX19267343 |
