|
| Status |
Public on Apr 05, 2024 |
| Title |
gNT_Veh [CtrlFS1] |
| Sample type |
SRA |
| |
|
| Source name |
gNT_Veh
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP/AR cells
cell type: prostate cancer cell line
genotype: gNT
treatment: Vehicle DMSO
time: 6 days
|
| Treatment protocol |
When treated with 10 µM enzalutamide, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum.
|
| Growth protocol |
LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LNCaP/AR cells transduced with Caspase 9 and different sgRNA constructs were treated with enzalutamide or vehicle for 6 days before the total RNA was extracted using Trizol.
RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
countTable.fpkm.txt
|
| Data processing |
Bulk RNAseq:
Adapter trimming and quality trimming was performed with trimgalore (v0.5.0), and ribosomal RNA was removed using SortMeRNA (v4.1.0), using the original FASTQ files.
Trimmed and filtered reads were aligned to reference (GRCh38) with STAR (vSTAR2.6.1d). FeatureCounts (v1.6.4) was used for gene counts, biotype counts, and rRNA estimation.
Reads counts.csv files for genes and transcripts were generated by StringTie (v1.3.5), and RSeQC (v3.0.0) was used for generating RNA quality control metrics.
Reads counts from all samples were normalized using the R package DESeq2 1.26. The vst command in DESeq2 were also used to perform the variance stabilizing transformation.
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 25, 2023 |
| Last update date |
Apr 05, 2024 |
| Contact name |
Ping Mu |
| E-mail(s) |
muping817@gmail.com
|
| Organization name |
University of Texas Southwestern Medical Cente
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE230601 |
Overcoming Lineage Plasticity and AR-Targeted Therapy Resistance in ZNF397-Deficient Prostate Cancer via TET2 Inhibition [RNA-seq] |
| GSE230602 |
Overcoming Lineage Plasticity and AR-Targeted Therapy Resistance in ZNF397-Deficient Prostate Cancer via TET2 Inhibition |
|
| Relations |
| BioSample |
SAMN34371816 |
| SRA |
SRX20098613 |
