|
| Status |
Public on Jun 14, 2019 |
| Title |
DU145_CON2 (D0-2) |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DU145
genotype: wild type
|
| Treatment protocol |
Cell culture medium containing 2.5 uM pentamidine or vehicle
|
| Growth protocol |
Cells were cultured with vehicle or 2.5 uM pentamidine in 6-well plates (1000000 cells/well) at 37°C for 48 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from PC3 and DU145 cells treated with 2.5 uM pentamidine or vehicle using the TRIzol reagent (Invitrogen, 15596018) and mRNA was enriched by Oligo(dT) beads.
The enriched mRNA was fragmented into short fragments using the fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA fragments were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then these cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were then size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq 6000 PE150.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
DU145 cultured with vehicle in 6-well plates (1000000 cells/well) at 37°C for 48 hours
|
| Data processing |
Illumina Novaseq 6000 PE150 used for sequencing
Paired-end clean reads were aligned to the reference genome using HISAT2 (v2.1.0).
Differential expression analysis of two groups was performed using the DESeq R package (1.18.1).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Genes with |log2(FoldChange)| > 1 and adjusted Pvalue <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: All.ReadsCount.txt and All.FPKM.exp.txt includes ReadsCount and FPKM values for each Sample; DU145_PTMVSDU145_CON.All.txt includes FPKM values and statistical analysis data for pentamidine- and vehicle-treated DU145 cells; PC3_PTMVSPC3_CON.All.txt includes FPKM values and statistical analysis data for pentamidine- and vehicle-treated PC3 cells.
|
| |
|
| Submission date |
Jun 13, 2019 |
| Last update date |
Jun 14, 2019 |
| Contact name |
Lin Liu |
| E-mail(s) |
55319872@163.com
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
Renji‐Med X Clinical Stem Cell Research Center, Ren Ji Hospital
|
| Lab |
State Key Laboratory of Oncogenes and Related Genes
|
| Street address |
Shanghai
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
222110 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE132693 |
RNAseq of prostate cancer cells (PC3 and DU145) treated with 2.5 uM pentamidine or vehicle |
|
| Relations |
| BioSample |
SAMN12047800 |
| SRA |
SRX6061995 |
