|
| Status |
Public on Mar 04, 2020 |
| Title |
PC3-T-Veh-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Prostate cancer
xenograft: PC3
ar status: AR-
animal treatment: Vehicle
|
| Treatment protocol |
Cell cultures were treated with E7107 at 10nM for 6 hrs, and tumors were treated with E7107 at 5mg/kg/day for 5 days.
|
| Growth protocol |
Early passages of LNCaP and PC3 cells (obtained from ATCC) were grown in RPMI1640 medium supplemented with 7% serum. LAPC9-AI and PC3 xenograft models were maintained in castrated NSG male mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell cultures (LNCaP and PC3) treated with DMSO (D) or E7107 (E) for 6hrs in vitro, and tumors (LAPC9-AI and PC3) harvested 4hrs after Vehicle (C) or E7107 (E) injection were subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 23
|
| Data processing |
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.5.2).
The number of fragments in each known gene from GENCODE (version 25) was enumerated using STAR QuantMode (GeneCounts) function.
The normalized fragment count for each gene was calculated by R/Bioconductor package DESeq2 (version 1.18.1).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq2) for all the samples.
|
| |
|
| Submission date |
Mar 19, 2019 |
| Last update date |
Mar 04, 2020 |
| Contact name |
Dingxiao Zhang |
| E-mail(s) |
zdx1980@hnu.edu.cn
|
| Phone |
+86-15391542415
|
| Organization name |
Hunan University
|
| Department |
School of BioMedical Sciences
|
| Lab |
Zhang lab
|
| Street address |
Yuelushan
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410082 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE128515 |
Therapeutic targeting of splicing in aggressive prostate cancer |
|
| Relations |
| BioSample |
SAMN11165021 |
| SRA |
SRX5541098 |
