|
| Status |
Public on Apr 22, 2024 |
| Title |
LNCaP_FOXA2OE_cells, DHT 10nM repeat 3 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP_FOXA2OE
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP_FOXA2OE
cell type: prostate cancer cell line (generated from LNCaP)
treatment: 10 nM DHT
|
| Treatment protocol |
PC3,NCI-H660 cells were treated with vehicle versus ORY-1001, or C12 for 4hrs
|
| Growth protocol |
PC3,LNCaP cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. NCI-H660 cells were cultured in RPMI-1640 base medium supplemented with 5% FBS, 10nM β-estradiol, 10nM hydrocortisone, and 1% Insulin-Transferrin-Selenium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
RNA libraries for RNA-seq were prepared using TruSeq Strnd Total,RNA LT (Illumina) mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
LN_FOXA2OE_DHT_3_S24
LN_FOXA2OE_DHT_rawCount.txt
|
| Data processing |
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (v2.0.1) from GRCh37 Ensembl reference.
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Assembly: GRCh37
Supplementary files format and content: tab-deliminated text files include raw gene counts
|
| |
|
| Submission date |
May 15, 2023 |
| Last update date |
Apr 22, 2024 |
| Contact name |
Zifeng Wang |
| E-mail(s) |
wzifeng8@gmail.com
|
| Phone |
6174709887
|
| Organization name |
UMASS Boston
|
| Department |
CPCT
|
| Lab |
Changmeng Cai
|
| Street address |
100 Morrissey Blvd, ISC/4610
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE232554 |
FOXA2/AP-1 drives prostate cancer lineage plasticity [RNA-seq] |
| GSE232555 |
FOXA2/AP-1 drives prostate cancer lineage plasticity |
|
| Relations |
| BioSample |
SAMN35099616 |
| SRA |
SRX20356040 |
