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Sample GSM8015507 Query DataSets for GSM8015507
Status Public on Apr 22, 2024
Title DKO cells, siNC, repeat 1
Sample type SRA
Source name DKO (Pten-/-/Rb-/-) murine PCa cells
Organism Mus musculus
Characteristics cell line: DKO (Pten-/-/Rb-/-) murine PCa cells
cell type: Prostate cancer cell line
treatment: Negative control knockdown
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. DKO cells were cultured in DMEM base medium supplemented with 10% FBS
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 DKO_siFOXA2_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) /GRCm38 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/GRCm38
Supplementary files format and content: tab-deliminated text files include raw gene counts
Submission date Jan 12, 2024
Last update date Apr 22, 2024
Contact name Zifeng Wang
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 GPL30172
Series (2)
GSE232554 FOXA2/AP-1 drives prostate cancer lineage plasticity [RNA-seq]
GSE232555 FOXA2/AP-1 drives prostate cancer lineage plasticity
BioSample SAMN39423429
SRA SRX23203751

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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