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Sample GSM3963322 Query DataSets for GSM3963322
Status Public on Jul 12, 2022
Title SPOP F102C.1 shGLI3 -DHT repeat 1
Sample type SRA
Source name LNCaP prostate cancer cell line
Organism Homo sapiens
Characteristics cell line: LNCaP prostate cancer cell line
genotype: SPOP mutant
media type: Hormone deprived media
treatment: shGLI3 specific lentivirus treated
Treatment protocol All cells grown in hormone deprived media were transitioned to phenol red free and dextran-charcoal treated FBS containing media 10 days prior to RNA harvest. For all shGLI3 samples, cells were treated with shGLI3 lentivirus 6 days prior to transition to hormone deprived media.
Growth protocol LNCaP were cultured at 37C and 5% CO2 in standard or phenol red–free RPMI-1640 medium containing 10% standard or dextran-charcoal treated fetal bovine serum respectively
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol and Direct-zol RNA Miniprep kit (Zymo Reserach) according to the manufacturer’s instructions.
Total RNA samples about 1-2 mg were used for sequencing library preparation according to Illumina TruSeq stranded mRNA-seq Sample Preparation Guide. Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SR) sequencing protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description Clone 1 F102C LNCaP cells grown in hormone deprived media and treated with shGLI3 lentivirus
Data processing Illumina Casava v1.8.2 software used for base-calling for samples by HiSeq2000, and Illumina bcl2fastq software used for base-calling for samples by HiSeq3000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
Submission date Jul 22, 2019
Last update date Jul 14, 2022
Contact name YI ZOU
Organization name UTHSA-GCCRI
Street address 8403 Floyd Curl Drive
State/province TX
ZIP/Postal code 78229
Country USA
Platform ID GPL21290
Series (1)
GSE134682 Pathologically stabilized GLI3 promotes androgen-independent growth of SPOP mutant prostate cancer cells through reactivation of an AR signaling axis
BioSample SAMN12339740
SRA SRX6489938

Supplementary file Size Download File type/resource
GSM3963322_7_shGLI3_1_Genes_ReadCount.txt.gz 94.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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