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Sample GSM3916509 Query DataSets for GSM3916509
Status Public on Aug 26, 2019
Title Digitoxin-treated rep3
Sample type SRA
 
Source name PAIII tumor
Organism Rattus norvegicus
Characteristics treatment: digitoxin
Extracted molecule total RNA
Extraction protocol Samples of grossly dissected, frozen primary tumors were mounted on a cryostat chuck. Serial thick sections (300 micron) were then cut and mounted on cold slides. Ten random samples were micro-dissected from viable regions of the tumor in 300 micron thick sections with a 1 mm diameter micropunch device. The tumor samples were then soaked in RNA Later at four degrees Celsius overnight before isolation of total RNA.
One microgram of total RNA was input for library preparation using the TruSeq RNA Sample Prep Kit v2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description A12
Data processing FASTQ data were generated using CASAVA
Raw reads were analyzed and groomed using FASTQC and FASTQ Groomer
RPKM values for transcriptome expression levels were generated using Bowtie 2, TopHat 2 and Cufflinks 2.
RPKM values were used for Comparative Marker Selection and differential gene analysis by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample profiled.
 
Submission date Jul 02, 2019
Last update date Aug 26, 2019
Contact name Clifton Lee Dalgard
E-mail(s) cdalgard@usuhs.edu
Organization name Uniformed Services University
Department Anatomy Physiology & Genetics
Lab Dalgard
Street address 4301 Jones Bridge Road B2038
City Bethesda
State/province Maryland
ZIP/Postal code 20814
Country USA
 
Platform ID GPL10669
Series (1)
GSE133696 Digitoxin Inhibits Epithelial-to-Mesenchymal-Transition in Hereditary Castration Resistant Prostate Cancer
Relations
BioSample SAMN12187038
SRA SRX6388042

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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