|
| 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 |
