|
| Status |
Public on May 27, 2016 |
| Title |
shMyb |
| Sample type |
SRA |
| |
|
| Source name |
MiaPaCa
|
| Organism |
Homo sapiens |
| Characteristics |
cancer type: Pancreatic cancer
cell line: MiaPaCa
genotype/variation: MYB-silenced
|
| Treatment protocol |
MiaPaCa cells were transfected with short hairpin RNA (shRNA) expression constructs for Myb (pGFP-V-RS-shMYB) along with control plasmids (pGFP-V-RS-Scr), using FuGENE as a transfection reagent. Stable pooled population of transfected cells were selected in RPMI-media containing Puromycin (2 μg/ml), expanded and examined for stable MYB silencing.
|
| Growth protocol |
MiaPaCa cells were maintained as monolayer cultures in RPMI 1640 media supplemented with 10% fetal bovine serum and 100 µM each of penicillin and streptomycin in a humidified atmosphere of 5% CO2 at 370C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Purification Kit.
RNA libraries were prepared and sequencing was performed using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-sequencing and bioinformatics analysis were performed at the Genomics Core Facility at the Heflin Center for Genetics, University of Alabama at Birmingham as described by Jiang et al., PlosOne (2013)
Illumina Casava v1.8.2 software used for basecalling.
TopHat was used to align the raw RNA-Seq fastq reads to the human hg19 genome using the short read aligner Bowtie. Cufflinks was used to align the reads from TopHat to assemble transcripts, estimate their abundances and test for differential expression and regulation.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file including Scr and shMyb abundance measurements, Scr vs shMyb fold change, log2 (fold_change) and p-value values.
|
| |
|
| Submission date |
Sep 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ajay P Singh |
| E-mail(s) |
asingh@health.southalabama.edu
|
| Phone |
251-445-9843
|
| Organization name |
University of South Alabama Mitchell Cancer Institute
|
| Department |
Oncologic Sciences
|
| Street address |
1660 Springhill Ave
|
| City |
Mobile |
| State/province |
Alabama |
| ZIP/Postal code |
36604 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE61290 |
Myb-regulated transcriptome in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN03068239 |
| SRA |
SRX700854 |
