|
| Status |
Public on Jul 09, 2019 |
| Title |
Race-specific transcriptome and Long non-coding RNA of ADT-resistant African-American prostate cancer cell models. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The goals of this study are to compare NGS-derived Androgen Deprivation Therapy (ADT) resistant transcriptome to profiling (RNA-seq) to Androgen Deprivation Therapy (ADT) sensitive transcriptome in African American prostate cancer cells and validate by reverse transcription polymerase chain reaction (qRT–PCR) methods.
Method: Total RNA was extracted from different CaP cell who were ADT sensitive and ADT resistance. Total RNA was subjected to whole transcriptome sequencing analysis. Sequence reads
Results: We performed whole transcriptome RNA-Seq analysis through paired-end deep sequencing to systematically investigate the molecular features of different CaP cell models- RCC7/N, RCC7T/E, RCC7T/E-ADT, RCC7T/E-CD133, E006AA-hT and E006AA-hT-ADT We obtained an average of 23.85 million reads per sample, ranging from 22.86 to 24.93 million reads, with an average mapping rate of 98.29% to the reference human genome (UCSC version hg20). Next we performed Kal’s Z-test and generated Fold-Change (FC) values, p values and False Discovery Rate (FDR) values for measuring comparative gene expression profile. By applying stringent statistical threshold of greater than or equal to 2 FC, p value < 0.05 and FDR value < 1, we identified genes that were significantly differentially expressed in three different comparative groups.
Conclusions: "Our study represents the first detailed analysis of African American ADT resistant transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. "
|
| |
|
| Overall design |
Androgen resistant and Androgen sensitive mRNA profiles from African American prostate cancer of were generated by deep sequencing, in duplicate using Illumina HiSeq
|
| |
|
| Contributor(s) |
Ganaie AA, Saleem M, Konety BR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R21 CA184685 |
Novel gene that determines metastatic phenotype in African-American men |
UNIVERSITY OF MINNESOTA |
MOHAMMAD SALEEM BHAT |
| U54 MD008620 |
National Transdisciplinary Collaborative Center for African American Men's Health |
UNIVERSITY OF ALABAMA AT BIRMINGHAM |
BADRINATH R KONETY |
|
| |
| Submission date |
Jun 04, 2018 |
| Last update date |
Jul 11, 2019 |
| Contact name |
Mohammad Saleem |
| Organization name |
University of Minnesota
|
| Department |
Urology
|
| Lab |
Molecular Therapeutics and Cancer Health Disparity
|
| Street address |
2231 6th St SE
|
| City |
Minneapolis |
| State/province |
Mn |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA474510 |
| SRA |
SRP149717 |
Less...
More...