 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 10, 2018 |
| Title |
Next-generation Sequencing (NGS) identified genome-wide profiles of piwi-interacting RNAs (piRNAs) in human Epithelial Ovarian Cancers (EOCa) |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Purpose: The aim of this study is to identify known and novel small RNAs (Piwi-interacting RNAs and microRNAs) in normal ovary and epithelial ovarian malignancies by adopting high-throughput RNA sequencing (RNA-Seq) and unveil their possible functions in neoplastic pathways of the two most frequently observed and highly lethal subtypes of epithelial ovarian cancers, endometrioid ovarian cancer (ENOCa) and serous ovarian cancer (SOCa). The study has been performed in normal ovarian tissues as well as malignant tissues of these cancer subtypes.
Methods: 1 µg of total RNA was used as the starting material for library preparation as prescribed by Illumina Truseq small RNA library protocol. Small RNA sequencing was carried out by Genotypic Technology, Bangalore, India on Illumina Next-Seq 500 platform. Library preparation was done by performing 3' and 5' adapter ligation followed by reverse transcription of cDNA and amplification of the library. The construct of the library was fractionated to select 16-40 nucleotide insert of small RNAs using PAGE. The quality check of the library was done in Agilent Technologies 2100 Bioanalyzer using a DNA-specific chip, such as High Sensitivity DNA. The sequence reads that passed through Quality Check by FastQC and aligned to the human genome (hg19) were further analysed using in-house pipelines and set of known and novel piRNAs and miRNAs were identified. The sets of known piRNAs and miRNAs identified were assessed for their involvement in neoplastic processes of ovarian cancer subtypes by performing target analysis and GO enrichment studies.
Results: Using an in-house prediction pipeline, we mapped about 10-15 million sequence reads per sample to the human genome (hg19) and detected 256, 234 and 219 annotated piRNAs in ENOCa, SOCa, and normal ovary respectively; whereas the average number of known miRNAs present in each sample was estimated to be 480. The annotated piRNAs obtained from each sample exhibited varied length distribution between 26-32 nts.
Conclusions: For the first time, our study reported the presence of piRNAs in ENOCa, SOCa and normal ovarian tissue from the next-gen sequencing of small RNAs of 16-40 nts length. The extensive catalogue of human EOCa small RNAs (both piRNAs and miRNAs) detected in this study provides a useful resource to dissect complex neoplastic events that are possibly mediated by these ncRNAs, especially by piRNAs. Moreover, these piRNAs could be used as probable small RNA biomarkers for the EOCa.
|
| |
|
| Overall design |
Small RNA profile of human epithelial ovarian cancer and normal epithelial ovarian tissue was generated by deep sequencing using Illumina Next-Seq 500
|
| |
|
| Contributor(s) |
Singh G, Mallick B |
| Citation(s) |
29320577 |
| Submission date |
Jun 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dr. Bibekanand Mallick |
| E-mail(s) |
vivek.iitian@gmail.com
|
| Organization name |
National Institute of Technology
|
| Department |
Department of Life Science
|
| Lab |
RNAi & Functional Genomics Lab.
|
| Street address |
NIT Rourkela
|
| City |
Rourkela |
| State/province |
Odisha |
| ZIP/Postal code |
769008 |
| Country |
India |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (3) |
|
| Relations |
| BioProject |
PRJNA327030 |
| SRA |
SRP077450 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE83794_RAW.tar |
20.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
