|
| Status |
Public on Jan 10, 2018 |
| Title |
SOCa |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: serous ovarian cancer
disease: ovarian cancer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The tissue samples from two ovarian cancer patients and one healthy donor was surgically resected and immediately placed into RNAlater solution (Invitrogen) at room temperature. These samples were collected from the neighbouring hospitals in the state. The median age of the donors was 60 years. All patients provided written informed consent. The IEC approval has been taken to carry out this work. The resected ovarian cancer tissues were characterized as endometrioid and serous type from the tissue biopsy. The samples were stored at -80°C until next-generation sequencing and other experiments were performed. Total RNA was extracted from all three tissue samples (ENOCa, SOCa, and normal ovary) with the use of RNeasy Mini kit (Qiagen, USA) according to the manufacturer’s instructions. The purity of isolated RNA was evaluated using NanoDrop spectrophotometer (Thermo Scientific) by measuring absorbance at 260 nm and 280 nm. An aliquot of each the samples of ENOCa, SOCa, and normal ovary was also run on an Agilent RNA Bioanalyzer chip to check for RNA integrity number (RIN) and was found to be 7.7, 7 and 6.3 respectively.
The RNA libraries were constructed for sequencing following Illumina TruSeq Small RNA library protocol outlined in “TruSeq Small RNA Sample Preparation Guide” (Part # 15004197; Rev. F; February 2014) and using TruSeq Small RNA sample preparation kit (Illumina, # RS-200-0012). The library was size selected in the range of 145 – 165 bp.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
bcl2fastq software (Illumina) was used for converting image file to FASTq format.
Sequenced reads were trimmed for adaptor sequence using srna Work bench and Quality check of the generated data was done using the FASTqc software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of annotated piRNAs predicted for each Sample.
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE83794 |
Next-generation Sequencing (NGS) identified genome-wide profiles of piwi-interacting RNAs (piRNAs) in human Epithelial Ovarian Cancers (EOCa) |
|
| Relations |
| BioSample |
SAMN05300496 |
| SRA |
SRX1881632 |
