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Sample GSM2218898 Query DataSets for GSM2218898
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
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)
BioSample SAMN05300496
SRA SRX1881632

Supplementary file Size Download File type/resource
GSM2218898_SOCa_piRNAs.txt.gz 4.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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