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Sample GSM2895105 Query DataSets for GSM2895105
Status Public on Dec 20, 2017
Title 101(M)
Sample type SRA
 
Source name 101 (M-strain)
Organism Drosophila virilis
Characteristics tissue: Ovaries
strain: 101 (M-strain)
rna fraction: Gel extraction of small RNAs (21-29 nts)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from ovaries of 7-10 days old females using Extract RNA reagent (Evrogen, Russia). To prepare small RNA fraction for cloning, total RNA from ovaries (~ 25 µg) was separated, using 15% polyacrylamide gel electrophoresis containing 8 M Urea. After incubation in an ethidium bromide solution (0.5 µg/ml) gel fragments corresponding to the small RNA fraction were excised, using chemically synthesized RNA corresponding to 21 and 29 nts as size markers.
Cloning of small RNA libraries was performed by Illumina TruSeq Small RNA prep kit (Illumina, USA) according to the manufacturer’s protocol.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description small RNAs (21-29 nts)
Data processing As a result of deep-sequencing we obtained 5-14 million reads of small RNAs for each library. Pre-processing procedure included: 3’-adapter cropping, filtration of reads by length filtration (>18 nt) and quality (80% of nt have ≥ 20 Phred quality). Pre-processed reads were further subjected to subtraction of reads matching to all rRNA, tRNA, snRNA and miRNA sequences. The selected reads were mapped to the latest release of D. virilis genome by Bowtie (Langmead et al., 2009) with requiring of perfect match. In order to identify siRNAs and piRNAs, the sequenced reads were mapped to the canonical sequences of TEs obtained from combined libraries of annotated and computationally predicted D. virilis transposons and repeats sequences (Erwin et al., 2015). Length distribution and counting of siRNAs and piRNAs reads, nucleotide biases, ping-pong signatures, coverage of transposon sequence by piRNAs were analyzed with accordance to the well-described technique (Brennecke et al., 2007; Song et al., 2014) using custom scripts written in Python.
genome build: droVir2 (Aug, 2005)
Supplementary_files_format_and_content: Excel file with CPM
 
Submission date Dec 19, 2017
Last update date Dec 20, 2017
Contact name Sergei Funikov
E-mail(s) sergeyfunikov@gmail.com
Phone +79645866708
Organization name Engelhardt Insitute of Molecular Biology
Street address Vavilov str. 32
City Moscow
State/province Moscow
ZIP/Postal code 119991
Country Russia
 
Platform ID GPL20240
Series (1)
GSE108298 Stochastic gain of susceptibility suggests a novel mechanism of resistance to hybrid dysgenesis in Drosophila virilis
Relations
BioSample SAMN08204650
SRA SRX3485181

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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