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Sample GSM8208286 Query DataSets for GSM8208286
Status Public on May 30, 2024
Title D. melanogaster hmr2, ovaries, small RNA rep2
Sample type SRA
 
Source name ovaries
Organism Drosophila melanogaster
Characteristics tissue: ovaries
Extracted molecule other
Extraction protocol For small RNA libraries preparation RNA was extracted from 0-3 days old gonads of D. melanogaster Hmr2, D. simulans w501 and interspecific hybrids. Small RNA fraction (19-29 nt) was purified by 15% polyacrylamide gel from 20-30 μg total RNA.
Small RNA libraries were prepared using NEBNext Multiplex Small RNA Sample Prep Set for Illumina (#E7300S, NEB) and sequenced on NovaSeq 6000 in 100 bp single-end mode yielding 25-40 million single-end reads per library.
 
Library strategy ncRNA-Seq
Library source other
Library selection size fractionation
Instrument model Illumina NovaSeq 6000
 
Data processing For piRNA production analysis adapter sequences were removed by cutadapt 2.8. After quality control with FastQC rRNA, snRNA, snoRNA, and tRNA were filtered from libraries using bowtie (version 1.1.0) with -v 3 parameter. Unaligned reads were then filtered against microRNA set of D. simulans and D. melanogaster obtained from https://ftp.flybase.net/releases/current/dsim_r2.02/ and https://ftp.flybase.net/releases/current/dmel_r6.56/, resrespectively. Small piRNAs of 23–29 nt in length were selected using cutadapt 2.8. This piRNA fraction was mapped to Drosophila transposon canonical sequences v10.1 (https://github.com/bergmanlab/drosophila-transposons/) using bowtie version 1.1.0 with parameters -l 35 -n 3. Mapped reads were counted with htseq-count 2.0.0
Assembly: transposon canonical sequences v10.1 (https://github.com/bergmanlab/drosophila-transposons/)
Supplementary files format and content: piRNA counts for transposon canonical sequences obtained by htseq-count 2.0.0
 
Submission date Apr 15, 2024
Last update date May 30, 2024
Contact name Alexei A. Kotov
E-mail(s) kotov_alexei@mail.ru
Organization name Koltzov Institute of Developmental Biology of the Russian Academy of Sciences
Street address 26 Vavilov Street
City Moscow
ZIP/Postal code 119334
Country Russia
 
Platform ID GPL25244
Series (2)
GSE263983 Molecular insights into female hybrid sterility in interspecific crosses between Drosophila melanogaster and Drosophila simulans (small RNA-Seq)
GSE263985 Molecular insights into female hybrid sterility in interspecific crosses between Drosophila melanogaster and Drosophila simulans
Relations
BioSample SAMN40973255
SRA SRX24266701

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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