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| Status |
Public on May 30, 2024 |
| Title |
D. simulans w501, ovaries, small RNA rep1 |
| Sample type |
SRA |
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| Source name |
ovaries
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| Organism |
Drosophila simulans |
| Characteristics |
tissue: ovaries
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| 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.
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| Library strategy |
ncRNA-Seq |
| Library source |
other |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Apr 15, 2024 |
| Last update date |
May 30, 2024 |
| Contact name |
Alexei A. Kotov |
| E-mail(s) |
kotov_alexei@mail.ru
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| Organization name |
Koltzov Institute of Developmental Biology of the Russian Academy of Sciences
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| Street address |
26 Vavilov Street
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| City |
Moscow |
| ZIP/Postal code |
119334 |
| Country |
Russia |
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| Platform ID |
GPL33169 |
| 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 |
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| Relations |
| BioSample |
SAMN40973252 |
| SRA |
SRX24266704 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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