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| Status |
Public on May 30, 2024 |
| Title |
D. simulans w501, ovaries, rep2 |
| 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 |
polyA RNA |
| Extraction protocol |
For the preparation of RNA-seq libraries, RNA was isolated from D. melanogaster Hmr2, D. simulans w501 and interspecific hybrid ovaries with TRIzol Reagent (Invitrogen). PolyA selection was done using an Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific).
RNA-seq libraries were generated using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760, NEB) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, NEB #E7335, and Set 2, NEB #E7500) according to the manufacturer's instructions and sequenced on the Illumina NovaSeq 6000 SP platform (100 bp runs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
RNA-seq libraries of ovaries of hybrids and parental species were pseudo-aligned by kallisto v.0.50.0 (Bray et al., 2016) with following parameters: --single -l 100 -s 0.05. Merged transcriptome sets obtained from NCBI were used as reference (GCF_000001215.4 and GCF_016746395.2 assemblies for D. melanogaster and D. simulans, respectively). Quantified abundances of transcripts for protein-coding genes were imported with tximport v.1.24.0 (Soneson et al., 2015).
Assembly: GCF_000001215.4 and GCF_016746395.2 assemblies for D. melanogaster and D. simulans, respectively
Supplementary files format and content: Summarized transcript-level abundance, estimated counts and transcript lengths in csv format file
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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) |
| GSE263982 |
Molecular insights into female hybrid sterility in interspecific crosses between Drosophila melanogaster and Drosophila simulans (RNA-Seq) |
| GSE263985 |
Molecular insights into female hybrid sterility in interspecific crosses between Drosophila melanogaster and Drosophila simulans |
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| Relations |
| BioSample |
SAMN40972685 |
| SRA |
SRX24255766 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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