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| Status |
Public on Oct 15, 2024 |
| Title |
Drosophila_simulans_ag_NG_z19_130917_I1135 |
| Sample type |
SRA |
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| Source name |
accessory glands
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| Organism |
Drosophila simulans |
| Characteristics |
tissue: accessory glands
sample id: ag_NG_z19
library name: 130917_I1135
strain information: MD106
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
We isolated mRNA from total RNA using NEBNext Poly(A) mRNA magnetic isolation.
Constructed RNA-seq directional paired-end libraries using NEBNext Ultra Directional RNA Library prep kit. We quantified library size using NEBNext Library Quant Kit (New England BioLabs, Ipswich, MA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
dsim_ag_refonly_replicates.tpm
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| Data processing |
After quality filtering with trimmomatic, we obtained 10, 22, 38, and 54 million reads for each of the 4 or five libraries.
Mapped paired-end reads to the genome and annotation from each species using STAR v. 2.5.3 (Dobin et al. 2013).
Assemlbed reference-only transcripts using Stringtie v. 1.3.4 (Pertea et al. 2015) to estimate expression in Transcrpts per million (TPM).
Assembly: Flybase: Dmel_r6.12, Dsim_r2.02, Dyak_r1.05, Dana_r1.05 NCBI: Dbia_2.0, Dbip_2.0, Dele_2.0, Deug_2.0, Dfic_2.0, Dkik_2.0, Dtak_2.0
Supplementary files format and content: Tab delimmited TPM files. One column for each biological replicate
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| Submission date |
Aug 06, 2024 |
| Last update date |
Oct 15, 2024 |
| Contact name |
Ben Hopkins |
| E-mail(s) |
[email protected]
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| Organization name |
UC Davis
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| Department |
Evolution & Ecology
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| Street address |
One Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL22293 |
| Series (1) |
| GSE274048 |
RNA-seq samples from male sex organs in Drosophila |
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| Relations |
| BioSample |
SAMN43046691 |
| SRA |
SRX25615964 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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