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Status |
Public on Oct 15, 2024 |
Title |
Drosophila_ficusphila_ag_G_45_45_S93 |
Sample type |
SRA |
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Source name |
accessory glands
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Organism |
Drosophila ficusphila |
Characteristics |
tissue: accessory glands sample id: ag_G_45 library name: 45_S93 strain information: 631.0-iso1 (14025-0441.05)
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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 3000 |
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Description |
dfic_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) |
brhopkins92@gmail.com
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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 |
GPL34785 |
Series (1) |
GSE274048 |
RNA-seq samples from male sex organs in Drosophila |
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Relations |
BioSample |
SAMN43046759 |
SRA |
SRX25615872 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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