NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8442604 Query DataSets for GSM8442604
Status Public on Oct 15, 2024
Title Drosophila_ficusphila_testes_G_z8_131220_I433
Sample type SRA
 
Source name testes
Organism Drosophila ficusphila
Characteristics tissue: testes
sample id: testes_G_z8
library name: 131220_I433
strain information: 631.0-iso1 (14025-0441.05)
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description dfic_testes_refonly_replicates.tpm
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
 
Submission date Aug 06, 2024
Last update date Oct 15, 2024
Contact name Ben Hopkins
E-mail(s) brhopkins92@gmail.com
Organization name UC Davis
Department Evolution & Ecology
Street address One Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL34799
Series (1)
GSE274048 RNA-seq samples from male sex organs in Drosophila
Relations
BioSample SAMN43046645
SRA SRX25615938

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap