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Sample GSM3720906 Query DataSets for GSM3720906
Status Public on Jul 05, 2020
Title 5G14
Sample type SRA
 
Source name RNA-seq-testis
Organism Oryzias latipes
Characteristics strain: Hd-rR
tissue: testis
treatment: EE2
Treatment protocol Fertilized eggs were collected and exposed to EE2 (10 ng/L) or BPA (10 µg/L) through the incubation water over a period of 12 dpf in 50 ml glass petri-dishes. Exposures were static with daily renewal of test chemicals from fertilization through day 12.
Growth protocol The medaka strain Hd-rR was used and maintained under standard conditions
Extracted molecule total RNA
Extraction protocol Total RNA from each sample tissues were extracted using a commercial combo kit for RNA/DNA isolation (Qiagen, Carlsbad, CA) according to manufacturer’s instructions.
The quality control and RNA-seq library preparation was conducted by the DNA sequencing Core facility of the University of Missouri Columbia.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description EE2 Rep2
Data processing Sequencing reads from each sample were mapped to medaka reference transcripts (Ensembl version 95) using TopHat2 software with default parameters. Only uniquely mapped reads were used for subsequent analysis. Cufflinks software was used to conduct differentially expressed gene analysis on the raw count data. Technical replicates were merged together using the Samtools software.
 
Submission date Apr 12, 2019
Last update date Jul 05, 2020
Contact name Ramji Kumar Bhandari
E-mail(s) rkbhanda@uncg.edu
Organization name University of North Carolina Greensboro
Department Biology
Lab Bhandari Laboratory
Street address 321 McIver St
City Greensboro
State/province NC
ZIP/Postal code 27412
Country USA
 
Platform ID GPL23308
Series (1)
GSE129727 RNA-seq testis
Relations
BioSample SAMN11405765
SRA SRX5675043

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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