NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5542896 Query DataSets for GSM5542896
Status Public on Feb 27, 2022
Title MA6-Hd45-LU4: Pooled Male FHM High Liver RepD
Sample type SRA
 
Source name Liver tissue
Organism Pimephales promelas
Characteristics Sex: Male
tissue: Liver
treatment: 56.7µg FLX/L
replicate: D
exposure time: 96 hours
Treatment protocol Fathead minnows were exposed for 96 hours
Growth protocol Adult fathead minnows were exposed to graded aqueous fluoxetine concentrations (2.42, 10.7, 56.7 µg/L) in 20L tanks for 96 hours. Two males and three females were in each tank. Tanks were in a flow-through design maintained at 25°C and a 16:8h light:dark cycle
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tissue samples of individual fish using the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) in a QiaCube instrument (Qiagen). Pooled samples with an RNA Integrity Number (RIN) ≥ 9 were used for mRNA sequencing
Steps for generating libraries from total RNA included the following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs, Ipswich, MA, USA); cDNA synthesis was done using NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). Subsequent steps of library preparation were done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems, Wilmington, MA, USA). Determination of average fragment size was done with a LabChip GX (PerkinElmer, Waltham, MA, USA) instrument. Once libraries were normalized and pooled, they denatured in 0.02N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq (Illumina, San Diego, CA, USA) S4 lane using Xp protocol. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3.4.4. Program bcl2fastq2 v2.20 was applied to demultiplex samples and generate fastq reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing https://galaxy.ecotoxxplorer.ca/
Trim Galore! -- trimmed to a minimum phred score of 20 and a minimum sequence length of 35 bases per paired read
Kallisto quant -- alignment
Count data was normalized by use of the trimmed mean of M values approach (Robinson and Oshlack, 2010)
Genome_build: Fathead minnow reference transcriptome NCBI Acc# GCA_016745375.1
Supplementary_files_format_and_content: csv -- Differential expression results using DESeq2
 
Submission date Aug 27, 2021
Last update date Feb 27, 2022
Contact name Markus Hecker
E-mail(s) carly.colville@usask.ca, markus.hecker@usask.ca
Organization name University of Saskatchewan
Street address 44 Campus Drive
City Saskatoon
State/province SK
ZIP/Postal code S7N 5B3
Country Canada
 
Platform ID GPL30333
Series (1)
GSE182913 CHARACTERIZING TOXICITY PATHWAYS OF FLUOXETINE TO PREDICT ADVERSE OUTCOMES IN ADULT PIMEPHALES PROMELAS
Relations
BioSample SAMN21019961
SRA SRX11949296

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

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