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Sample GSM5468943 Query DataSets for GSM5468943
Status Public on Aug 31, 2022
Title U10: upstream7
Sample type SRA
 
Source name adult
Organism Pimephales promelas
Characteristics Sex: female
strain: WT
genotype: wild type
tissue: brain
treatment: upstream exposure
age: adult
exposure: 96 h
Treatment protocol 96 h exposure 100 m upstream and 100 m downstream of effluent outfall
Growth protocol Fish were fed TetraMin Tropical Flakes twice a day and were maintained at a 16:8 h light:dark cycle. Tanks were kept at 19-23° C.
Extracted molecule total RNA
Extraction protocol Brain tissues were homogenized in TRIzol and RNA-purified using the Direct-zol RNA MiniPrep (Zymo Research, R2051).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequence data was quality-assessed using FastQC v0.11.5
Illumina TruSeq 3’-anchored primers were clipped using Cutadapt v1.18
Quality-controlled data was pseudoaligned and sample-quantified against the GCF_016745375.1 GenBank release of the fathead minnow reference genome using Kallisto v0.45.0
Genome_build: reference genome
Supplementary_files_format_and_content: estimated counts, tsv text
 
Submission date Jul 23, 2021
Last update date Aug 31, 2022
Contact name Rebecca Klaper
E-mail(s) rklaper@uwm.edu
Organization name University of Wisconsin - Milwaukee
Street address 600 E Greenfield Avenue
City Milwaukee
State/province WI
ZIP/Postal code 53204
Country USA
 
Platform ID GPL30333
Series (1)
GSE180719 RNA-seq reveals potential gene biomarkers in Pimephales promelas for exposure to treated wastewater effluent
Relations
BioSample SAMN20360842
SRA SRX11533784

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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