|
| Status |
Public on Aug 31, 2022 |
| Title |
U16: upstream12 |
| Sample type |
SRA |
| |
|
| Source name |
adult
|
| Organism |
Pimephales promelas |
| Characteristics |
Sex: male
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 |
SAMN20360837 |
| SRA |
SRX11533789 |
