 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 12, 2021 |
| Title |
pooled (20) whole embryos water control repE |
| Sample type |
SRA |
| |
|
| Source name |
whole body tissue
|
| Organism |
Pimephales promelas |
| Characteristics |
age: 7-days post-fertilization
treatment: water control
tissue: whole body tissue
|
| Treatment protocol |
Embryos were exposed (waterborne) from 6-hrs post-fertilization to 7-days post-fertilization in a static renewal condition (at least 50% test solution renewal per day)
|
| Growth protocol |
Fathead minnow embryos (<6 hrs post-fertilization; 20 embryos each replicates) were exposed to graded concentrations (measured concentrations: water control, 0.19, 0.74, 3.38, 10.2, 47.2 µg/L ) of FLX in glass petri dishes, maintained at (23 oC, 16:8 light:dark cycle)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from pools of 20 larvae using QIAGEN RNeasy plus universal mini kit following the manufacturer's protocol
Libraries were generated from 250 ng of total RNA. mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps were done using 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). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ME6_kallisto_countfile_fhm-els-flx.csv
flx-0-e
|
| Data processing |
Raw files were trimmed using Trimmomatic v0.38
Trimmed fastq files were pseudoaligned to the referencefathead minnow transcriptome (NCBI Acc# GCA_016745375.1) using Kallisto
Only features with at least 5 counts per million in at least 3 samples were kept for differential expression analyses. Significance of differentially expressed genes were assessed using DESeq2 in R, with a cut-off FDR (Benjamini-Hochberg) < 0.05 and an effect size threshold |FC| ≥ 1.5
Genome_build: fathead minnow (Pimephales promelas) reference transcriptome NCBI Acc# GCA_016745375.1 from Martinson, J., Bencic, D.C., Toth, G.P., Kostich, M.S., Flick, R.W., See, M.J., Lattier, D., Biales, A.D., Huang, W., n.d. De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure. https://doi.org/10.1101/2021.02.24.432777
Supplementary_files_format_and_content: csv - raw counts of all samples
Supplementary_files_format_and_content: tabular - differential expression results using DESeq2
|
| |
|
| Submission date |
Jun 30, 2021 |
| Last update date |
Dec 13, 2021 |
| Contact name |
Markus Hecker |
| E-mail(s) |
ajames.alcaraz@usask.ca, markus.hecker@usask.ca
|
| Organization name |
University of Saskatchewan
|
| Department |
Toxicology
|
| Lab |
Predictive Aquatic Toxicology Research Lab
|
| Street address |
44 Campus Drive
|
| City |
Saskatoon |
| State/province |
Saskatchewan |
| ZIP/Postal code |
S7N5B3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL30333 |
| Series (1) |
| GSE179232 |
Comparative analysis of transcriptomic points-of-departure (tPODs) and adverse apical responses in embryo-larval fathead minnows exposed to fluoxetine |
|
| Relations |
| BioSample |
SAMN19976059 |
| SRA |
SRX11322302 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5411895_flx-water-e.tabular.txt.gz |
847.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
