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| Status |
Public on Sep 02, 2022 |
| Title |
pooled (20) whole embryos solvent control RepD |
| Sample type |
SRA |
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| Source name |
whole embryo bodies
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| Organism |
Pimephales promelas |
| Characteristics |
tissue: whole embryo bodies
age: 7-days post-fertilization
treatment: ethanol (EtOH)
treatment (measured concentration): solvent control
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| Treatment protocol |
Embryos were exposed via maternal transfer and reared in cllean water for 7-days post-fertilization in a flow-through system.
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| Growth protocol |
Fathead minnow embryos (20 embryos per replicate) were maternally exposed to graded concentrations (measured concentrations: solvent control, 0.576, 1.77, 5.89 mg/kg ) of HBCD and reared in glass petri dishes in clean water, maintained at (23 oC, 16:8 light:dark cycle)
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ME8-WT7-SDP
ME8_transcript1.txt
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| Data processing |
https://galaxy.ecotoxxplorer.ca/
Raw files were trimmed to a minimum phred score of 20 and a minimum sequence length of 35 bases per paired read using Trim Galore!
Trimmed fastq files were pseudoaligned to the reference fathead minnow transcriptome (NCBI Acc# GCA_016745375.1) using Kallisto quant
Only features with at least 20 counts per million in at least 5 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
Assembly: 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 - differential expression results using DESeq2
Supplementary files format and content: tabular - raw counts of all samples
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| Submission date |
Aug 30, 2022 |
| Last update date |
Sep 02, 2022 |
| Contact name |
Susari Malala Irugal Bandaralage |
| E-mail(s) |
shi339@mail.usask.ca
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| Phone |
6394713449
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| Organization name |
University of Saskatchewan
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| Department |
Toxicology
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| Street address |
44 Campus Drive
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| City |
Sasaktoon |
| State/province |
Saskatchewan |
| ZIP/Postal code |
S7N 5B3 |
| Country |
Canada |
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| Platform ID |
GPL30333 |
| Series (1) |
| GSE212295 |
Embryo/ larval toxicity and key gene expression signatures of maternally transferred hexabromocyclododecane (HBCD) in Pimephales promelas |
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| Relations |
| BioSample |
SAMN30589524 |
| SRA |
SRX17320966 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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