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| Status |
Public on Dec 18, 2024 |
| Title |
Zebrafish embryos, dose 0, replicate E |
| Sample type |
SRA |
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| Source name |
whole embryo
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| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
developmental stage: protuding mouth
strain: AB wild type
age: 120h post-fertilization
treatment: 0 µg/L DBP exposure
biological replicate: E
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| Treatment protocol |
Commercial DBP (99% purity, CAS no. 84-74-2; Sigma-Aldrich, USA) was prepared as a solvent-free stock solution in fish water at 5.4 mg/L. Stock and fish water DBP concentrations were quantified one day before exposure using UPLC-UV with a detection limit of 3 µg/L. The analysis, performed on a 10 µL injection volume, used an Acquity UPLC HSS T3 column (2.5 µm, 2.1x100 mm; Waters, Germany) with a mobile phase of 60% acetonitrile and 40% H₂O at a flow rate of 8 mL/min and 25 °C. DBP concentrations in fish water were below the limit of detection. Stock solutions were stored in the dark at 26 °C and remained stable throughout the experiment. Test solutions were freshly prepared daily in oxygenated fish water by serial dilution of the stock solution to achieve a dose gradient [0, 5, 10, 30, 100 µg/L]. Glassware was exclusively used to prevent contamination by phthalates or plasticizers. Zebrafish embryos (256-cell stage) were randomly assigned to glass beakers containing 60 mL of test solution, with 30 embryos per beaker and five replicates per dose. Embryos were maintained in a climate-controlled chamber at 26 (±0.5) °C under a 14:10 light/dark cycle. Exposure was semi-dynamic, with daily renewal of one-third of the solution volume using freshly prepared test solutions. After 120 hours of exposure, pools of 10 embryos (‘protruding mouth’ stage) were flash-frozen in liquid nitrogen and stored at −80 °C for RNA extraction.
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| Growth protocol |
Zebrafish (Danio rerio) embryos (AB strain) were obtained from the Luxembourg Centre for Systems Biomedicine (LCSB) aquatic plateform (Luxembourg University, Belval, Luxembourg). They were collected within 1 hour after spawn, placed in standardized fish water at 26°C (NF EN ISO 7346-2 (1998), pre-oxygenated by bubbling for 12h) and transferred to the LIEC facilities (Metz, France).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Rneasy mini extraction kit (Qiagen).
Quality and integrity assessment: After quality and integrity assessment of extracted RNA by NanoDrop (Thermo Fisher Scientific, Waltham, MA) and by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), the 3 higher quality RNA samples per condition (A260/A280 > 1.7, A260/A230 > 2, RIN >8.8) were selected for high throughput mRNA sequencing.
RNA libraries were prepared from 250 ng total RNA using UltraTMII Directional RNA library Prep kit (New England Biolabs) and library size was checked by the DNA 1000 Assay Kit of the Bioanalyzer 2100 system. Libraries were sequenced on a NextSeq500 Illumina sequencer with 1x 75 bp single reads, providing 40 to 57 million reads for each sample. Library preparation, quality check and sequencing were performed by Helixio, France.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Library name: Sample 3
Column name in raw_counts_All_Samples.csv : 0E
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| Data processing |
Raw mRNAseq data processing was performed on the Galaxy french server provided by the ‘Institut Français de Bioinformatique’ (IFB). Raw reads were filtered according to size (>55 bp) and quality parameters (mean Phred score >20 on 5’ and 3’ bases and on a 4 pb sliding window) using Trimmomatic, leading to keep 87 to 92% of total reads according to the sample.
Cleaned reads were mapped to the zebrafish reference transcriptome GCRz11 and quantified using Salmon quant (v. 1.5.1)
Assembly: GCRz11
Supplementary files format and content: raw_counts_All_Samples.csv includes raw counts for each Sample
Supplementary files format and content: xx_TPM.csv files include TPM values for each Sample
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| Submission date |
Dec 10, 2024 |
| Last update date |
Dec 18, 2024 |
| Contact name |
Sophie Prud'homme |
| E-mail(s) |
[email protected]
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| Organization name |
Université de Lorraine
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| Department |
Toxicologie de l'Environnement
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| Lab |
LIEC
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| Street address |
Bâtiment IBISE, Rue Claude Bernard, Metz
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| City |
Metz |
| ZIP/Postal code |
57070 |
| Country |
France |
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| Platform ID |
GPL20828 |
| Series (1) |
| GSE283957 |
Dose-dependent effects of dibutyl phthalate on embryonic development in zebrafish (Danio rerio): The value of integrating concentration gradients in transcriptomic analyses |
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| Relations |
| BioSample |
SAMN45447685 |
| SRA |
SRX27029357 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8674866_dbp0E_TPM.csv.gz |
715.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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