|
| Status |
Public on Jul 20, 2024 |
| Title |
PFAS-11_replicate-2 [run64_s028] |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish embyonic total RNA
|
| Organism |
Danio rerio |
| Characteristics |
strain: Tropical 5D Wildtype
age: 48 hours post fertilization
pooled organisms: 10 whole embryos
treatment: Perfluorohexanesulfonamide (PFAS-11)
|
| Treatment protocol |
At 6 hours post-fertilization (hpf), animals were statically exposed to chemicalsusing an HP D300 digital dispenser to dispense stocks into individual wells of the 96-well plates, all normalized to 1% DMSO, and plates were sealed.
|
| Growth protocol |
Animals were dechorionated at 4 hours post-fertilization (hpf) and then kept in 96-well plates in 100µLembryo medium consisting of 15 mM NaCl, 0.5 mM KCl, 1 mM MgSO4, 0.15 mM KH2PO4, 0.05 mM Na2HPO4, and 0.7 mM NaHCO3(Westerfield, 2000) at 28°C in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from pooled animals in Eppendorf safe-lock tubes by euthanizing on ice, immediately removing excess water, homogenizing in 200 µL RNAzol®RT (Molecular Research Center) with 100 µL 0.5 mm zirconium oxide beads (Next Advance) using a Bullet Blender® (Next Advance) at speed 8 for 3 minutes. After homogenization, 300 µL RNAzol® was added, and samples were stored at -80 °C. Isolation was performed using Direct-zol RNA MiniPrep kit (Zymo, Cat no. R2052) and optional DNase I digestion step.
RNA libraries for RNA-seq were prepared usingLexogen QuantSeq 3' mRNA-seq FWD kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Total RNA isolated from zebrafish embryos treated with 28 µM Perfluorohexanesulfonamide (PFAS-11; CAS 41997-13-1; 1% DMSO) from 6-48 hpf
2022MAR25All_Raw_Counts_Table_-_NOT_Concatenated_-_Sample_number_-_Experiments_A-B
FINAL_Raw_Counts_with_lowest_35th_percentile_genes_removed_-_Experiments_A-B
Differential_Gene_Expression_Experiments_A-B
|
| Data processing |
STAR for genome mapping and alignment (parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate).
HTSeq for gene-level counts (parameters: -m intersection-nonempty -s yes -f bam -r pos).
For experiments A&B, genes with low counts were removed (i.e., genes with zero counts for all samples (9.9% of 32,521 genes), genes that were in the lowest 35th percentile of counts for all samples (4.8%)). Multidimensional scaling analysis in R (metaMDS function, vegan package) identified 1 outlier (PFAS-5_replicate-1) that was removed.
For experiment C, all genes with zero count were removed but low count genes were not removed. Control-C_48h_replicate-2 and Nafion byproduct 2_48h_replicate-3 were identified as outliers and removed.
DESeq2 for differential expression analysis (experiments A&B analyzed together, with sequencing runs collapsed by sample and samples contrasted to appropriate controls).
Assembly: GRCz11
Supplementary files format and content: .xlsx with read counts, filtered files and gene expression for all samples.
|
| |
|
| Submission date |
Dec 26, 2023 |
| Last update date |
Jul 20, 2024 |
| Contact name |
Robyn Leigh Tanguay |
| E-mail(s) |
[email protected]
|
| Phone |
5417376514
|
| Organization name |
Oregon State University
|
| Department |
Environmental Molecular toxicology
|
| Lab |
SARL
|
| Street address |
28645 E hwy34
|
| City |
Corvallis |
| State/province |
Oregon |
| ZIP/Postal code |
97333 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE252004 |
Structurally Diverse PFAS Produce Unique Transcriptomic Changes Linked to Developmental Toxicity in Zebrafish |
|
| Relations |
| BioSample |
SAMN39120311 |
| SRA |
SRX23022857 |
