|
| Status |
Public on Apr 21, 2021 |
| Title |
wfikkn1-mut-DMSO-rep4_S12 |
| Sample type |
SRA |
| |
|
| Source name |
48 hpf whole zebrafish
|
| Organism |
Danio rerio |
| Characteristics |
strain: wfikkn1 mutant
agent: 0.1% DMSO
developmental stage: 48 hpf
|
| Treatment protocol |
The two zebraifsh lines were exposed to either 0.1 % DMSO (vehicle control) or 1 ng/mL TCDD (chemical) for 1 hour at 4 hpf. Exposures were conducted in 20 mL glass vials with 100 uL/embryo exposure solution. To ensure even mixing, vials were placed on a rocker for the duration of the exposure, and every 15 minutes were manually shaken. After exposure, zebrafish were rinsed three times with embryo media (EM) and grown to 48 hpf in 60 mm Petridishes with at 28.5˚C. Each individual biorep (n=9 fish) was in a different Petridish.
|
| Growth protocol |
Tropical 5D wildtype zebrafish and wfikkn1 mutant zebrafish embryos were grown to 4 hpf in glass petridishes at 28.5˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 48 hpf whole embryos using RNAzol (Molecular Research Center, Inc; Cincinnati, OH) and a bullet blender with 0.5 mM zirconium oxide beads (Next Advance, Averill Park, New York) as recommended by the manufacturer. The RNA was purified using the Direct-zol MiniPrep kit (Zymo Research; Irvine, CA) and included an in-column DNase 1 digestion. RNA quality and quantity was assessed using a SynergyMix microplate reader with the Gen5 Take3 module. RNA integrity was confirmed (RIN score > 8) with an Agilent Bioanalyzer 2100.
Total RNA samples were sent to Oregon State University Center for Genome Research and Biocomputing Core facilities for library preparation and sequencing. Samples were prepared using the Robotic PolyA Enrichment Library Prep and Robotic Stranded RNA Library Prep Kits (WaferGen, Fremont, CA).
Libraries were randomized across 6 lanes and sequenced with 100bp single-end reads using the Illumina HiSeq 3000. Raw sequence reads were quality checked prior to processing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
fastqc file of wfikkn1 mutant_DMSO rep4
Count_matrix.txt
wfikkn1mut_DMSO--WT_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--wfikkn1mut_DMSO_log2_sig_log_ratios.xlsx
wfikkn1mut_TCDD--WT_TCDD_log2_sig_log_ratios.xlsx
WT_TCDD--WT_DMSO_log2-1_sig_log_ratios.xlsx
|
| Data processing |
Reads were trimmed using Cutadapt (version 1.8.1) to remove the adapter sequencesTrimmed files were aligned using HISAT2 (version 2.2.0) against the zebrafish build 11 (Danio rerio GRCz11 release 97) genome
Number of mapped reads was counted, sorted, and converted to BAM files using Samtools (version 1.10)
Read counts were estimated using HTSeq (version 0.12.4)
Normalization of counts and differential expression analysis were conducted using Bioconductor's edgeR
Genome_build: Outliers (WT DMSO 2 and WT TCDD 2) were removed after multidimensional scaling
|
| |
|
| Submission date |
Apr 20, 2021 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Christopher Michael Sullivan |
| Organization name |
Oregon State University
|
| Department |
Environmental & Molecular Toxicology
|
| Lab |
Robert L. Tanguay
|
| Street address |
Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97333 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE172418 |
TCDD exposure in control and wfikkn1mutant zebrafish at 48 hpf |
|
| Relations |
| BioSample |
SAMN18810557 |
| SRA |
SRX10644272 |
