 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 17, 2024 |
| Title |
Identifying suitable experimental designs to determining differentially expressed genes and benchmark doses from transcriptomic dose-response studies in zebrafish embryos |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To identify suitable experimental designsfor toxicology experiments (i.e., sample size, pool size, number of biological replicates, and number of doses), we exposed zebrafish embryos to 0.1% dimethyl sulfoxide for 4-120 hours post fertilization. We then created 96 samples to examine the impact of pool size comprised of 1, 5, 10, and 20 zebrafish embryos each (n = 24). From these, total RNA extraction was extracted and transcriptomic analyses were done using the TempO-Seq S1500+ Surrogate Assay platform. Samples were sequencing on an Illumina NextSeq 2000. The data were simulated to conduct power analyses exploring suitable study designs for identification of differentially expressed genes and for benchmark dose analysis. The aim was to identify a feasible pool size and sample size that would yield an acceptable false discovery rate for these analyses.
|
| |
|
| Overall design |
Samples were comprised of different pool sizes of embryos (i.e., 1, 5, 10, and 20 embryos per sample, indicated by Z1, Z5, Z10, and Z20) to identify optimal experimental designs for the dose-response study. Each pool size included 24 samples and a total of 96 samples were sequenced on the TempO-Seq S1500+ Surrogate assay platform. This study consisted of 12 extraction batches with 8 samples per batch and 3 batches per pool size.
|
| |
|
| Contributor(s) |
Lee H, Stead J, Williams A, Atlas E, Mennigen J, O'Brien J, Yauk C |
| Citation(s) |
38530926 |
| Submission date |
Apr 20, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
John Stead |
| E-mail(s) |
john.stead@carleton.ca
|
| Organization name |
Carleton University
|
| Department |
Department of Neuroscience
|
| Street address |
1125 Colonel By Drive
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1S 5B6 |
| Country |
Canada |
| |
|
| Platforms (1) |
|
| Samples (96)
|
|
| Relations |
| BioProject |
PRJNA957853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE230213_count_table.csv.gz |
441.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...