|
| Status |
Public on Apr 17, 2024 |
| Title |
P05_4 [Z5_B1_4_S12] |
| Sample type |
SRA |
| |
|
| Source name |
whole_embryo
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole_embryo
developmental stage: 120-hours post fertilization
treatment: DMSO
duration of_chemical_exposure: 5 days
chemical: DMSO
chemical long_name: Dimethyl sulfoxide
dose: 0.10%
rna extraction_batch: 8
rna extraction_date: 2022-12-17
chemical exposure_dates: 12-Dec-22_17-Dec-22
i7 index_id: AAGACTCTT
i5 index_id: AAGACTCTT
library well: D8
protocol: TempO-Seq
|
| Treatment protocol |
Zebrafish embryos were exposed from 3-4 hours post fertilization (hpf) to 120 hpf in 16 ml Petri-dish of 0.1 % dimethylsulfoxide (DMSO) and chemical renewal of 8 ml was daily in every Petri-dish.
|
| Growth protocol |
Zebrafish embryos were cultured in water from the ZebTEC housing system (Techniplast, Montreal, Canada) maintaining a temperature of 28 Celsius degrees, pH of 7.4, and conductivity of 2-400μS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using a Qiagen Mini kit (Qiagen, Toronto, Canada), followed by the manufacter's protocol
RNA libraries were prepared in a 96-sample TempO-Seq S1500+ Zebrafish Surrogate Assay panel (BioSpyder Technologies, California, USA). Each sample was diluted with an equal volume of 2X Enhanced Lysis Buffer. All samples were annealed with detector oligo probes and sequentially processed in digestion, ligation, and amplification steps according to the manufacturer’s protocol. Equal amounts of each sample’s libraries were pooled in a 1.5 ml microtube and purified using NucleoSpin® Gel and PCR Cleanup Kits (Macherey-Nagel, Düren, Germany). Purified pooled libraries were sequenced on an Illumina NextSeq 2000 using a P2 Reagent kit and a 100 cycle flow cell (Illumina, USA).
TempO-Seq S1500+ Zebrafish Surrogate Assay - Index E set was used
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Base calling was performed by bcl2fastq v 2.20
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10a
Gene counts were performed with RSEM v1.3.3
Normalization was performed with DESeq2 v1.31.15
Assembly: Biospyder Zebrafish S1500+ Surrogate Gene Set
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the STAR alignments
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL30614 |
| Series (1) |
| GSE230213 |
Identifying suitable experimental designs to determining differentially expressed genes and benchmark doses from transcriptomic dose-response studies in zebrafish embryos |
|
| Relations |
| BioSample |
SAMN34272217 |
| SRA |
SRX20030804 |
