Dataset: Transcriptomic responses to saxitoxin

Name: Genetic accessions, treatment information, and methodology from laboratory experiments studying transcriptomic responses to saxitoxin in zebrafish (Danio rerio)
Published: 2022-09-27
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.881469.1

Temporal Extent: 2022

Project:

WHCOHH - Cellular and Molecular Mechanisms Underlying Long-Term Effects of Early Life Exposure to HAB Toxins (WHCOHH HAB toxins)

Program:

Woods Hole Center for Oceans and Human Health (WHCOHH)

Principal Investigator:

Neelakanteswar Aluru (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Mark Hahn (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-09-27

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Genetic accessions, treatment information, and methodology from laboratory experiments studying transcriptomic responses to saxitoxin in zebrafish (Danio rerio)

Abstract:

This dataset contains genetic accessions, treatment information, and methodology from laboratory experiments involving developmental exposure to low-level saxitoxin and how it affects neuronal gene expression in zebrafish (Danio rerio).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-09-27	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.881469.1	2022-09-28

Description

The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible through GEO Series accession number GSE204989 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE204989).

Sequence Read Archive (SRA) data, BioSamples, and GEO holdings can be accessed from the NCBI BioProject PRJNA843039 (http://www.ncbi.nlm.nih.gov/bioproject/PRJNA843039).

Methods & Sampling

Adult zebrafish (Tupfel-Long fin wild type strain) were raised under ambient conditions (temperature 28.5 degrees, photoperiod 10:14 light/dark) in Redfield zebrafish facility. Embryos used in the experiment were obtained by tank breeding of the adults. Embryos were injected with saxitoxin or vehicle control at 6 hours post-fertilization.

Zebrafish embryos were exposed to saxitoxin (STX; 24 or 48 pg) or vehicle (0.3 mM HCl) at 6 hours post fertilization (hpf) via microinjection. We examined transcriptional profiles in embryos at 24, 36 and 48 hpf using RNA sequencing.

Sampling and analytical procedures:
Total RNA was isolated from embryos at 3 developmental time points and RNAseq was carried out using Illumina platform.

Organism scientific name: Danio rerio
LSID (Life Sciences Identifier) = urn:lsid:marinespecies.org:taxname:1026595
NCBI:txid903980

Data Processing Description

RNAseq data was pre-processed and mapped to the zebrafish genome (GRCz10) using STAR aligner. HTseq-count was used to obtain read counts. Statistical analysis was done using edgeR.

Data Files

File

Treatment and NCBI accession information
filename: treatments_accessions.csv

(Comma Separated Values (.csv), 1.05 KB)
MD5:0de81a7c5514a6e42a314011f6f6d093

Treatment information, and NCBI accession identifiers for BioSamples, and holdings in the Sequence Read Archive (SRA).  

Parameters:

Run,NCBI Sequence Read Archive (SRA) Run identifier

BioSample,NCBI BioSample identifier

Experiment,NCBI Sequence Read Archive (SRA) Experiment identifier

Sample_Name,Sample name

Treatment,Treatment type (Control or Saxitoxin)

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1314642
National Institutes of Health	NIH-P01ES021923

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2000

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

None available yet

Database

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Dataset: Transcriptomic responses to saxitoxin