GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE60167

Query DataSets for GSE60167

Status

Public on Aug 01, 2015

Title

Natural Variation in Fish Transcriptomes: Comparative Analysis of the Zebrafish (Danio rerio)

Sample organism

Danio rerio

Experiment type

Third-party reanalysis
Expression profiling by array

Summary

Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations. Little effort, however, has been made in this area. Leveraging the transcriptomics data from a number of our toxicogenomics studies conducted over the years, we conducted a meta-analysis of nearly 600 microarrays generated from the ovary tissue of untreated, reproductively mature fathead minnow and zebrafish samples. As expected, there was considerable batch-to-batch transcriptomic variation; this “batch-effect” appeared to impact the fish transcriptomes randomly. The overall level of variation within-batch was quite low in fish ovary tissue, making it a suitable system for studying chemical stressors with subtle biological effects. The within-batch variation, however, differed considerably among individual genes and molecular pathways. This difference in variability is probably both technical and biological, thus suggesting a need to take into account both the expression levels and variance in evaluating and interpreting the transcriptional impact on genes and pathways by experimental conditions. There was significant conservation of both the genomes and transcriptomes between fathead minnow and zebrafish. The conservation to such a degree would enable not only a comparative biology approach in studying the mechanisms of action underlying environmental stressors, but also effective sharing of a large amount of existing public transcriptomics data for future development of toxicogenomics applications.

Overall design

RNA from treated and control samples were directly hybridized on individual arrays.
This study is a reanalysis of ovary Samples from GSE38070. The data processing is different and consisted of:
Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer?s protocol and recommendations. Data processing was conducted using R package Limma in the order of backgroundCorrect("normexp"), normalizeWithinArrays("loess"), and normalizeBetweenArrays("quantile"). Various types of control probes were filtered out. Each expression value represents the average of its duplicated probes. Only intensity data from control channel were utilized in the study after channel splitting.
The supplementary files attached contain log2 ratios(M) and log2 intensities (A) after backgroundCorrect("normexp"), normalizeWithinArrays("loess"), and normalizeBetweenArrays("quantile") in Limma; various types of control probes were filtered

Contributor(s)

Wang R, Bencic DC, Garcia-Reyero N, Perkins EJ, Villeneuve DL, Ankley GT, Biales AD

Citation(s)

25493933, 26822894

Submission date

Aug 06, 2014

Last update date

Oct 18, 2019

Contact name

Rong-Lin Wang

E-mail(s)

wang.rong-lin@epa.gov

Phone

513-569-7862

Organization name

US EPA

Street address

26 W MLK Dr

City

Cincinnati

ZIP/Postal code

45268

Country

USA

This SubSeries is part of SuperSeries:

GSE60202

Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)

Relations

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE60167_DREovary80samples.A.txt.gz	9.2 Mb	(ftp)(http)	TXT
GSE60167_DREovary80samples.M.txt.gz	9.1 Mb	(ftp)(http)	TXT
GSE60167_sample_key_association.txt.gz	1.0 Kb	(ftp)(http)	TXT
Processed data are available on Series record