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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
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)
Reanalysis of GSM933410
Reanalysis of GSM933411
Reanalysis of GSM933412
Reanalysis of GSM933413
Reanalysis of GSM933414
Reanalysis of GSM933445
Reanalysis of GSM933446
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Reanalysis of GSM933460
Reanalysis of GSM933461
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Reanalysis of GSM933495
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Reanalysis of GSM933500
Reanalysis of GSM933501
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Reanalysis of GSM933515
Reanalysis of GSM933516
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Reanalysis of GSM933550
Reanalysis of GSM933551
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Reanalysis of GSM933564
Reanalysis of GSM933560
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Reanalysis of GSM933578
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Reanalysis of GSM933599
Reanalysis of GSM933625
Reanalysis of GSM933626
Reanalysis of GSM933632
Reanalysis of GSM933628
Reanalysis of GSM933634
Reanalysis of GSM933650
Reanalysis of GSM933651
Reanalysis of GSM933652
Reanalysis of GSM933653
Reanalysis of GSM933654
Reanalysis of GSM933660
Reanalysis of GSM933661
Reanalysis of GSM933662
Reanalysis of GSM933663
Reanalysis of GSM933664
BioProject PRJNA257740

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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

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