Hello everyone,
This post will help everyone who is interested in analyzing and comparing zebrafish samples. Attached I will be posting a descriptive table that identifies the exposure category, GEO accession series, platform, sample IDs, number of samples, treatment conditions and gender.
All samples were extracted from the NCBI GEO website. The raw data was downloaded individually from their respective samples. The platform and series matrix were joined and matched according to sample IDs to gene IDs to expression intensities using excel and R studio.
Brief summary of the experiment design:Series Title: Trancriptome Kinetics of Arsenic-induced Adaptive Response in Zebrafish Liver.
Series Accession Number: GSE 3048
Platform: GPL 2715
Expression Profile: Microarray
Organism: Zebrafish
CH1: Cy5--> Treated sample RNA
CH2: Cy3-->Reference pooled sample (male and female) liver RNA
The arrays contain 16,416 oligonucleotide probes. The probes were designed by Compugen and synthesized by Sigma Genesis. The array also contains 172 spots representing the same beta-actin probe as controls. In order to estimate a suitable concentration for the arsenic experiment, the adult zebrafish were treated with different concentrations of arsenic V. Basis from the toxicology test, (ran with different concentrations) the concentration of 15ppm As V was utilized to treat the adult zebrafish. For the microarray study , Fish liver samples were sampled at (8,24,48,and 96 hours) from which they were separated into three pooled samples at each time point. During the initial design steps, reference RNA was obtained by pooling equal amounts of male and female total RNA extractred from the livers tissues of wildtype zebrafish.
Please fell free to comment below if there are any questions that you may encounter
Thanks, and have a great week
Best,
Juan Carlos Morales, MPH | Environmental Health Sciences
U.S. Department of Energy Doctoral Fellow - Graduate Research Assistant
Systems Biology Group
Robert Stempel College of Public Health & Social Work
Florida International University
11200 S.W. 8th Street, AHC 5 353 . Miami, FL 33199
Tel. 305.348.3994 Mobile 786.282.4458 E:
jumorale@fiu.edu