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Series GSE9745 Query DataSets for GSE9745
Status Public on Apr 01, 2008
Title Hepatic Transcriptional Profiling of Hatchling Chicks and Market-age Broiler Chickens during Fasting and Re-feeding
Organism Gallus gallus
Experiment type Expression profiling by array
Summary This study integrates global transcriptional profiling and the metabolic perturbation induced by fasting and re-feeding. Genetic control of growth and development should be revealed by systematic modeling of metabolic and regulatory pathways. Chicken oligo arrays were used for transcriptional profiling in two time-course experiments. Two critical developmental stages were chosen: immediately after hatchling (Wk1) and prior to marketing of broiler chickens (Wk6). Only male chickens were used to simplify the experimental design. A RNA reference design was employed for microarray hybridization using two reference RNA pools derived from all individuals sampled at either Wk1 or Wk6. Microarray data was acquired using GenePix Pro software. Loess normalization and a linear mixed model were applied in data processing using the R statistical package with LIMMA software [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3]. The results show hundreds of differentially expressed genes, which are regulated by age and the metabolic perturbation of fasting and re-feeding. Numerous common genes were found at both developmental stages (Wk1 and Wk6) that could be candidates for controlling growth and development of chickens. Differential expression revealed by either microarray or qRT-PCR analyses of selected genes was highly consistent. QRT-PCR verification of genes acutely depressed by fasting includes AGO1, ANGTPL3, ATPCL, FASN, FAT, ME1, PPARG, SCD1, SREBP1 and THRSPA. Genes up-regulated by fasting were ALDOB, IL-15, LDHB, LIPIN2, PANK1, PPARA and UPP2. These genes are functionally assigned to metabolic enzymes, transcription factors, acute phase proteins, immune factors and involved in various pathways (i.e., fatty acid and amino acid metabolism, glycolysis, growth factor signaling and immune defense).
Keywords: Hepatic transcripts, oligo-array, chicken, metabolic perturbation, fasting and re-feeding
 
Overall design A reference RNA design was used for microarray hybridizations, where the same reference RNA pool was co-hybridized to each target sample on an microarray. The reference RNA pool was made from an equal amount of high-quality amplified RNA (aRNA), derived from all liver samples within each experiment (Wk1 = 50 samples and Wk6 = 30 samples). The reference RNA pool was labeled with Alexa 647 while each target sample was labeled with Alexa 555.
 
Contributor(s) Trakooljul N, Porter TE, Cogburn LA
Citation(s) 32005146
Submission date Nov 30, 2007
Last update date Feb 10, 2020
Contact name Larry Albert Cogburn
E-mail(s) cogburn@udel.edu
Phone 302-831-1335
Organization name University of Delaware
Department Animal and Food Sciences
Lab Avian Functional Genomics
Street address 531 South College Ave.
City Newark
State/province DE
ZIP/Postal code 19717
Country USA
 
Platforms (1)
GPL6049 Arizona Gallus gallus 20.7K Oligo Array v1.0
Samples (80)
GSM244284 Chicken liver, newly hatched, replicate 1
GSM244285 Chicken liver, one day old, fed, replicate 1
GSM244286 Chicken liver, one day old, fast, replicate 1
Relations
BioProject PRJNA103665

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
GSE9745_RAW.tar 123.5 Mb (http)(custom) TAR (of GPR)
Raw data provided as supplementary file
Processed data included within Sample table

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