Location: Nutrition, Growth and PhysiologyTitle: Transcriptomic and bioinformatics analysis of the early time-course of the response to prostaglandin F2 alpha in the bovine corpus luteum
|TALBOTT, HEATHER - Nebraska Medical Center|
|HOU, XIAOYING - Nebraska Medical Center|
|QUI, FANG - Nebraska Medical Center|
|ZHANG, PAN - Nebraska Medical Center|
|GUDA, CHITTIBABU - Nebraska Medical Center|
|YU, FANG - Nebraska Medical Center|
|Cushman, Robert - Bob|
|WOOD, JENNIFER - University Of Nebraska|
|WANG, CHENG - Nebraska Medical Center|
|CUPP, ANDREA - University Of Nebraska|
|DAVIS, JOHN - Nebraska Medical Center|
Submitted to: Data in Brief
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/24/2017
Publication Date: 10/1/2017
Publication URL: https://handle.nal.usda.gov/10113/5852164
Citation: Talbott, H., Hou, X., Qui, F., Zhang, P., Guda, C., Yu, F., Cushman, R.A., Wood, J.R., Wang, C., Cupp, A.S., Davis, J.S. 2017. Transcriptomic and bioinformatics analysis of the early time-course of the response to prostaglandin F2 alpha in the bovine corpus luteum. Data in Brief. 14:695-706. https://doi.org/10.1016/j.dib.2017.08.026.
Interpretive Summary: The ability to control regression of the corpus luteum (CL) is an important component in protocols to synchronize estrus for artificial insemination. Synchronization of estrus increases efficiency of artificial insemination because detection of estrus is easier when large groups of cows express behavioral estrus at the same time and labor can be concentrated into a shorter breeding season. Improper response to the hormone that causes regression of the CL, prostaglandin F2' (PGF2'), can cause inefficiencies in synchronization of estrus. Global transcript profiling was applied to identify the normal cascade of physiological events that occur in the CL in response to a luteolytic dose of PGF2'. Differentially expressed genes were analyzed with multiple pathway analysis programs to compare the physiological pathways that were predicted with each program. Additionally, we combined our data with the data from three previously published studies to perform a meta-analysis and more accurately characterize and validate these pathways. This work is an example of how the use of multiple pathway analysis programs combined with meta-analysis of multiple independent datasets can increase the accuracy of our understanding of functional genomics. The earliest response to PGF2' is an increase in transcripts for cytokines and genes involved in activation of immune cells which ultimately leads to programmed cell death in the cells of the corpus luteum.
Technical Abstract: RNA expression analysis was performed on the corpus luteum tissue at five time points after prostaglandin F2 alpha treatment of midcycle cows using an Affymetrix Bovine Gene v1 Array. The normalized linear microarray data was uploaded to the NCBI GEO repository (GSE94069). Subsequent statistical analysis determined differentially expressed transcripts ± 1.5-fold change from saline control with P = 0.05. Gene ontology of differentially expressed transcripts was annotated by DAVID and Panther. Physiological characteristics of the study animals are presented in a figure. Bioinformatic analysis by Ingenuity Pathway Analysis was curated, compiled, and presented in tables. A dataset comparison with similar microarray analyses was performed and bioinformatics analysis by Ingenuity Pathway Analysis, DAVID, Panther, and String of differentially expressed genes from each dataset as well as the differentially expressed genes common to all three datasets were curated, compiled, and presented in tables. Finally, a table comparing four bioinformatics tools’ predictions of functions associated with genes common to all three datasets is presented. These data have been further analyzed and interpreted in the companion article “Early transcriptome responses of the bovine mid-cycle corpus luteum to prostaglandin F2 alpha includes cytokine signaling”.