Transcriptomic and bioinformatics analysis of the early time-course of the response to prostaglandin F2 alpha in the bovine corpus luteum
Heather Talbott,
Xiaoying Hou,
Fang Qiu,
Pan Zhang,
Chittibabu Guda,
Fang Yu,
Robert A. Cushman,
Jennifer R. Wood,
Cheng Wang,
Andrea S. Cupp,
John S. Davis
Affiliations
Heather Talbott
Olson Center for Women’s Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA
Xiaoying Hou
Olson Center for Women’s Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA
Fang Qiu
Biostatistics Department, University of Nebraska Medical Center, 984375 Nebraska Medical Center, Omaha, NE 68198-4375, USA
Pan Zhang
Olson Center for Women’s Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA
Chittibabu Guda
Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198-5805, USA
Fang Yu
Biostatistics Department, University of Nebraska Medical Center, 984375 Nebraska Medical Center, Omaha, NE 68198-4375, USA
Robert A. Cushman
Nutrition and Environmental Management Research Unit, Department of Agriculture, P.O. Box 166 (State Spur 18D)/USDA-ARS-PA-USMARC, Clay Center, NE 68933, USA
Jennifer R. Wood
Department of Animal Science, University of Nebraska—Lincoln, P.O. Box 830908, C203 ANSC, Lincoln, NE 68583-0908, USA
Cheng Wang
Olson Center for Women’s Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA
Andrea S. Cupp
Department of Animal Science, University of Nebraska—Lincoln, P.O. Box 830908, C203 ANSC, Lincoln, NE 68583-0908, USA
John S. Davis
Olson Center for Women’s Health/Obstetrics and Gynecology Department, University of Nebraska Medical Center, 989450 Nebraska Medical Center, Omaha, NE 68198-9450, USA
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” [1].
