Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003]. Male and female rats of the F3 generation of Vinclozolin and Control lineages were selected out of litters from untreated F2 generation. One animal from each lineage (Control and Vinclozolin) were pair-housed (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the behavioral study until sacrifice at age of 11 months.
Growth protocol
Male and female rats of the F3 generation of Vinclozolin (Vinclozolin-Lineage) and DMSO Control (Control-Lineage) Lineages were selected out of litters from untreated F2 generation mothers at Washington State University according to established protocols (Anway et al., 2005). On postnatal day (PND) 22, one day after weaning, animals were shipped to the University of Texas. Upon arriving at the University of Texas, one animal from each Lineage (Control and Vinclozolin) was pair-housed (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the behavioral study. All rats were sacrificed at age of 11 months and certain brain areas samples were collected as 3 mm tissue punches and put into Trizol™ reagent (Invitrogen, USA) and kept at -20 degrees Celsius until RNA isolation.
Extracted molecule
total RNA
Extraction protocol
RNA was isolated from individual animal tissue homogenate in 750 ul Trizol™ reagent (Invitrogen, USA), according to manufacturer’s instructions.
Label
biotin
Label protocol
Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).
Hybridization protocol
Following fragmentation, ssDNA were hybridized on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
Description
Treatment-Sex Group: EnCTX-F-Con Marina-EnCTX-Con-Fm-1-021210-109.CEL Entorhinal cortex from F3-generation control lineage (vehicle) female 11 months old rat brain
Data processing
The data for each of the 12 studied male or female brain areas (F-Amy, F-CngCTX, F-EnCTX, F-Hipp, F-OlfB, F-POAH ,M-Amy, M-CngCTX, M-EnCTX, M-Hipp, M-OlfB, M-POAH) were pre-processed and analyzed as a separate group (12 groups, 9-12 chips per group) with Partek Genomic Suite 6.5 beta software (Partek Inc. St. Louis MO) in August-October of 2010 using RMA GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.
Gene Bionetworks Involved in Epigenetic Transgenerational Inheritance of Environmentally Altered Sexual Selection: Role of Epigenetics in Evolutionary Biology
Data table header descriptions
ID_REF
VALUE
Logarithm of signal values, base 2, pre-processed with RMA, GC-content adjusted algorithm - each of the 12 bran areas separately. Scan date batch effect was removed if applicable.
