Abstract
A Drosophila melanogaster genome-wide transcriptome dataset is available for studies on temporal patterns of gene expression. Gene expression was measured using two-dye color oligonucleotide arrays derived from Version 2 of the Drosophila Genomics Resource Center. A total of 15,158 oligonucleotide probes corresponded to a high proportion of the coding genes in the genome. The source of the flies was a highly genetically heterogeneous population maintained in an overlapping generation population regime. This regime was designed to maintain life history traits so that they were similar to those found in natural populations. Flies collected for the cohorts were obtained in a short period of time in a carefully controlled manner before virgin females and males were allowed to mate. Mated females were introduced into two large population cages in unusually high numbers (approximately 12,000 per cage) for a Drosophila laboratory longevity study. Samples were taken weekly from each cohort for 11 weeks; only a small proportion of surviving flies were present at the last two collection time points and thus they were exceptionally old compared to those collected in early-to-midlife samples. The data set is useful for studies of temporal patterns of gene expression as flies age. The very large size of each cohort, and relatively frequent incidence of temporal samples, allows for a fine-scale study of gene expression from young to very old flies.
Highlights
Two-color Version 2 DGRC (Drosophila Genomics Resource Center) oligonucleotide microarray RNA extraction, Bioanalysis of RNA using Agilent 2100 Bioanalyzer, cDNA microarray analysis, data analysis with Linear Models for Microarray Analysis (LIMMA) package in Bioconductor, Gene Set Enrichment Analysis (GSEA) Raw data: TAR; Normalized data: SOFT, MINIML, and TXT Age and survival
Two 30x20x10 cages with $ 12,000 once mated females were sampled weekly for $ 11 weeks and cDNA microarray analysis performed on all collections
A longitudinal cohort genome-wide transcriptome data set of adult female D. melanogaster aging has been generated, which is valuable for future studies of temporal variation of gene expression on a fine temporal scale
Summary
The flies for the present study were based on a set of lines derived from a natural population in the University of California Davis Wolfskill Experimental Orchards near Winters, California. Twenty inbred lines were crossed in all possible combinations, including reciprocal crosses, and a standard number of progeny per cross used to establish a large laboratory base population of at least 10,000 adults. The number of lines (20) used as a source of genetic variation in this study, and the crossing scheme, was based on the goal of generating a large genetically heterogeneous laboratory base population. The base population was kept in the laboratory for approximately 16 months whereupon it provided the large number of genetically heterogeneous outbred flies used for the two cohorts in the present study. The motivation was an attempt to represent natural genetic variation, to the extent possible, in a large long-term (quasi-equilibrium) laboratory population
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