Transcriptomics,Genomics

Dataset Information

27

Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Larva)


ABSTRACT: A key feature of Nasonia are their form of sex determination, called haplodiploidy. Females are diploid and develop from fertilized eggs, whereas males are haploid and develop parthenogenetically from unfertilized eggs. This form of sex determination is exploited by this experiment, by knowing the sex of the organisms from the earliest stages of development, so to trace the transcriptomes of sexual development of an insect. We conducted three replicates each using RNA from independent biological extractions of male and female early embryo (0-10 hrs), late embryo (18-30 hrs), 1st instar larvae, and pupae. Additional experiments were performed comparing transcription in adult males, adult females, testis and the female reproductive tract. Overall design: We conducted two-color competitive hybridizations that measure differential expression from three replicates, each using RNA from independent biological extractions. Transcriptional active regions (TARs) were defined by stringing together overlapping probes showing fluorescence above a 1% false positive rate (FPR). Positive probes were joined into a TAR if they were adjacent (maxgap=0, no intermittent non-positive probe) and a TAR's length had to be at least 45 bp (minrun=45, mid-point first positive probe to mid-point last positive probe, resulting in at least 3 adjacent positive probes for a TAR). The data analysis to measure differential expression of Official Gene Set (OGS) 2.0 annotated genes (http://arthropods.eugenes.org/EvidentialGene/nasonia/), their exons and of unannotated TARs was performed using the statistical software package R and Bioconductor with additions and modifications. The signal distributions across chips, samples and replicates were adjusted to be equal according to the mean fluorescence of the random probes on each array. All probes including random probes were quantile-normalized across replicates. Expression-level scores were assigned for each predicted gene based on the median log2 fluorescence over background intensity of probes falling within the exon boundaries.

INSTRUMENT(S): NimbleGen Nasonia vitripennis 1.0 Whole-genome Tiling Array Set (1 of 4) [080222_Nvit1_JC_ChIP_HX1]

SUBMITTER: Justin Choi  

PROVIDER: GSE46080 | GEO | 2018-04-15

REPOSITORIES: GEO

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