Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 12
Release date: Apr 15 2018
Last update date: Apr 16 2018
Access: Public
Dataset link Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Adult)

Experimental Protocol


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.

Repositories


GEO

GSE46082

BioProject

PRJNA197232

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Contact


Justin Choi