GSE113932
Transcriptome of Acacia cornigera extrafloral nectaries
Nectaries are the glands responsible for nectar secretion. In the tree Acacia cornigera, extrafloral nectaries produce nectar primarily consumed by mutualistic ant colonies.  To understand the genetic programming underlying nectar production, and in particular the connection of the jasmonic acid pathway with the mutualistic ants, extrafloral nectaries tissue was collected at ten time points and conditions, with RNA being isolated and subjected to Illumina RNA-seq analysis. Overall design: Samples from Acacia cornigera extrafloral nectaries were taken in May, 2014, in Puerto Escondido, Oaxaca, Mexico, and stored in liquid nitrogen before further processing.  The first six sample types are from different times of day (9am, noon, 2pm, 3pm, and 8am), the last four sample types are under different conditions perturbing the condition of mutualistic ant colonies (Pseudomyrmex ferrugineus).  Samples were in triplicate but not all replicates passed quality control steps.  Exfloral nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Each biological replicate was represented by nectaries pooled from different individual plants. RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for barcoded library creation and Illumina HiSeq 2500 sequencing. Twenty-four TruSeq RNA v2 libraries were created and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. Pooled libraries generated over 800 M reads and the average quality scores were above Q30.