Project name: Thlaspi arvense

Description: Nectaries are the glands responsible for nectar secretion. To understand the genetic programming underlying nectar production, nectaries were collected from Thlaspi arvense cultivar MN108 at two developmental time points, with RNA being isolated and subjected to Illumina RNA-seq analysis.Overall design: Thlaspi arvense cultivar MN108 plants were grown on Sun Gro LC8 soil under a 16 hr day/8 hr night cycle, photosynthetic photon flux of 150 μmol m-2 s-1, and a temperature of 21°C. Two types of RNA samples were prepared from pennycress nectaries: mature nectaries (equivalent to Stage 14–15 flowers from Arabidopsis thaliana), and immature nectaries (equivalent to Stage 11–12 flowers from Arabidopsis thaliana). Mature nectaries secrete nectar, whereas immature nectaries are pre-secretory. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 40 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4–8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Up to four nectaries were collected per flower, with approximately 100 nectaries being processed as a single RNA sample. Each biological replicate was represented by nectaries pooled from different sets of plants. RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro 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. Six TruSeq RNA v2 libraries were created (triplicate samples for immature and mature nectaries) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two lanes to achieve the equivalent of 1 lane output. This generated ≥120 M reads for each lane and the average quality scores were above Q30.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Other

Last updated: 2017-03-16