Transcriptome analysis of various tissues in wild species S. pimpinellifolium, LA1589

Experiment description: Transcriptome analysis of 12 tissues in wild species S. pimpinellifolium, LA1589 using Illumina RNA-seq. The tissues include: newly developed leaves around 5 mm long, mature green leaflets, flower buds 10 days before anthesis or younger, flowers at anthesis, 10 days post anthesis (DPA) fruit, 20 DPA fruit, and breaker stage ripening fruit. Another set of 10 DPA fruit were collected in a separate greenhouse for comparison. The following tissues were collected from seeds that were germinated and grown for 7 days in a petridish under growing lights: whole root, hypocotyl from below the cotyledons to above the root zone, cotyledons, and vegetative meristems. RPKM values are an average of 4 replicates. Stand-specific libraries prepared from total RNA and sequences of 51 bp were generated on an Illumina HiSeq2000.

Author: Jason Van Houten

Contact: Esther van der Knaap (, Department of Horticulture and Crop Science, Ohio State University