E-MTAB-3646 - RNA-seq Transcriptional Profiling of Herbaspirillum seropedicae Colonizing Bread Wheat (Triticum aestivum) Roots

Status
Released on 3 July 2016, last updated on 28 December 2016
Organism
Herbaspirillum seropedicae SmR1
Samples (4)
Protocols (5)
Description
H. seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize and promote plant growth wheat seedlings growing hydroponically in Hoagland’s medium were inoculated with H. seropedicae the bacteria and incubated for 3 days. mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of bacteria attached to the root and planktonic revealed an extensive metabolic adaptation to the epiphytic life style.
Experiment types
RNA-seq of coding RNA, growth condition design, replicate design, validation by reverse transcription PCR design
Contacts
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-3646.idf.txt
Sample and data relationshipE-MTAB-3646.sdrf.txt
Links