Study : Solanum tuberosum subsp. andigenum Transcriptome or Gene expression

Identification

• Name: Solanum tuberosum subsp. andigenum Transcriptome or Gene expression
• Identifier: dXJuOkVWQS9zdHVkeS9QUkpOQTI5MDgwMA==
• Data link: Link to this study on EBI European Nucleotide Archive
• Description: To better understand the function of the phloem in plants, we have combined laser capture microdissection (LCM) and RNA-seq for an in-depth transcriptional profile of phloem-associated cells of both petioles and stems of potato. Out of the 27k transcripts assembled that we identified, approximately 15K were present in phloem-associated cells of petiole and stem with greater than ten reads. Approximately 22% of the transcripts in phloem cells contained at least one binding motif for Pumilio, Nova, or polypyrimidine tract-binding proteins in their downstream sequences. Highlighting the predominance of binding processes identified in the gene ontology analysis of active genes from phloem cells, 78% of the 464 RNA-binding proteins present in the potato genome were detected in our phloem transcriptome. As a reasonable alternative when phloem sap collection is not possible, LCM can be used to isolate RNA from specific cell types, and along with RNA-seq, provides practical access to expression profiles of phloem tissue.
• Data files: SRR2131060; SRR2131063; SRR2131065; SRR2131061; SRR2131062; SRR2131064; SRR2126855; SRR2126856; SRR2126915; SRR2126975; SRR2127278; SRR2127279; SRR2127280; SRR2127289; ERZ1140749; ERZ287806; ERZ318252; ERZ594485; ERZ1140721; ERZ287800; ERZ318247; ERZ594299; ERZ1140720; ERZ1140738; ERZ1140739; ERZ1140755; ERZ287796; ERZ287799; ERZ287801; ERZ287803; ERZ318248; ERZ318249; ERZ318250; ERZ318255