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Rhizome Project Meeting: RNA-seq and Transcriptome Analysis Methods

This document provides a comprehensive overview of the Rhizome Project meeting held on May 4, 2011, at the Institute of Biological Chemistry, Washington State University. Led by Min-Jeong Kim, the meeting discussed methodologies for gene analysis using mRNA, microarray, and RNA sequencing (RNA-seq). Key topics included total RNA purification with Qiagen kits, cDNA library preparation, sequencing data analysis, and transcriptome analysis of rhizome parts. The collaboration with NCGR for sequencing and the integration of multiplexed RNA-seq methodologies were also highlighted.

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Rhizome Project Meeting: RNA-seq and Transcriptome Analysis Methods

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Presentation Transcript

  1. Rhizome Project Meeting(1)5-4-2011 Min-Jeong Kim Gang Lab Institute of Biological Chemistry Washington State University Pullman, WA

  2. Approach gene A gene B mRNA microarray RNA-seq Intensity of spot Number of sequence Expression level

  3. Work Flow Flow cell

  4. Total RNA Purification Tissuelyser II Qiagen RNA mini kit www.qiagen.com

  5. mRNA Isolation Total RNA www.invitrogen.com

  6. cDNA Library

  7. Cluster Generation with cBot (1) Attach DNA to flow cell surface Prepare DNA sample

  8. Cluster Generation with cBot (2) Bridge amplification Fragments become double stranded

  9. Sequencing and Data Analysis Align data Sequencing by synthesis(SBS)

  10. Progress on Specific Species * Some are not available in the database

  11. Transcriptome Analysis of Rhizome Parts

  12. Multiplexed RNA-seq Multiplexed sequencing Adding the sequence index to a library Clustering Pooling 5 replicates in a tube

  13. Interaction/Relationship with NCGR Sequencing Contig Library Flow cell Blast Database

  14. Thank You

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