Transcriptomics-Tobacco

Tobacco Pipeline Target

• Get the differentially expressed Genes in tobacco leaf
• Author: Guru and Rajkumar and et al
• Timeline
  • Sequencing of ESTs: SEP 2009
  • Assemble / pre annotation: NOV 2009
  • Printing Array  : JAN 2010
  • Combining the protein data: MAR 2010
  • Re annotation of hybridised genes  : APR 2010
  • Consenses of the 2 data for the selected genes (MAY 2010)
  • Validate selected genes (100) by RT: JUN 2010
  • Manuscript (after approval): JUL 2010
  • Lab validation of selected genes: DEC 2010
  • Get the final list of genes characterised : JAN 2011
  • Manuscript MAR 2011

Strategy

• Flavour +/- tobacco samples
• Extract mRNA and made ESTs
• Sequencing and EST short reads
• Assemble the EST reads (contigs and singlets)
• Annotated the contigs
• Meaningful EST picces wer

Implementation

1. Some Tools
   1. gth_run
   2. trim_seq | Filter "N", size
   3. multifasta-fastas
   4. Mapping ESTs on tgi