Transcriptomics-Tobacco: Difference between revisions
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=Implementation= | =Implementation= | ||
* Mapping ESTs on tgi | |||
* Some Tools | |||
** [[gth_run]] | |||
** [[trim_seq]] | Filter "N", size | |||
** [[multifasta-fastas]] | |||
Revision as of 16:10, 4 January 2010
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
Scientific Assumptions
Strategy
- Gene Prediction
- 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 pieces
- Implanted them on micro array
- Further annotate them to spot reliable genes to the existing models
- Use the contrasting samples to hybridise them to assign gene status and differentially expressed
- Validate the identified genes
Implementation
- Mapping ESTs on tgi
- Some Tools
- gth_run
- trim_seq | Filter "N", size
- multifasta-fastas