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Lab Meeting Presentation

Lab Meeting Presentation. Ping HU. Experiments for Arabidopsis. Design Primers to check the Twinscan annotation of Arabidopsis Compare the unconfirmed Arabidopsis annotation and the Twinscan predictions. Categorization of Twinscan Predictions. Total Prediction: 30634/Total annotation: 28581.

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Lab Meeting Presentation

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  1. Lab Meeting Presentation Ping HU

  2. Experiments for Arabidopsis • Design Primers to check the Twinscan annotation of Arabidopsis • Compare the unconfirmed Arabidopsis annotation and the Twinscan predictions

  3. Categorization of Twinscan Predictions Total Prediction: 30634/Total annotation: 28581 Identical to ann: 15063 Not Identical to ann: 15588 Overlap with confirmed ann: 3246 Not overlap with confirmed ann: 12342 Not overlap with any ann: 4394 Overlap with other ann: 7948 Same start/Same stop 2358 Diff start/Same stop 2770 Same start/Diff stop 1879 Diff start/Diff stop 941

  4. UTR Primer Designs • Plate 1: from non-overlapped Twinscan predictions • Plate 2: • Half from non-overlapped TIGR unconfirmed annotation • Half from annotations which differs at the internal structures (same start and stop codon)

  5. Current result from plate 1 • 21 of 90 PCR products have splice sites confirmed (23%) • Problem: • genomic contamination from total RNA • PCR purification

  6. Try to improve cDNA quality • mRNA purification • still have genomic contamination • Yield is very low and could not detect some of the genes

  7. Dnase I treatment Problems • Dnase I treatment: be careful about the time and Rnase contamination

  8. Comparison of three methods M 1 2 3 M 1 2 3 1 2 3 1 2 3

  9. PCR purification : need to improve • Check concentration and use SAP and EdonucleaseI treatment

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