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August 20, 2007

BDGP modENCODE Data Production. August 20, 2007. BDGP Data Production. Project Goals 21,000 RACE experiments 6,000 cDNA’s from directed screening and full insert sequencing 3,000 RT-PCR experiments and insert sequencing Data Tracking Requirements

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August 20, 2007

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  1. BDGP modENCODE Data Production August 20, 2007

  2. BDGP Data Production Project Goals • 21,000 RACE experiments • 6,000 cDNA’s from directed screening and full insert sequencing • 3,000 RT-PCR experiments and insert sequencing Data Tracking Requirements • Identification of genomic regions for interrogation • Tracking and associations of experiments • Analysis of experimental data • Submission of results to GenBank and DCC

  3. Data Resources • The identification of experiments is based on • existing resources • Affymetrix microarray data • BDGP EST/cDNA clones

  4. Embryonic RNA Expression on Genome Tiling Arrays Manak et al., (2006) Nat. Genet. 38(10):1151-8.

  5. BDGP EST and cDNA Projects Data Resources • Project Resources • 295,379 BDGP EST end sequences • 109,398 Exelixis EST end sequences • 15,015 BDGP clone full length sequences • Production tracking and analysis in an • integrated database LIMS

  6. BDGP Production Tracking Existing production tracking through an internal web-based LIMS system

  7. Production Data Workflow Benchwork Registration Gel Processing Clone Data Processing

  8. BDGP Data Analysis

  9. BDGP 5’ RACE Identification of 5’ 2,074 RACE primers from set of CG’s from Ohler et al. 96 selected for experiments

  10. Directed cDNA Screening using iPCR • The congo exon screen is a model for the 5’ RACE, directed cDNA, and RT-PCR screening • congo: 41,564 protein coding exons from comparative analysis from Manolis Kellis • 434 exons did not overlap Rel 4.3 annotations or existing EST/cDNA data • 267 (61.5%) completed full insert sequencing

  11. Identification of Exon Primer Design and Experiment Registration PCR Plate Production Cloning, end and internal sequencing Assembly and Analysis of screen data Full insert sequencing of positive matches cDNA Clone Capture using iPCR

  12. Computationally predicted conserved exons validated by cDNA screening and sequencing I. Gene modifications II. Identification of New Genes Predictions - Kellis

  13. BDGP Data Production • The remaining work on the LIMS and data production system: • Completion of migration from EST/cDNA project to new code. • Identification and prioritization of experiments • Integration of microarray data • Specification of success • Definition of data transfer to DCC

  14. BDGP Data Production

  15. cDNA Sequencing Corrects Gene Models

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