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BIF-30806 Group Project

BIF-30806 Group Project. Group ( A) rabidopsis : David Nieuwenhuijse Matthew Price Qianqian Zhang Thijs Slijkhuis. Species: Caenorhabditis elegans. Nematode worm Genome of ~100M bp (completed 2002) ~20,000 genes. Project choice: Advanced Project.

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BIF-30806 Group Project

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  1. BIF-30806 Group Project Group (A)rabidopsis: David Nieuwenhuijse Matthew Price Qianqian ZhangThijsSlijkhuis

  2. Species: Caenorhabditiselegans • Nematode worm • Genome of ~100M bp(completed 2002) • ~20,000 genes

  3. Project choice: Advanced Project • Investigation of differences in gene expression over multiple conditions

  4. Project Overview

  5. Datasets to use • We will use four different conditions, corresponding to four different life-stages of the organism (L2, L3, L4 & YA) • For each life-stage, there are 2-3 datasets (runs) of transcript reads, available on the NCBI SRA online database. • Reference Genome also required

  6. Dataset preparation • .sra files are first converted to .fastq files via fastq-dump • .fastqrun-files are merged together to create a single .fastq file per stadia, via command-line script (cat) • Reference genome selected from Ensembl database, after a Ref. genome from Wormbase failed to work

  7. Pipeline Overview Transcript reads .fastqfile TopHat program Readssplice-alignedto genome Reference genome .gtf file CuffLinks program Reconstructed transcriptome  Complete Transcriptome quantified(4 files) CuffMerge program Merged transcriptome file CuffDiff program Differential gene expression

  8. Project Task Delegation

  9. Problem Management

  10. Data Validation • Run the pipeline on another closely-related organism for comparable results? • Do the biological explanations of the gene expression make sense in light of the conditional contexts?

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