Pathogen Exposure

Pathogen exposure post-adulthood N2 tiling_array (Waterston project, Reinke subgroup)

General Description

Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commercially available genome tiling arrays. To understand how bacterial pathogens taken up by C. elegans may affect transcription, we grew young adult worms on various pathogenic bacterial strains for either 24 or 48 hours and measured transcription levels. Simultaneously, young adult worms were also grown on non-pathogenic bacteria (OP50) as controls.

Protocols

  1. Growth and isolation: Worm growth, Worm staging and isolation, Growth_condition_assay, RNA_isolation
  2. Sample preparation: cDNA amplification (with Dnase treatment), Labeling_of_cDNA_for_Tiling_Arrays, Affy_Hybridization_and_Scanning
  3. Data Analysis: Tiling_Array_Signal_Extraction, Tiling_Array_Normalization_and_Smoothing, Tiling_Array_TAR_analysis
  4. Other Protocols: Growth_condition_assay, cDNA amplification (with Dnase treatment), Affy_Hybridization_and_Scanning

Experimental Reagents

  1. Growth Conditions: P. luminescens (Hb) 24h/48h exposure, E. faecalis (OG1RF) 24h/48h exposure, S. marcescens (Db11) 24h/48h exposure, E. coli (OP50) 24h/48h exposure
  2. Arrays: Affymetrix GeneChip C. elegans tiling 1.0R array, GPL5634

Sample Details

  1. Animals/Lines: Caenorhabditis elegans, Young Adult, N2


Release Date: 2009-07-14