Tiling array (Waterston project, Reinke subgroup)
Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method.
- Growth and isolation: Worm growth, Worm staging and isolation, RNA_isolation
- Sample preparation: cDNA amplification (with Dnase treatment), Labeling_of_cDNA_for_Tiling_Arrays, Affy_Hybridization_and_Scanning
- Data Analysis: Tiling_Array_Signal_Extraction, Tiling_Array_Normalization_and_Smoothing, Tiling_Array_TAR_analysis
- Other Protocols: cDNA amplification (with Dnase treatment), Affy_Hybridization_and_Scanning
- Arrays: Affymetrix GeneChip C. elegans tiling 1.0R array, GPL5634
- Animals/Lines: Caenorhabditis elegans, early embryo, N2, late embryo 20dC 4.5 hours post-early embryo, N2, larva mid-L1 25dC 4.0 hrs post-L1, N2, mid-L2, N2, mid-L3, N2, mid-L4, N2, Male larva mid-L4 25dC 30 hrs post-L1, N2, CB4689, Young Adult 20dC 42 hr post-L1, Gonad (hermaphrodite), N2, Young Adult, N2