mRNA microarray N2 Mixed Embryos

Lieb SDQ4051_LEM2_N2_MXEMB (Lieb project, Lieb subgroup)

General Description

To complement our extensive ChIP-chip characterization of chromosomal regulators in C. elegans, in select experiments we also isolate total RNA from parallel cultures of staged animals. Labeled cDNA will be prepared and used to probe either gene-specific microarrays, or genomic tiling microarrays to assess the transcriptional state of genomic sequences flanking the protein-binding regions localized by ChIP-chip and ChIP-seq. To investigate possible correlations between putative regulatory proteins and transcription state, data from such experiments (i.e., protein binding sites and steady-state mRNA levels) will be integrated during downstream analysis.

Protocols

  1. Growth and isolation: Worm embryo RNA extraction:JL:1, Worm embryo growth and harvest:JL:5, Worm embryo RNA extraction:JL:2, Worm embryo growth and harvest:JL:3
  2. Sample preparation: NimbleGen RNA labeling:JL:1, NimbleGen RNA scanning:JL:1, NimbleGen RNA hybridization:JL:1
  3. Data Analysis: RMA Averaging of 4-plex array:JL:1, NimbleGen RNA data normalization:JL:1

Release Date: 2010-12-22