ALR-1 Combined (GFP ChIP)

Identification of Transcription Factor ALR-1::GFP Binding Regions in L2 (Snyder project, Snyder subgroup)

General Description

Synchronized L2 larvae from C. elegans strain OP200 (a transgenic strain engineered to express a gene fusion between alr-1 and GFP) were treated with the cross-linking reagent formaldehyde. After lysis and sonication, the chromatin was immunoprecipitated with an affinity-purified antibody that recognizes GFP. The bound DNA was purified and sequenced in an Illumina GA-2. A sample of the input DNA was sequenced in parallel. The ChIP-seq data generated by this experiment was analyzed using the PeakSeq peak-calling algorithm to predict protein binding sites in the C. elegans genome.

Protocols

  1. Growth and isolation: Worm Growth and Harvest
  2. Sample preparation: Illumina Deep Sequencing, ChIP
  3. Data Analysis: Illumina Data Merging, Skip Illumina Data Merging, Illumina Data Analysis, Peak Calling

Experimental Reagents

    Growth Conditions:
  1. Antibodies: Anti-eGFP

Sample Details

  1. Animals/Lines: L2


Release Date: 2009-11-26 Track 3156