NHR-237 Combined (GFP ChIP)

Identification of Transcription Factor NHR-237::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, and L3 larvae C. elegans (Snyder project, Snyder subgroup)

Details

Synchronized C. elegans from various developmental stages of strain OP228 (a transgenic strain engineered to express a gene fusion between nhr-237 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.

General Description

We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.

Protocols

  1. Growth and isolation: Plated Worm Growth and Harvest
  2. Sample preparation: ChIP, Illumina Deep Sequencing
  3. Data Analysis: Illumina Data Merging, Skip Illumina Data Merging
  4. Other Protocols: Peak Calling, Illumina Data Analysis, ChIP-seq replicate verification

Experimental Reagents

    Antibodies: Anti-eGFP

Sample Details

    Animals/Lines: L3, L2, L1 26dC, Embryo


Release Date: 2013-04-09 Submission 3849
Release Date: 2013-04-04 Submission 3850
Release Date: 2013-04-16 Submission 3852
Release Date: 2013-04-16 Submission 3853