PHA-4 Combined (GFP ChIP)

Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans (Snyder project, Snyder subgroup)


Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 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.


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

Experimental Reagents

    Growth Conditions:
  1. Antibodies: Anti-eGFP, Anti-eGFP

Sample Details

  1. Animals/Lines: starved L1, fed L1, Young Adult, late embryo, embryo, L2, L4, L3
  2. External Links: GSM363860, GSM363863, GSM363862, GSM363861

Release Date: 2011-02-02 Submission 3158
Release Date: 2009-11-27 Submission 585
Release Date: 2009-11-27 Submission 582
Release Date: 2009-11-27 Submission 584
Release Date: 2011-02-13 Submission 3161
Release Date: 2013-04-18 Submission 4033 (Temporarily withheld; track not shown)
Release Date: 2013-05-15 Submission 3215
Release Date: 2013-04-18 Submission 2945