GEI-11 Combined (GFP ChIP)

Identification of Transcription Factor GEI-11::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, and Young Adult C. elegans (Snyder project, Snyder subgroup)

Details

Synchronized C. elegans from various developmental stages of strain OP179 (a transgenic strain engineered to express a gene fusion between gei-11 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, Worm Growth and Harvest
  2. Sample preparation: Illumina Deep Sequencing, ChIP, ChIP, Illumina Deep Sequencing
  3. Data Analysis: Illumina Data Merging, Skip Illumina Data Merging, Illumina Data Analysis, Peak Calling
  4. Other Protocols: Illumina Data Analysis, Illumina Data Analysis, Peak Calling, ChIP-seq replicate verification

Experimental Reagents

  1. Antibodies: Anti-eGFP, Anti-eGFP

Sample Details

  1. Animals/Lines: Young adult, L4, L3, L2, fed L1, Embryo


Release Date: 2011-05-07 Submission 3149
Release Date: 2009-11-28 Submission 2451
Release Date: 2013-09-16 Submission 4037
Release Date: 2013-04-23 Submission 3067
Release Date: 2011-09-13 Submission 3066
Release Date: 2013-04-22 Submission 3373