ZFP-1 ChIP-chip arrays

Transcription and Chromatin(Lieb project, Lieb subgroup)

Synchronized C. elegans mixed embryos from strains RB774 (which contains a zfp-1 knockout allele) and N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes chromatin-associated protein ZFP-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.



General Description

The focus of our analysis will be elements that specify nucleosome
positioning and occupancy, control domains of gene expression, induce
repression of the X chromosome, guide mitotic segregation and genome
duplication, govern homolog pairing and recombination during meiosis,
and organize chromosome positioning within the nucleus. Our 126
strategically selected targets include RNA polymerase II isoforms,
dosage-compensation proteins, centromere components, homolog-pairing
facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the
biology of the targets and perform ChIP-chip analysis on mutant and RNAi
extracts lacking selected target proteins.

Protocols

  1. Growth and isolation: Worm embryo extraction:JL:1, Worm embryo growth and harvest:JL:5, Worm embryo extraction:JL:2, Worm embryo growth and harvest:JL:3, Worm embryo growth and harvest:JL:5, Worm embryo extraction:JL:2, Worm embryo growth and harvest:JL:1
  2. Sample preparation: ChIP-chip label hyb nimblegen:JL:1, ChIP-chip scanning nimblegen:JL:2, Worm Chromatin Immunoprecipitation:JL:MBJ1, Worm Chromatin Immunoprecipitation:JL:MBJ5, Worm LM-PCR Amplification:JL:MBJ1, ChIP-chip label hyb nimblegen:JL:2, ChIP-chip scanning nimblegen:JL:1
  3. Other Protocols: ChIP-chip normalization standard MA2C:JL:1, ChIP-chip peak finding over reps MA2C:JL:1, ChIP-chip normalization standard MA2C:JL:2, ChIP-chip normalization standard zscore:JL:2, ChIP-chip peak finding MA2C:JL:1, ChIP-chip peak finding MA2C:JL:1

Sample Details

    Animals/Lines:


Release Date: 2010-06-21