Histone Modifications (H3K9) ChIP-chip arrays

H3K9 modifications (Lieb project, Ahringer subgroup)

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. 126 strategically selected targets include key histone modifications, histone variants, 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, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.


  1. Growth and isolation: Worm embryo growth and harvest:JL:SS6, Worm L3 extraction:JL:PK1, Worm embryo extraction:JL:SS2, Worm embryo growth and harvest:JL:SS3, Worm embryo extraction:JL:SS5, Worm embryo growth and harvest:JL:SS4, Worm embryo extraction:JL:SS4, Worm embryo growth and harvest:JL:SS2, Worm L3 extraction:JL:PK1
  2. Sample preparation: Worm LM-PCR Amplification for ChIP-chip:JL:SS1, ChIP-chip scanning nimblegen:JL:1, ChIP-chip label hyb nimblegen:JL:1, Worm LM-PCR Amplification for ChIP-chip:JL:SS2, ChIP-chip scanning nimblegen:JL:1, Worm Chromatin Immunoprecipitation:JL:SS1, Worm Chromatin Immunoprecipitation:JL:SS4, ChIP-chip label hyb nimblegen:JL:2, Worm LM-PCR Amplification for ChIP-chip:JL:IL1, Worm Chromatin Immunoprecipitation:JL:5, Worm LM-PCR Amplification for ChIP-chip:JL:PK1, Worm Chromatin Immunoprecipitation:JL:SS2, ChIP-chip scanning nimblegen:JL:2, Worm chromatin immunoprecipitation:JL:IL2, Worm Chromatin Immunoprecipitation:JL:PK1, ChIP-chip label hyb nimblegen:JL:1
  3. Other Protocols: ChIP-chip normalization standard zscore:JL:2, ChIP-chip normalization standard nimblegen:JL:1, ChIP-chip normalization standard MA2C:JL:1

Experimental Reagents

  1. Antibodies: HK00008_H3K9me2:6D11, C. elegans UP07442_H3K9ME3 rabbit polyclonal antibody, No Antibody Control, ab9045_H3K9me1:291918, ab8896_H3K9me1:104560, HK00009 H3K9me3:2F3, No Antibody Control, WA305-34819 H3K4me3
  2. Arrays: 080922_MODENCODE_CE_CHIP_HX1, 080922_MODENCODE_CE_CHIP_HX1, NimbleGen modEncode_CE_chip, NimbleGen C elegans ChIP HX1

Sample Details

  1. Animals/Lines: Early Stage Embryos, Early Stage Embryos

Related modENCODE submissions:

Release Date: 2009-10-07