Histone Modifications ChIP-chip arrays

Histone modifications(Lieb project, Ahringer subgroup)

General Description

Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 9. 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.

Protocols

  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 L3 extraction:JL:PK1, Worm embryo growth and harvest:JL:SS2
  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:SS4, Worm Chromatin Immunoprecipitation:JL:SS1, 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

    Growth Conditions:
  1. Antibodies: AB3594 H3K79me2:346021, C. elegans AB9050_H3K36ME3 rabbit polyclonal antibody, C. elegans UP07442_H3K9ME3 rabbit polyclonal antibody, HK00008_H3K9me2:6D11, No Antibody Control, WA308-34809_H3K4me2, HK00013 H3K27me3:1E7:JL:1, HK00009 H3K9me3:2F3, No Antibody Control, AB9049 H3K36me2:608457, HK00001 H3K36me3:13C9, AB2621 H3K79me3:361576, C. elegans AR0169_H3K4ME3 rabbit polyclonal antibody, WA305-34819 H3K4me3, HK00012_H3K36me2:2C3
  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


    External Links

  1. DCC-2539 Ahringer_L3_Worm_Samples_1
  2. DCC-2540 Ahringer_L3_Worm_Samples_2


Release Date: 2009-09-22