MRG-1 ChIP-chip arrays

Transcription and Chromatin(Lieb project, Strome 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 the chromodomain-containing protein MRG-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.

Protocols

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

Experimental Reagents

    Growth Conditions:
  1. Antibodies: C. elegans JA00002_IGG rabbit polyclonal antibody, SDQ0791_MES4, SDQ0790_MRG1, SGF3165_FLAG
  2. Arrays: NimbleGen DesignName2007-05-17_C_elegans_ChIP_03, 080922_MODENCODE_CE_CHIP_HX1, NimbleGen DesignName2007-05-17_C_elegans_ChIP_02, NimbleGen C elegans ChIP HX1, NimbleGen modEncode_CE_chip, NimbleGen DesignName2007-05-17_C_elegans_ChIP_01

Sample Details

  1. Animals/Lines: Early Stage Embryos

External Links

  1. DCC-2539 Ahringer_L3_Worm_Samples
  2. Data Analysis: ChIP-chip_peak_finding_ChIPOTle:JL:SE1


Release Date: 2009-09-22