ChIP-chip computed peaks

ChIP-chip array computed peaks (Lieb project, Desai subgroup)

General Description

Synchronized C. elegans 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 dosage compensation and condensin protein DPY-26. 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.


  1. Growth and isolation: Worm embryo extraction:JL:SE1, Worm embryo extraction:JL:1, Worm embryo growth and harvest:JL:SE1, Worm embryo growth and harvest:JL:SS1, Worm embryo extraction vCW1, Worm embryo extraction:JL:SS1, Worm embryo growth and harvest vCW1
  2. Sample preparation: ChIP-chip label hyb nimblegen v1, Worm Chromatin Immunoprecipitation:JL:5, Worm LM-PCR Amplification for ChIP-chip:JL:SS1, ChIP-chip scanning nimblegen:JL:1, Worm chromatin immunoprecipitation:JL:SS1, Worm LM-PCR Amplification for ChIP-chip v1, Worm Chromatin Immunoprecipitation vCW1, Worm Chromatin Immunoprecipitation:JL:4.1
  3. Other Protocols: ChIP-chip normalization standard nimblegen:JL:1, ChIP-chip normalization standard zscore:JL:2, ChIP-chip normalization standard zscore v1

Experimental Reagents

    Growth Conditions:
  1. Antibodies: JL0004_MIX1, JL00003_DPY26, JL0005_SDC2, SGF3165_FLAG, C. elegans HTZ-1 mouse polycolonal
  2. Arrays: NimbleGen DesignName2007-05-17_C_elegans_ChIP_03, NimbleGen DesignName2006-05-08 C elegans SXGA 1, NimbleGen DesignName2007-05-17_C_elegans_ChIP_02, NimbleGen DesignName2006-05-08 C elegans SXGA 2, NimbleGen C elegans ChIP HX1, NimbleGen DesignName2007-05-17_C_elegans_ChIP_01

Sample Details

  1. Animals/Lines: Mixed Stage Embryos, Early Stage Embryos
  2. External Links: GSM257465, GSM257584, GSM409468, GSM257587, GSM409469, GSM403972, GSM403974, GSM257582, GSM409467, GSM403973, GSM257575

  1. Data Analysis: ChIP-chip peak finding ChIPOTle vCW1, ChIP-chip_peak_finding_ChIPOTle:JL:SE1, ChIP-chip peak finding ChIPOTle:JL:SE2

Release Date: 2009-11-30