Dosage Compensation ChIP-chip arrays

Dosage Compensation and Chromosome Organization (Lieb project, Ahringer 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 antibodies that recognize the dosage compensation and condensin proteins. 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 germlineless adult soma extract:JL:2.2, Worm embryo extraction:JL:SE1, Worm embryo extraction:JL:1, Worm_embryo_growth_and_harvest:JL:1, Worm embryo extraction:JL:2, Worm embryo extraction:JL:2, Worm embryo growth and harvest:JL:1, Worm embryo extraction:JL:3, Worm embryo growth and harvest:JL:SE1, Worm embryo growth and harvest:JL:SS3, Worm embryo extraction:JL:SS2, Worm embryo growth and harvest:JL:5, Worm embryo growth and harvest:JL:SS4, Worm embryo growth and harvest:JL:3, Worm L4 growth and harvest:JL:SE1
  2. Sample preparation: Worm Whole Genome Amplification for ChIP-chip:JL:2, Worm Chromatin Immunoprecipitation:JL:1, Worm Chromatin Immunoprecipitation:JL:5, Worm LM-PCR Amplification for ChIP-chip:JL:KI1, Worm Chromatin Immunoprecipitation:JL:SS2, ChIP-chip scanning nimblegen:JL:1, ChIP-chip label hyb nimblegen:JL:1, Worm Chromatin Immunoprecipitation:JL:PK1, Worm LM-PCR Amplification for ChIP-chip:JL:SS2, ChIP-chip scanning nimblegen:JL:2, Worm LM-PCR Amplification for ChIP-chip:JL:1, Worm Chromatin Immunoprecipitation:JL:4.1, ChIP-chip label hyb nimblegen:JL:2
  3. Other Protocols: ChIP-chip normalization standard nimblegen:JL:1, ChIP-chip normalization standard zscore:JL:2

Experimental Reagents

    Growth Conditions:
  1. Antibodies: JL00003_DPY26, JL00001_DPY27, SDQ3148_SDC2, C. elegans SS00050_IGG rabbit polyclonal antibody, JL0005_SDC2, JL00012_DPY28, No Antibody Control, JL00002_SDC3, JL00001_DPY27, SDQ3146_SDC2, JL0004_MIX1, JL00002_SDC3, JL00001_DPY27
  2. Arrays: 080922_MODENCODE_CE_CHIP_HX1, NimbleGen C elegans ChIP HX1, 080922_MODENCODE_CE_CHIP_HX1, NimbleGen DesignName2006-07-18 C elegans ChIP03, NimbleGen C elegans ChIP HX1

Sample Details

  1. Animals/Lines: Mixed Stage Embryos, Mixed Stage Embryos, L4 Larval Stage, Early Stage Embryos


  1. External Links: GSM403974, GSM403972, GSM409468, GSM409467, GSM403973, GSM409469


  1. Data Analysis: ChIP-chip peak finding ChIPOTle:JL:SE2


Release Date: 2009-11-27