Polymerase II Isoforms ChIP-chip arrays

RNA Polymerase II Isoforms (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 either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. 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 growth and harvest:JL:SS6, Worm embryo extraction:JL:SS2, Worm embryo extraction vCW1, Worm embryo growth and harvest vCW1, Worm L4 growth and harvest:JL:SE1, Worm embryo growth and harvest:JL:SS2
  2. Sample preparation: Worm Whole Genome Amplification for ChIP-chip:JL:2, ChIP-chip label hyb nimblegen v1, 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, ChIP-chip scanning nimblegen v1, Worm LM-PCR Amplification for ChIP-chip v1, Worm Chromatin Immunoprecipitation vCW1, Worm LM-PCR Amplification for ChIP-chip:JL:1, Worm Chromatin Immunoprecipitation:JL:4.1
  3. Other Protocols: ChIP-chip normalization standard zscore:JL:2, ChIP-chip normalization standard nimblegen:JL:1, ChIP-chip normalization standard zscore v1

Experimental Reagents

    Growth Conditions:
  1. Antibodies: No Antibody Control, Ab:8WG16:JL:CVMMS126R, ABAB817_8WG16
  2. Arrays: NimbleGen DesignName2007-05-17_C_elegans_ChIP_02, NimbleGen modEncode_CE_chip, NimbleGen C elegans ChIP HX1, NimbleGen DesignName2007-05-17_C_elegans_ChIP_01, NimbleGen DesignName2006-05-08 C elegans SXGA 1, 080922_MODENCODE_CE_CHIP_HX1, NimbleGen DesignName2007-05-17_C_elegans_ChIP_03, NimbleGen DesignName2006-05-08 C elegans SXGA 2

Sample Details

  1. Animals/Lines: L4 Larval Stage, Early Stage Embryos, Mixed Stage Embryos
  2. External Links: GSM257638, GSM257637, GSM257654, GSM257642


Release Date: 2008-07-28