Histone Modifications in H4K20 (ChIP-Seq)

Histone Modifications in H4K20 (ChIP-seq) (Lieb project, Lieb subgroup)

Details

Synchronized C. elegans mixed stage embryos from strains YPT41, N2, and TY1072 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 methylated on lysine 20. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call binding peaks with the MACS algorithm to generate the track showing sequence features.

General Description

The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include key histone modifications and histone variants. We will integrate information generated with existing knowledge on the biology of the targets and perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins.

Protocols

  1. Growth and isolation: Worm embryo growth and harvest v1, modENCODE N2 embryos culture protocol_v5, Worm embryo extraction vSE2, worm_embryo_extraction_v5
  2. Sample preparation: Worm chromatin immunoprecipitation v4.1, worm_chromatin_immunoprecipitation_v5, Sequencing Illumina Library Preparation vSE2, Homebrew_Solexa_SE_prep, Illumina_DNA_Sequencing:JL:1
  3. Other Protocols: ChIP-seq_alignment-BWA:JL:1

Experimental Reagents

  1. Antibodies: NASP-1, H4K20me1
  1. External Links: GEO:TMPID:6011_chip_rep1, GEO:TMPID:6011_chip_rep2, GEO:TMPID:6011_input_rep1, GEO:TMPID:6011_input_rep2, GSM1195437, GSM1195438, GSM1195435, GSM1195436, GSM1217403, GSM1217404, GSM1217401, GSM1217402


Release Date: 2013-06-06 Submission 6011
Release Date: 2013-06-04 Submission 6210
Release Date: 2013-05-27 Submission 6211