Histone Modifications in H3K27 (ChIP-Seq)

Histone Modifications in H3K27 (ChIP-seq) (Lieb project, Dernburg subgroup)

Details

Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipiitated with an affinity-purified polyclonal antibody that recognizes histone H3 acetylated on lysine 27, histone H3 methylated on lysine 27, or histone H3 trimethylated on lysine 27. 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_adult_growth_and_harvest_vHP2, Worm_adult_purified_germline_extract_v1, Worm_germline_enriched_adult_extract_vHP1, worm_embryo_growth_and_harvest_vSS5, worm_embryo_growth_and_harvest_vSS4, worm_embryo_extraction_vSS2
  2. Sample preparation: Worm_chromatin_immunoprecipitation_vACD1, worm_chromatin_immunoprecipitation_vSS4, Homebrew_Solexa_SE_prep, Truseq Library prep vACD1, Illumina_DNA_Sequencing:JL:1
  3. Other Protocols: ChIP-seq_alignment-BWA:JL:1

Experimental Reagents

  1. Antibodies: H3K27ac, H3K27me1, H3K27me3, H3K27me3
  1. External Links: GEO:TMPID:3921_chip_rep1, GEO:TMPID:3921_chip_rep2, GEO:TMPID:3921_input_rep1, GEO:TMPID:3921_input_rep2, GSM1206354, GSM1206355, GSM1206352, GSM1206353, GSM1217459, GSM1217460, GSM1217457, GSM1217458, GSM1206350, GSM1206351, GSM1206348, GSM1206349, GSM1206366, GSM1206367, GSM1206364, GSM1206365


Release Date: 2013-06-18 Submission 3921
Release Date: 2013-06-12 Submission 5160
Release Date: 2013-05-24 Submission 6254
Release Date: 2013-06-13 Submission 5159
Release Date: 2013-06-12 Submission 5163