Histone Modifications in H3K4 (ChIP-Seq)

Histone Modifications in H3K4 (ChIP-seq) (Lieb project, Strome and Dernburg subgroups)

Details

Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 dimethylated on lysine 4, histone H3 methylated on lysine 4, or histone H3 trimethylated on lysine 4. 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_vSS5, worm_embryo_growth_and_harvest_vSS4, Worm_adult_growth_and_harvest_vHP2, Worm_adult_growth_and_harvest_germCW1, Extract Preparation Dual Crosslinking vACD1, worm_embryo_extraction_vSS2, Worm_germline_enriched_adult_extract_vHP1, Worm_adult_purified_germline_extract_v1
  2. Sample preparation: worm_chromatin_immunoprecipitation_vSS4, Worm chromatin immunoprecipitation vACD1, Worm chromatin immunoprecipitation:JL:IL2, Worm_chromatin_immunoprecipitation_vCW2, Homebrew_Solexa_SE_prep, Truseq Library prep vACD1, Illumina TruSeq Library Preparation:JL:JA1:JL:1, Illumina_DNA_Sequencing:JL:1
  3. Other Protocols: ChIP-seq_alignment-BWA:JL:1

Experimental Reagents

  1. Antibodies: H3K4me2, H3K4me1, H3K4me3, H3K4me1
  1. External Links: GSM1206346, GSM1206347, GSM1206344, GSM1206345, GSM1217451, GSM1217452, GSM1217449, GSM1217450, GSM1206370, GSM1206371, GSM1206368, GSM1206369, GSM1217351, GSM1217352, GSM1217349, GSM1217350, GSM1217363, GSM1217364, GSM1217361, GSM1217362, GSM1217261, GSM1217262, GSM1217259, GSM1217260


Release Date: 2013-06-12 Submission 5157
Release Date: 2013-05-27 Submission 6246
Release Date: 2013-06-05 Submission 5166
Release Date: 2013-05-17 Submission 5245
Release Date: 2013-06-03 Submission 5153
Release Date: 2013-06-06 Submission 5158