Histone Modifications (H3K27) ChIP-Seq

seq-UP07448_H3K27me1:24439_N2_L3 (Lieb project, Ahringer subgroup)

Details

seq-UP07448_H3K27me1_24439_N2_L3 (Lieb project, Ahringer subgroup)

Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated 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_L3_Formaldehyde_Extract Preparation_vPK2, Worm L3 growth and harvest:JL:PK1
  2. Sample preparation: Illumina_DNA_Sequencing:JL:1, Worm chromatin immunoprecipitation:JL:IL2, Illumina TruSeq Library Preparation:JL:JA1:JL:1
  3. Other Protocols: Histone_Replicates_QC, ChIP-seq_alignment-BWA:JL:1, BEADS_Normalization

Experimental Reagents

    Antibodies:
  1. External Links: GEO:TMPID:5044_input_rep1, GEO:TMPID:5044_chip_rep2, GEO:TMPID:5044_input_rep2, GEO:TMPID:5044_chip_rep1


Release Date: 2013-05-30 Submission 5044