Dosage Compensation ChIP-Seq

Dosage Compensation ChIP-Seq (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 dpy-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

ChIP-seq analysis of 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. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.

Protocols

  1. Growth and isolation: Worm_L3_growth_and_harvest:JL:PK1, Worm_L3_extraction:JL:PK1
  2. Sample preparation: Worm_chromatin_immunoprecipitation:JL:IL2, Illumina_Library_Preparation_ChIPseq:JL:JA1, Illumina_DNA_Sequencing:JL:1
  3. Other Protocols: ChIP-seq_alignment-BWA:JL:1, ChIP-Seq_MACS_Peak-calling_over_reps:JL:1, ChIP-Seq_MACS_Peak-calling:JL:1

Experimental Reagents

  1. Antibodies: DPY-27 , and 7 more.

Sample Details

  1. Animals/Lines: Caenorhabditis elegans
  2. External Links: GSM706165 , and 99 more.


Release Date: 2011-08-24