Insulators in Oregon strain

Solexa.SU(HW)-HB.14-16 hr OR embryo (Karpen project, Karpen subgroup)

Nuclei were isolated from staged Drosophila Oregon R embryos, 14-16 hr after egg laying that had been crosslinked with formaldehyde. After lysis and sonication the chromatin was immunoprecipitated with an affinity-purified antibody that recognizes the chromosomal insulator protein Su(Hw). The resulting fragments were used to create libraries and sequenced on the Illumina platform. Short reads were aligned to the reference genome using Bowtie, and peaks for each replicate were called using SPP (using sequence from the Input material as a comparison control). Statistically significant regions of enrichment from the two biological replicates were then combined and used to call the cumulative peaks.

Details

General Description

We aim to determine the locations of 125 chromosomal proteins across
the Drosophila melanogaster genome. The proteins under study are
involved in basic chromosomal functions such as DNA replication, gene
expression, gene silencing, and inheritance. We will perform Chromatin
ImmunoPrecipitation (ChIP) using the Illumina NGS platform. We will
initially assay localizations using chromatin from three cell lines
and two embryonic stages, and will then extend the analysis of a
subset of proteins to four additional animal tissues/stages

Protocols

Growth and isolation: Cage population, Chromatin prep from fixed D.m. embryos
Sample preparation: Illumina sequencing, ChIP
Data Analysis: Bowtie alignment
Other Protocols: SPP Peak calling

Experimental Reagents

Antibodies:

Sample Details

Animals/Lines:

Release Date: 2013-03-06 Submission 3958 Release Date: 2013-03-06 Submission 3958