ArticleChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2016
Data analysis algorithm for DamID-seq profiling of chromatin proteins in Drosophila melanogaster.
Article in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
7 citing papers in PubMed.
- Article
- DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm.Development (Cambridge, England) · 2021Article
- Article
- DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis.Epigenetics & chromatin · 2018Article
- Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis.Epigenetics & chromatin · 2018Article
- Genome-wide analysis of SU(VAR)3-9 distribution in chromosomes of Drosophila melanogaster.Chromosoma · 2018Article
- Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile.Epigenetics & chromatin · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of gene expression regulation typically requires identification of genomic sites bound by regulatory proteins. For this purpose, chromatin immunoprecipitation (ChIP) and Dam identification (DamID) methods can be applied to cell lines, whole organisms, or enriched cell populations. In this work, we present modifications to the experimental DamID protocol, as well as a custom data processing algorithm, that allow to confidently identify genomic sites enriched with the proteins of interest. This algorithm is implemented in Perl and is also available as executable files, thereby making DamID analysis relatively straightforward. Finally, we demonstrate how this pipeline performs when fed with real experimental data.
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Registered trials
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