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Drosophila melanogaster

ABSTRACT: damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets

PROVIDER: PRJNA284767 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2038537.fastq.gz	Fastqsanger.gz
	SRR2038538.fastq.gz	Fastqsanger.gz

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damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets

Project description:DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalisation based on read-counts alone can lead to high background and the loss of bound signal. DamID-seq thus presents novel challenges in terms of normalisation and background minimisation. We describe here damidseq_pipeline, a software pipeline that performs automatic normalisation and background reduction on multiple DamID-seq FASTQ or BAM datasets. Single replicate profiling of pol II occupancy in 3rd instar larval neuroblasts of Drosophila

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Project description:Analysis of gene expression regulation typically requires identification of genomic sites where regulatory proteins bind. For this purpose, ChIP and DamID methods applied to cell lines or model organisms are now routinely used, even in selected cell types. In this work, we present modifications to experimental DamID protocol, as well as a custom data processing algorithm that allows 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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