Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

ABSTRACT: Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

PROVIDER: PRJNA305508 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2983110.fastq.gz	Fastqsanger.gz
	SRR2983120.fastq.gz	Fastqsanger.gz
	SRR2983111.fastq.gz	Fastqsanger.gz
	SRR2983121.fastq.gz	Fastqsanger.gz
	SRR2983112.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 22

Similar Datasets

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [DamID-seq]

Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. We determined DamID scores for Polycomb, normalized by Dam only control, for Drosophila larval central brain, larval fat bodies and repo+ glial cells of larval central brain. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.

2016-03-17 | E-GEOD-75831 | biostudies-arrayexpress

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [DamID-seq]

2016-03-17 | GSE75831 | GEO

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [RNA-seq]

2016-03-17 | GSE75833 | GEO

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [RNA-seq]

Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. RNA sequencing of 3 samples, each using 2 biological replicates.

2016-03-17 | E-GEOD-75833 | biostudies-arrayexpress

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila.

Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity, it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila Here, we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress possible toxic effects of Dam. In addition, we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. These new DamID tools will be valuable for the mapping of binding patterns of chromatin proteins in Drosophila tissues and especially in cell lineages.

| S-EPMC4937306 | biostudies-literature

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-03-17 | GSE75835 | GEO

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-17 | E-GEOD-75835 | biostudies-arrayexpress

Tissue-specific DamID profiling of chromatin proteins in Drosophila melanogaster

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.

2016-08-30 | GSE86205 | GEO

Drosophila melanogaster

Project description:Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [DamID-seq]

| PRJNA305509 | ENA

Mapping SET1B Chromatin Interactions with DamID using DamMapper, a Comprehensive Snakemake Workflow

Project description:Background DNA adenine methyltransferase identification followed by sequencing (DamID-seq) is a powerful method used to map genome-wide chromatin-protein interactions. However, the bioinformatic analysis of DamID-seq data presents significant challenges due to the inherent complexities of the data and a notable lack of comprehensive software solutions for data-processing and downstream analysis. Results To address these challenges, we present a comprehensive bioinformatic workflow for DamID-seq data analysis, DamMapper, using the Snakemake workflow management system. Key features include straightforward processing of multiple biological replicates, visualisation of quality control figures, such as a correlation heatmaps and principal component analysis (PCA) plotting, and robust code quality maintained through continuous integration (CI). Reproducibility is ensured across diverse computational environments, including cloud computing and high-performance computing (HPC) clusters, through the implementation of software environments (Conda) and containerisation (Docker/Apptainer). We validated this workflow using a previously published DamID-seq dataset and Furthermore, we apply it to analyse novel datasets for proteins involved in the hypoxia response, specifically the transcription factor HIF-1α and the histone methyltransferase SET1B. This application reveals a strong concordance between our HIF-1α DamID-seq results and ChIP-seq data, and importantly, provides the first genome-wide DNA binding map for SET1B. Conclusions This work provides a validated, reproducible, and feature-rich workflow that overcomes common hurdles in DamID-seq data analysis. By streamlining the processing and ensuring robustness, DamMapper facilitates reliable analysis and enables new biological discoveries, as demonstrated by the characterization of SET1B binding sites. The workflow is available under the MIT license at: https://github.com/niekwit/damid-seq.

2025-08-21 | GSE296995 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data