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Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [DamID]

ABSTRACT: To investigate the mechanisms of gene regulation during Drosophila spermatogenesis, we obtained genome-wide binding profiles of the proteins involved in gene regulation during drosophila spermatogenesis using germline-specific DamID-Seq approach.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE97176 | GEO | 2017/03/30

SECONDARY ACCESSION(S): PRJNA380896

REPOSITORIES: GEO

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Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [RNA-Seq]

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Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [ChIP-Seq]

Project description:To investigate the mechanisms of gene regulation during Drosophila spermatogenesis, we studied the effects of comr and can mutations on the chromatin of the cells in Drosophila testes by H3K27me3 ChIP-Seq.

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Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis

Project description:Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis

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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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Identifying targets of DSX with DamID-seq

Project description:We have adapted the DamID protocol for use with high throughput sequencing. We have used DamID to identify the positions within the Drosophila genome where the transcription factor DSX is bound. We sequenced DpnI-digested genomic DNA from fly tissues containing UAS-Dam (control) or UAS-Dam-DsxF or UAS-Dam-DsxM. We have performed DamID-seq on adult male and female fatbody and on ovary. We used two biological replicates for each tissue and sex.

2014-10-30 | E-GEOD-27269 | biostudies-arrayexpress

Identifying targets of DSX with DamID-seq

2014-10-30 | GSE27269 | GEO

Genome-wide DNA-binding analysis for Stat92E in Drosophila testis by DamID

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DamID data for Comr binding in drosophila testes

Project description:Comr protein was found to be a major regulator of gene activity in drosophila spermatocytes. We obtained Comr binding profile to determine targets of Comr. Comr binding in drosophila male germ line cells was determined using DamID technique.

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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.

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