Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Gon4l-associated genomic regions by DamID-seq

ABSTRACT: We report DNA adenine methyltransferase identification (DamID)-sequencing data to identify Gon4l-associated genomic regions in wild-type (WT) tailbud (TB) stage zebrafish embryos. Methylated, and therefore Gon4l-proximal, gDNA was isolated from embryos expressing a Gon4l-Dam fusion and compared to that from embryos expressing GFP-Dam control.

ORGANISM(S): Danio rerio

PROVIDER: GSE96576 | GEO | 2017/09/13

SECONDARY ACCESSION(S): PRJNA379067

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and Su(H) in wildtype, seq overexpressed and ttk-RNAi intestinal progenitor cells by DamID

Project description:Purpose: Genome-wide DNA-binding analysis for Ttk in intestinal progenitor cells and comparing Su(H) binding sites between seq overexpressed and ttk-RNAi intestinal progenitor cells in Drosophila midgut by DNA adenine methyltransferase identification(DamID) Methods: Dam(Ctrl) , Ttk-Dam transgenes, Su(H)-Dam, Su(H)-Dam&seq and Su(H)-Dam&ttk-RNAi were expressed in intestinal progenitor cells by esg-Gal4.The guts within 2 days was used for DNA adenine methyltransferase identification (DamID), followed by deep sequencing analysis Results: Ttk suppresses neural specific Notch targets through suppressing Seq in intestinal progenitor cells

2021-02-23 | GSE130941 | GEO

DamID experiment looking at Dichaete-bound regions in 2-7h old Drosophila embryos

Project description:Dichaete is a developmentally important transcription factor, known to be involved in basic biological processes including segmentation and nervous system development among others. The aim of this experiment was to gain further insight into the role of Dichaete during early embryogenesis, by finding out where in the genome it's binding using the DamID technique. 3 independent biological replicates. Embryos between 2-7 h old were collected. The sample embryos contained a Dichaete-Dam methylase fusion, while the control embryos had a Dam methylase only to simulate the background level of methylation not specific to transcription factor binding.

2013-07-22 | E-GEOD-49013 | biostudies-arrayexpress

Identification of HP1 protein binding sites in Drosophila Kc cells using DamID

Project description:Heterochromatin protein HP1 is thought to play key role in chromatin structure and gene regulation. We performed a genome-wide mapping of HP1 target genes in the non-polytenic Drosophila Kc cells by using DamID. This approach is based on the ability of a chromatin protein fused to Escherichia coli DNA adenine methyltransferase (Dam) to methylate the native binding site of the chromatin protein. Dam-fusion proteins are expressed at very low levels to avoid mistargeting. Subsequently, methylated DNA fragments are isolated, labeled (using Cy3 or Cy5) and hybridized to a microarray. Methylated DNA fragments from cells transfected with Dam alone served as reference. Genomic binding sites of the protein can then be identified based on the targeted methylation pattern. For detailed background information on DamID, see: van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-8 (2001); van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8 (2000). We performed three independent replicates. We used for this study a cDNA array developed by the GeneCore facility in EMBL (Heidelberg, Germany), covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.

2007-07-05 | E-MEXP-864 | biostudies-arrayexpress

PolyA+ expression profiling of tubulin Gal4 driven targeted DamID in Drosophila melanogaster adults and gonads

Project description:Targeted DamID (TaDa) measures gene expression using a DNA adenine methyltransferase (Dam) fused to RNA polymerase II (Dam Pol II) to methylate DNA as the genome is transcribed (Southall, Gold et al. 2013, PMID: 23792147). Here we use traditional Illumina RNA-Seq to determine if a cell’s expression profile is affected by Dam Pol II expression. Twenty-four hours prior to collection, we ubiquitously drove UAS Dam or UAS Dam Pol II using a tubulin (tub) GAL4 regulated by a temperature sensitive tub GAL80[ts] (McGuire et al. 2003, PMID: 14657498) in adult Drosophila melanogaster (taxon: 7227) whole males, whole females, testes, and ovaries.

2018-06-13 | GSE115694 | GEO

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.

2014-10-30 | GSE27269 | GEO

Identifying targets of DSX with DamID-seq

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

LMN-1-DamID in N2 and set-25(n5021) met-2(n4256) mutant early C. elegans embryos

Project description:We asked if the perinuclear position of chromosome arms in C. elegans depends on the histone methyltransferases MET-2 and SET-25. To this end, we performed LMN-1-DamID in wild-type (N2) and mutant (set-25 met-2) strains. LMN-1-DamID signal on chromosome arms was significantly reduced in the mutant. Three biological replicas were performed for each genotype. For one replica dyes were swapped. For each replica methylated DNA amplified from a strain expressing LMN-1-Dam was competitively hybridized against DNA amplified from a strain expressing GFP-Dam.

2012-09-04 | E-GEOD-37226 | biostudies-arrayexpress

Identification of Rx2 binding loci in medaka by iDamID-seq

Project description:We have improved the DamID method to make it applicable for vertebrate life specimens. We use iDamID-seq to profile the binding profile of the transcription factor Rx2 in medaka embryos at stage 22 of development. We compare two replicates of the fusion Dam-Rx2 against two replicates of the fusion Dam-GFP as control. Medaka embryos at 1-cell stage were injected with mRNA transcribed in vitro from one of the two Dam fusions. The embryos were allowed to grow in normal conditions up to stage 22. The genomic DNA was isolated and treated to extract only the DpnI fragments that had adenine methylation. These fragments were subjected to deep sequencing.

2016-10-06 | E-MTAB-4610 | biostudies-arrayexpress

C. elegans L4 hypodermal RNA polymerase DamID

Project description:To adapt RNA polymerase DamID (RAPID) for FLP-mediated spatial control in Caenorhabditis elegans, we inserted a Dam::rpb-6 fusion gene downstream of a FRT-flanked mCh::his-58 cassette and under control of the hsp-16.41 promoter. We introduced a single copy of this construct into the C. elegans genome and crossed the resulting line with a dpy-7p::FLP driver to enable basal Dam::rpb-6 expression in the hypodermis. Nematodes were cultured at 20 degrees Celcius to ensure low levels of Dam::RPB-6 expression in the hypodermis and total genomic DNA was purified from L4 larvae. DNA from animals expressing GFP::Dam was used to control for unspecific methylation. The genome-wide association profile of Dam::RPB-6 was determined by deep sequencing, which revealed a list of 2331 protein coding genes with FDR < 0.05. Original RAPID reference: Gomez-Saldivar et al (2020) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Genetics 216, 931–945. doi:10.1534/genetics.120.303774

2022-09-30 | GSE214300 | GEO

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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