Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Using DNA Affinity Purification sequencing (DAP-seq) to identify in vitro binding sites of transcription factors potentially involved in aromatic degradation

ABSTRACT: The genome-wide binding sites of 44 transcription factors from the aromatic metabolizing Alphaproteobacterium Novosphingobium aromaticivorans were identified using DNA Affinity Purification sequencing (DAP-seq). We report 32 of these transcription factors have at least one area of enrichment. These data will be valuable for better understanding of aromatic metabolism.

ORGANISM(S): Novosphingobium aromaticivorans

PROVIDER: GSE291618 | GEO | 2025/03/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The DNA affinity purification DAP-Seq assay [ChIP-seq]

Project description:As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.

2016-05-25 | GSE60142 | GEO

Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce aromatic diketones

Project description:Aromatic diketones are a major product of formic acid lignin depolymerization. Novosphingobium aromaticivorans can degrade these diketones, but the enzymes used in this process were unknown. We used RNA-Seq to identify aromatic dimer dehydrogenases as potential candidates for the initial reduction of the aromatic G-diketone, then verified this using in vitro enzyme assays.

2021-05-22 | GSE174697 | GEO

Identification of NAC094-targeted genes using DNA affinity purification sequencing (DAP-seq)

Project description:To identify binding sites and nodule SAGs that are directly targeted by NAC094, we used DAP-seq, which allows the capture of the NAC094 regulatory targets at the whole-genome scale. A total of 2,819 binding peaks corresponding to 2,721 genes were identified from two repeats of the DAP-seq experiment.

2023-03-23 | GSE197359 | GEO

DNA affinity purification sequencing (DAP-seq) data of LEAFY (LFY)

Project description:In this study, we use DNA affinity purification sequencing to identiy genome-wide binding of LFY transcription factor, a master regulator of flower development in Arabidopsis. We generated two sets of data, one using genomic DNA from plant tissue, thus retain DNA methylation, as probe for DNA affinity purification (DAP-seq dataset), and the other using PCR amplified genomic DNA (without DNA methylation; AmpDAP-seq dataset).

2021-03-25 | GSE160013 | GEO

sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI

Project description:In this study, we applied sequential DNA affinity purification sequencing (seq-DAP-seq) to identiy genome-wide binding of a heterocomplex formed by two transcription factors of the MADS familly SEP3 and AG(AP1-I) (AG with its I domain switched with that of AP1). We compared the genome wide binding of SEP3-AG(AP1-I) to that of our previously published SEP3-AG data

2021-07-08 | GSE166205 | GEO

Mapping genome-wide binding profile of ChCUC1 by DNA Affinity Purification sequencing (DAP-seq)

Project description:The mechanism underlying CUC genes regulating leaf marginal patterning remains largely unknown. To this end, we employed DAP-seq to identify the downstream regulating genes of ChCUC1. The aim of this project is to map genome-wide CUC genes binding sites.

2024-05-31 | GSE241208 | GEO

Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce aromatic diketones

Project description:Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce aromatic diketones

| PRJNA731907 | ENA

DNA affinity purification sequencing (DAP-seq) data of LEAFY (LFY)

Project description:DNA affinity purification sequencing (DAP-seq) data of LEAFY (LFY)

| PRJNA671605 | ENA

Identification of NAC094-targeted genes using DNA affinity purification sequencing (DAP-seq)

Project description:Identification of NAC094-targeted genes using DNA affinity purification sequencing (DAP-seq)

| PRJNA810032 | ENA

sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI

Project description:sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI