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

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

PROVIDER: PRJNA671605 | ENA |

REPOSITORIES: ENA

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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

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

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

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Transcription profiling of Arabidopsis thaliana LFY mutant plants transformed with different LFY orthologs to investigate evolutionary divergence of LFY function

Project description:The aim of this experiment is to test the ability of the ortholog of Arabidopsis LFY gene from flowering and non flowering species to complement an Arabidopsis LFY mutant. Plants expressing, in a homozygous lfy12 background, the open reading frame of LFY orthologs under the control of Arabidopsis LFY promoter were synchronously induced to flower by growing plants in short days for 30 days then shifting them to Long Day for an additional 8 days. Shoot apices were dissected at either d0 or d8 in long days. Two biological replicates were performed. The following genotypes were used: Col - wild type arabidopsis; reference strain LFY (lfy12; LFY::AthLFY) - Arabidopsis UNI (lfy12; LFY::UNI) - Pisum ALF (lfy12; LFY::ALF) - Petunia WelNDLY (lfy12; LFY::WelNDLY) - Welwitschia mirabilis CrLFY1 (lfy12; LFY::CrLFY1) - Ceratopteris richardii CrLFY2 (lfy12; LFY::CrLFY2) - Ceratopteris richardii lfy-2; weak lfy allele lfy-9; intermediate leafy allele lfy-12; strong leafy allele.

2009-07-23 | E-MEXP-2258 | biostudies-arrayexpress

LFY is pioneer transcription factor [RNA-seq]

Project description:This study identified LEAFY (LFY) as a pioneer transcription factor. We made use of 35S:LFY-GR, an inducible version of the LFY protein fused to the rat glucocorticoid hormone binding domain. In root explants, steroid activated LFY-GR triggers synchronous and abundant flower induction (PMID: 15225291). We combined LFY ChIP-seq, MNase-seq before and after LFY binding and time-course RNA-seq in 35S:LFY-GR root explants to characterize the role of LFY as a pioneer transcription factor.

2020-12-15 | GSE141703 | GEO

LFY is pioneer transcription factor [MNase-seq]

2020-12-15 | GSE141705 | GEO

LFY is pioneer transcription factor [ChIP-seq]

2020-10-27 | GSE141704 | 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

Deciphering the regulatory network of the NAC transcription factor FvRIF, a master regulator in controlling strawberry fruit ripening [DAP-seq]

Project description:To better understand FvRIF-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to unravel FvRIF binding sites at the genome level. For DAP-seq analysis, the recombinant FvRIF fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA ‘input’ negative control libraries were prepared and submitted for deep sequencing.

2023-11-08 | GSE220785 | GEO

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