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Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [gene expression]

ABSTRACT: Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [gene expression]

PROVIDER: PRJNA632774 | ENA |

REPOSITORIES: ENA

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Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites

Project description:Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites

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Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [ChIP-chip]

Project description:Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [ChIP-chip]

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Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [gene expression]

Project description:ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor that is a member of the B3 domain family and is involved in seed development. To understand how it controls development, we mapped genome-wide binding sites by ChIP-chip and combined this data wi Ran Tian, Fangfang Wang, Qiaolin Zheng, Venus Niza, A. Bruce Downie and Sharyn E. Perry (2020)

2020-05-27 | GSE150558 | GEO

Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites [ChIP-chip]

Project description:ABSCISIC ACID INSENSITIVE3 (ABI3) is a transcription factor that is a member of the B3 domain family and is involved in seed development. To understand how it controls development, we mapped genome-wide binding sites by ChIP-chip and combined this data with transcriptomic data obtained by microarrays. Ran Tian, Fangfang Wang, Qiaolin Zheng, Venus Niza, A. Bruce Downie and Sharyn E. Perry (2020)

2020-05-27 | GSE150559 | GEO

ABI3 Network Walking

Project description:Deciphering gene regulatory networks (GRNs) is a key for understanding gene expression regulations in living systems. Here, we describe the investigation of the ABSCISIC ACID INSENSITIVE 3 (ABI3) plant transcription factor GRN vicinity by a technique called Network Walking. The method involves transient transformation of protoplasts and inducible nuclear re-localization of transcription factors along with transcriptomic analysis. This genome-wide approach allowed the de novo recovery of i) direct and indirect ABI3 target genes, ii) cis-binding site preference, and iii) biological processes regulated by this canonical abscisic acid response factor. This work improves our knowledge of ABI3 action by inferring network motifs (such as Feed Forwar Loops) under its influence. The novel high-throughput-oriented technique will help accelerate GRN systems investigations in plants, as well as in other organisms. This work studies ABI3 direct and indirect targets by a technique named Network Walking. Root/protoplasts were treated with or without dexamethasone (DEX) and cycloheximide (CHX). 3 reps each.

2013-01-01 | E-GEOD-33344 | biostudies-arrayexpress

ABI3 TARGET approach

2013-01-01 | GSE33344 | GEO

Direct and indirect targets of Arabidopsis ABI3: genome wide binding sites

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

2020-05-27 | GSE150561 | GEO

Direct and indirect effects of a social supergene

Project description:Direct and indirect effects of a social supergene

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Determining ELL2 direct targets via ChIPseq

Project description:Determining ELL2 direct targets via ChIPseq

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Transcription profiling of Strongyloides ratti larval stage 2 (L2) direct vs indirect development

Project description:S. ratti Isofemale line ED321 Heterogonic predominantly undergoes indirect development; isofemale line ED5 Homogonic predominantly undergoes direct development. Therefore, L2 stages of ED321 Heterogonic and of ED5 Homogonic are destined for indirect (i.e. L2 indirect) and direct (i.e. L2 direct) development, respectively; these sources of material were used in this comparison. To do this, for both isofemale lines, rats were infected with ED321 Heterogonic or ED5 Homogonic and faeces collected on days 5, 6, 7 and 8 p.i. and cultured for 24 h at 19oC, after which larvae were prepared with a Baermann funnel held for 6 h at 19oC, larvae were concentrated and cleaned by sucrose flotation, as above. In excess of 75,000 worms were routinely isolated from three infected hosts. The experimental design used, was to have at least three biological replicates for each sample (i.e. three independent preparations of the relevant worm samples and their RNA) and to have at least three technical replicates (i.e. independent, separate cDNA synthesis, amplification and hybridization etc.) for each biological replicate. For each hybridisation a dye-swap was used i.e. each sample to be used in a hybridisation was labelled, separately, with each of the two dyes.

2022-11-22 | E-MEXP-709 | biostudies-arrayexpress

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