Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

44 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Arabidopsis thaliana seedlings to investigate ZAT14 inducible misexpression - TRANSPLANTA collection

ABSTRACT: To identify targets of the C2H2 zinc finger protein ZINC 34 FINGER OF ARABIDOPSIS THALIANA 14 (ZAT14, AT5G03510), we used an estradiol-inducible system for inducible expression of ZAT14, comparing gene expression in estradiol-treated plants and mock-treated 5-day old seedlings 8 hours after estradiol or mock treatment.

INSTRUMENT(S): Sigma-Aldrich, NextSeq 500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Plant Systems Biology data submission

PROVIDER: E-MTAB-12843 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Repressive ZINC FINGER OF ARABIDOPSIS THALIANA proteins promote programmed cell death in the Arabidopsis columella root cap.

Feng Qiangnan Q Cubría-Radío Marta M Vavrdová Tereza T De Winter Freya F Schilling Neeltje N Huysmans Marlies M Nanda Amrit K AK Melnyk Charles W CW Nowack Moritz K MK Nowack Moritz K MK

Plant physiology 20230501 2

Developmental programmed cell death (dPCD) controls a plethora of functions in plant growth and reproduction. In the root cap of Arabidopsis (Arabidopsis thaliana), dPCD functions to control organ size in balance with the continuous stem cell activity in the root meristem. Key regulators of root cap dPCD including SOMBRERO/ANAC033 (SMB) belong to the NAC family of transcription factors. Here, we identify the C2H2 zinc finger protein ZINC FINGER OF ARABIDOPSIS THALIANA 14 ZAT14 as part of the gen ...[more]

PMID: 36852889

Similar Datasets

RNA-seq of Arabidopsis thaliana seedlings to investigate SMB inducible misexpression

Project description:To identify targets of the NAC transcription factor SOMBRERO (SMB, AT1G79580), we used a dexamethasone-inducible p35S::SMB-GR line (DOI: 10.1105/tpc.109.072272), comparing gene expression in dexamethasone-treated and mock-treated 5-day old seedlings 6 hours after estradiol or mock treatment.

2023-04-22 | E-MTAB-12844 | biostudies-arrayexpress

The PXC3 receptor-like kinase constitutively interacts with BAK1 and is involved in vascular development in Arabidopsis.

Project description:We designed an experiment to identify BAK1 interactors considering that it could be a coreceptor for the GOLVEN6 (GLV6) signaling peptide involved in lateral root organogenesis in Arabidopsis thaliana. A BAK1pro:BAK1-GFP/bak1-4 line crossed to an estradiol-inducible GLV6 overexpression line (BAK1pro:BAK1-GFP/bak1-4xiGLV6) was treated with mock or estradiol followed by affinity purification mass spectrometry (AP-MS) experiments using anti-GFP beads in microsomal-enriched fractions. Statistical analysis of estradiol-treated vs. mock seedlings did not reveal significant differences. Nevertheless, we remarked that regardless of the treatment, several LRR-RLKs co-eluted with BAK1-GFP, comprising known, as well as, unknown interactors. We confirmed interaction of BAK1 with these LRR-RLKs by BIFC and identified the PXC3 receptor as a BAK1 constitutive interactor, which was further verified by co-IP.

2022-02-17 | PXD026487 | Pride

RNA-seq GLV6 overexpression during lateral root initiation in Arabidopsis thaliana

Project description:The goal of this experiment was to identify the downstream targets of the GOLVEN6 peptide signaling pathway in Arabidopsis thaliana, specifically during lateral root initiation. Using an estradiol inducible GLV6 overexpression construct in wildtype and rgi1rgi5 double mutant (mutant in receptors for the GLV6 peptide) backgrounds, in combination with gravistimulation induced lateral root formation, the RGI receptor dependent transcriptional effects of GLV6 overexpression were characterized. An estradiol inducible GLV6 overexpression line in a wildtype (iGLV6) and in an rgi1rgi5 double receptor mutant background (rgi1rgi5/iGLV6) were used. 4-day old seedlings of both lines were gravistimulated (vertically grown seedlings were turned counterclockwise by 90°) to induce lateral root initiation in the resulting root bends. 8h after gravistimulation, seedlings of both lines were treated with 2µM of estradiol to induce GLV6 overexpression, or DMSO as a mock treatment. 3h and 6h after treatment, root bends were dissected and collected for RNA-sequencing. This yielded a total of 8 samples per replicate; 3h mock treated iGLV6 (IM3), 3h estradiol treated iGLV6 (IE3), 3h mock treated rgi1rgi5/iGLV6 (RM3), 3h estradiol treated rgi1rgi5/iGLV6 (RE3), 6h mock treated iGLV6 (IM6), 6h estradiol treated iGLV6 (IE6), 6h mock treated rgi1rgi5/iGLV6 (RM6), 6h estradiol treated rgi1rgi5/iGLV6 (RE6). For each sample, 4 replicates were obtained. This setup enabled the comparison of the GLV6 induced transcriptional effects between wildtype and rgi1rgi5 mutants at 2 time points after treatment, in samples that are strongly enriched for lateral root initiation events.

2022-02-13 | E-MTAB-10891 | biostudies-arrayexpress

Transcription factor ATAF1 integrates carbon starvation responses with trehalose metabolism

Project description:Global transcriptome patterns were obtained from ATAF1-IOE seedlings at 1 h, 2 h and 5 h after estradiol induction or mock treatment, and from mature ATAF1-IOE leaves at 5 h after estradiol induction or mock treatment. To identify genes rapidly responding to elevated ATAF1 expression estradiol induction experiments were performed on ATAF1-IOE seedlings after 1 h, 2 h and 5 h of ATAF1 induction. In addition, expression profiles were obtained from mature leaves after 5 h of ATAF1 induction.

2014-08-30 | E-GEOD-54676 | biostudies-arrayexpress

Inducible overexpression analysis of KUODA1 in Arabidopsis seedlings

Project description:To identify potenital target genes of the transcription factor KUODA1 (AT5G47390), we performed expression profiling using an estradiol inducible overexpression system. Estradiol-treatment allows for the nuclear translocation of the constitutively expressed chimeric transcription factor XVE and subsequent expression of KUA1 from the LexA promoter. Stable trangenic T3 seedlings were grown for 14 days and either treated with 15 M-BM-5M estradiol or ethanol (mock) for 4 hours. Two mock and two estradiol treated samples were used for RNA isolation and hybridization.

2013-12-31 | E-GEOD-50520 | biostudies-arrayexpress

Identification of Direct Targets of RPX a NAC transcription factor of Arabidopsis thaliana

Project description:To determine the role of RPX on cell proliferation and organ development, we performed microarray experiments in search of RPX target genes by using an estradiol-inducible RPX protein. Estradiol-treatment allows for the nuclear translocation of the constitutively expressed chimeric transcription factor XVE and subsequent expression of RPX from the LexA promoter. Stable transgenic T3 seedlings were either treated with 10 uM estradiol or ethanol (mock) for 2 hours. Three mock and three estradiol treated samples were used for RNA isolation and hybridization.

2012-03-30 | E-GEOD-34837 | biostudies-arrayexpress

RNAseq of Arabidopsis plants lacking E2 ubiquitin conjugating enzymes UBC35 and UBC36

Project description:This RNAseq experiment aims at determining the reprogramming of gene expression upon loss of K63 polyubiquitin chain formation. Twelve-day-old plants expressing a beta-estradiol inducible artificial microRNA targeting the two plant E2 enzymes catalyzing K63 polyubiquitin chain formation were mock-treated or beta-estradiol-treated (5microM). Total RNAs from whole seedings were extracted and subjected to RNA-seq analyses. Genes that are differentially regulated between non-treated (uninduced) and treated (induced with beta-estradiol) were identified.

2020-01-01 | E-MTAB-8437 | biostudies-arrayexpress

Rhizogenic Agrobacterium protein RolB interacts with the TOPLESS and NINJA repressor proteins to reprogram plant jasmonate signaling (rolB overexpression)

Project description:RNA sequencing was performed to compare the gene expression in tomato hairy root lines transformed with the inducible rolB, rolBmEAR2 or GFP overexpression constructs, 24 h after mock and β-estradiol treatments. This set-up allowed us to map the general RolB targets as well as the specific targets of the RolB-mediated inhibition of the TPL function.

2022-07-08 | E-MTAB-11880 | biostudies-arrayexpress

Bifunctional Activity of members of the Arabidopsis NF-YA Transcription Factor Family

Project description:Five members of the Arabidopsis thaliana NF-YA gene family are strongly induced by several stress conditions via transcriptional and miR169-related posttranscriptional mechanisms. These transcription factors participate in gene regulation via two different mechanisms, one depending on binding to the CCAAT-box in the promoter of regulated genes and the other, independent of the CCAAT-box, in which NF-YA prevents the interaction of the NF-YB/YC heterodimer with transcription factors. Three biological and two technical (in swap) replicates for each genotype were obtained for each treatment (DMSO (mock) and estradiol 24h after induction). Mock samples were pooled and used as a reference.

2012-04-24 | E-GEOD-36092 | biostudies-arrayexpress

Multiplexed proteome dynamics profiling of Estradiol and SERMs

Project description:Investigation of proteostatic effects of Estradiol, raloxifen and GW7604 in MCF7 cells.

2018-05-02 | PXD008636 | Pride