Similar Datasets
Project description:ChIP-seq data were used to analyze ASR3 target genes
| PRJNA812914 | ENA
Project description:Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the transgenic plants overexpressing 4D09 effector gene from the cyst nematode Heterodera schachtii and the wild-type (C24). Also, Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the transgenic plants overexpressing 14-3-3Ɛ gene from Arabidopsis and the wild-type (Col-0). Wild-type (Arabidopsis thaliana, ecotypes C24 and Col-0 ), and the transgenic plants overexpressing 4D09 effector gene or overexpressing 14-3-3Ɛ gene from Arabidopsis were grown in vertical culture dishes on modified Knop’s medium for 2 weeks and then root tissues were collected for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tarek Hewezi. The equivalent experiment is AT144 at PLEXdb.]
2016-01-21 | GSE43853 | GEO
Project description:To obtain better insight into the underlying mechanism of melatonin in switchgrass growth, flowering and defence, we performed proteomics analyses between transgenic lines overexpressing melatonin biosynthesis genes and transgenic control (expressing only the empty vector) plants.
2021-10-12 | PXD029065 |
Project description:To reveal the regulatory network of ThERF1 in response to abiotic stress, we have employed an Agilent Arabidopsis gene expression microarray to study the expression profile changes between Wild-type and transgenic plants overexpressing ThERF1 under salt stress. A total of 154 and 307 differentially expressed genes with p-value < 0.05 and ≥ 2-fold change were significantly up- and down- regulated in ThERF1-transformed plants under salt stress treatment.
2014-05-21 | GSE57847 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has been utilized for systems-based analysis of rice plants. The goals of this study were to compare the transcriptome between non-transgenic (NT) control and OsTZF8 overexpressing transgenic plants. Methods: Total RNAs were extracted from the whole plants of OsTZF8 overexpressing plants (T4 generation, line number #20) and non-transgenic (NT) plant using RNeasy plant mini kit (Qiagen, Germany) according to the manufacturer’s instruction. cDNA libraries were prepared from total RNAs using TruSeq RNA sample Prep kit (v2) (Macrogen, Korea). Two biological replicates were analyzed by RNA-sequencing analysis. Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). Conclusions: Our study has identified downstream candidate genes regulated by overexpression of OsTZF8.
2020-11-05 | GSE135940 | GEO
Project description:To reveal the regulatory network of ThERF1 in response to abiotic stress, we have employed an Agilent Arabidopsis gene expression microarray to study the expression profile changes between Wild-type and transgenic plants overexpressing ThERF1 under salt stress. A total of 154 and 307 differentially expressed genes with p-value < 0.05 and M-bM-^IM-% 2-fold change were significantly up- and down- regulated in ThERF1-transformed plants under salt stress treatment. Four-week-old seedlings of Wild-type and ThERF1-transformed Arabidopsis plants treated with 120 mM NaCl for 6 h were immediately harvested for RNA isolation. The Agilent Arabidopsis (V4) gene expression microarray (4M-CM-^W 44K, Design ID: 021169) was employed to compare the gene expression profiles of Wild-type and transgenic plants with three independent biological replicates.
2014-05-21 | E-GEOD-57847 | biostudies-arrayexpress
Project description:Entry into the S phase of the cell cycle is controlled by the E2F transcitption factors that induce the transcription of genes required for cell cycle progression and DNA replication. To identify E2F target genes of Arabidopsis on a genome-wide scale, the transcriptome of wild-type plants was compared with that one of plants ectopically expressing the E2Fa-DPa genes. In four independent experiments, E2Fa-DPa overexpressing plants were grown side-to-side with wild type (Col-0) plants. RNA was extracted from 6-day-old seedlings. Each biological sample was harvested and processed independently, and finally all probed individually to Affymetrix ATH1 microarrays, resulting into 8 hybridization signals for each probeset. Experimenter name = Lieven De Veylder Experimenter phone = +32 9 3313961 Experimenter fax = +32 9 3313809 Experimenter address = Technologiepark 927 Experimenter address = B-9052 Gent Experimenter zip/postal_code = B-9052 Experimenter country = Belgium Keywords: genetic_modification_design
2006-08-15 | GSE5529 | GEO
Project description:Direct target genes of VND7 were explored with inducible expression system using glucocorticoid receptor (GR). Transgenic plants expressing 35S:VND7-VP16-GR were treated with dexamethazone (DEX) and/or protein synthesis inhibitor cycloheximide (CHX). A number of genes related to the formation of vascular vessel was induced by DEX even in the presence of CHX. Total RNAs of the transgenic plants expressing 35S:VND7-VP16-GR treated with DEX plus CHX and those treated with CHX only were compared. As a control experiment, transgenic plants harboring empty vector were treated similarly and the total RNAs were compared similarly to identify genes merely induced by DEX treatment itself.
2011-03-31 | E-GEOD-24169 | biostudies-arrayexpress
Project description:High mobility group (HMG) proteins play an important role in regulation of gene transcription through modulate the structure of DNA. In this study, OsHMGB707, a HMG gene localized in rice drought resistance QTL interval, was isolated and the function on rice stress resistance was identified. Overexpression of OsHMGB707 significantly enhanced the drought resistance of the transgenic rice plants, whereas the OsHMGB707-RNAi transgenic rice plants exhibited slightly decrease in drought stress tolerance. To search the downstream genes regulated by OsHMGB707, we performed microarray analysis of the OsHMGB707-overexpressing, OsHMGB707-RNAi and wild-type plants under both normal conditions using Affymetrix Rice Genome Genechip. 21-day-old plants of the OsHMGB707-overexpressing line OE1, OsHMGB707-RNAi line RNAi1 as well as the wild-type plants were used in the normal condition.
2019-05-08 | GSE130821 | GEO
Project description:The aim was to identify early target genes of the senescence-associated transcription factor: ORS1. For this purpose we used DEX-inducible system and studied the expression profile 5h after treatment using Affymetrix microarray. Keywords: genetic modification Arabidopsis 46 day-old transgenic plants (Arabidopsis C24 background, inducible overexpression) were sprayed with 30µM DEX for 5h. As control mock (0.05% ethanol) treated ORS1-inducible over-expression plants were used. Whole rosettes were harvested 5h after induction and used for expression profiling using Affymetrix near-full genome ATH1 arrays. Experiment performed in two biological replications.
2010-12-01 | E-GEOD-22836 | biostudies-arrayexpress