Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcript profiling of the roots and leaves of opt3-2 mutant and wild type Arabidopsis

ABSTRACT: Illumina 100bp single end sequencing was used to profile the transcriptomes of wild type (Columbia) and opt3-2 mutant Arabdiopsis leaves and roots under hydroponic conditions ( 4 weeks old, bolting stage). Sequencing resulted in 381 million uniquely mapping reads accross 36 libraries. Each sample was barcoded and divided into three sequencing lanes, while each genotype/tissue combination is represented by 3 biological replicates consisting of 3-4 individual plants (2 genotypes x 2 tissues x 3 biological replicates x 3 technical replicates = 36 libraries). Our results show the leaves and roots of the opt3-2 mutant have different iron sensing transcriptional programs in place which is independent of the iron status of the plant.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE79275 | GEO | 2018/09/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic study of soybean (Glycine max) in response to zinc deficiency

Project description:We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified Zn-deficiency responsive genes. At least 20 genes that are potentially involved Zn homeostasis were significantly changed by Zn deficiency, including 7 ZIP (ZRT, IRT-related protein) transporter genes, 3 nicotianamine synthase genes, and 7 metallothionein genes. At least 48 genes encoding likely Zn-binding proteins were found to be responsive to Zn deficiency in leaves or roots. Eighty-five transcription factor genes were significantly changed by Zn deficiency in leaves or roots, including 5 bZIP members and 10 Golden 2-like members. In addition, some other groups of genes which are possibly related to reactive oxygen species scavenging, calcium and hormone signaling, and protein phosphorylation and dephosphorylation also differentially expressed under Zn deficiency.

2019-03-30 | GSE111799 | GEO

Root and shoot Jamonic Acid induction in Brassica oleraceae

Project description:Brassica oleraceae plants were treated with jasmonic acid either at the roots or two leaves. An acidic (HCl) water sollution with the same pH as the jasmonic acid sollution was also applied to two leaves of the root jasmonic acid treated plants, and to the roots of leaf jasmonic acid treated plants. Control plants received a mock treatment on roots and leaves with acidic water of the same pH as the jasmonic acid sollution. The whole root system and two systemic leaves were harvested separately at 6, 18 and 30 h after treatment. For each time point, tissue and treatment, three biological replicates (except two replicates for 'Root-Cont-18h' sample) were made consisting of pooled tissue samples from 10 plants. Gene expression was analyzed in both tissues using the 29,000 element Arabidopsis Oligonucleotide Microarrays (Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set version 3.0).

2012-12-18 | GSE38784 | GEO

Expression data from Arabidopsis Col and rglg1/2 mutant in response to Fe deficiency

Project description:Iron is an essential element for almost all organisms, catalyzing numerous essential redox reactions by virtue of its unique electrochemical properties. Iron levels in cells need to be carefully balanced. Rglg1/2 is an Arabidopsis mutant which display a pleiotropic phenotype partly resembling iron-deficient plants.To dissect global transcriptional regulation of gene expression in iron-deficient plants, we conducted genome-wide proteomic and transcriptomic surveys of leaves and roots from iron-sufficient and iron-deficient Col-0 wild-type plants and rglg1 rglg2 double mutants.

2016-10-30 | GSE63946 | GEO

Gene expression changes in leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering.

Project description:Illumina technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering. Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France). Raw reads were filtered and trimmed using erne-filter command. Filtered reads from each library were aligned to P. trichocarpa (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1) using TopHat2 v2.12.

2023-09-12 | GSE175506 | GEO

Iron Deficiency Triggered Transcriptome Changes in Bread Wheat

Project description:Iron (Fe) plays a pivotal role in several metabolic and biosynthetic pathways essential for plant growth. Fe deficiency in plants severely affects the overall crop yield. Despite several studies on iron deficiency responses in different plant species, these mechanisms remain unclear in the allohexaploid wheat, which is the most widely cultivated commercial crop. In order to gain a comprehensive insight into molecular responses of bread wheat when exposed to iron deficiency, we studied transcriptomic changes in the roots and flag leaves of wheat plants subjected to iron-deficient and iron-sufficient conditions during early grain filling.

2020-11-24 | GSE162027 | GEO

Trx knockdown in intestinal stem cells (ISCs) of Drosophila melanogaster

Project description:Male flies were crossed to virgins of genotype yw;esg-Gal4,UAS-GFP;tub-Gal80ts/Tm3,Sb. Progeny was collected and aged 3-4 days before shifting for 7 days to 29 degrees to induce RNAi expression. Guts were dissected for 2 biological replicates/condition, each containing 80-100 guts, dissociated and GFP-positive cells were FACS-sorted. RNA was isolated using the PicoPure RNA-isolation kit and libraries were generated. Sequencing was done by distributing the 4 libraries over 5 lanes on the Illumina HiSeq2000 platform.

2021-04-02 | GSE163406 | GEO

Iron_deficiency gene expression in Arabidopsis wild type and yellow stripe1-like1/3 (ysl1ysl3) double mutants.

Project description:When iron is withdrawn from the growth medium of plants, large changes in gene expression have been observed. A double mutant with T-DNA insertions in the Arabidopsis yellow stripe1-like1 (At4g24120) and yellow stripe3-like (At5g53550) genes shows strong iron-related phenotypes. This study is intended to uncover the gene expression changes that occur in leaves and roots of the double mutant compared to wild type plants.

2017-01-01 | GSE92716 | GEO

Epigenome analysis of hESCs undergoing neuronal differentiation [methylation array]

Project description:Genome wide DNA methylation profiling of human embryonic stem cells (hESCs) at day 0, and day 7, 13 and 20 of neuronal differentiation. The Illumina Infinium MethylationEPIC_v-1-0_B3 was used to obtain DNA methylation profiles accross approximately 850k CpGs in differentiating cells. Samples included 6 day 0 replicates, 6 day 7 replicates, 4 day 13 replicates and 6 day 20 replicates.

2022-10-13 | GSE192854 | GEO

RNA-seq analysis of Arabidopsis roots of Col-0, fls2 and UBQ10::mCitrine-IMA1 in response to +Fe, +Fe+flg22, -Fe and -Fe+flg22

Project description:We reported the flg22-triggered immune responses in roots affect the iron deficiency responses and may link to the function of FLS2 and IMA1 in the root. To identify the underlying mechanism of how the root transcriptome profiles respond to +Fe, +Fe+flg22, -Fe, -Fe+flg22 respectively, and if the flg22 responses is dependent on the function of FLS2 and IMA1 in the root, we performed an mRNA-seq experiments in Col-0, fls2 and UBQ10::mCitrine-IMA1 with different treatments. The differentially expressed genes in response to +Fe, +Fe+flg22, -Fe, -Fe+flg22 were analyzed. It has 36 samples in total, with 3 biogical replicates for each condition and each genotype.

2023-10-09 | GSE213557 | GEO

Early drought-responsive changes in pepper leaves and roots

Project description:Drought is one of the major factor that limits crop production and reduces yield. To understand the early response of plants under nearly natural conditions, pepper plants were grown in a greenhouse and drought stressed by withholding water for one week. Plants adapted to the decreasing water content of the substrate by adjustment of their osmotic potential in roots by accumulation of raffinose, glucose, galactinol and proline. In contrast in leaves levels of fructose, sucrose and also galactinol increased. Due to the water deficit cadaverine, putrescine, spermidine and spermine accumulated in leaves whereas the concentration of polyamines was reduced in roots. These polyamines are suggested to rather act as stress protectants than for osmotic adjustment. To understand the molecular basis of the response to this early drought stress better, four suppression subtractive hybridisation libraries from leaves and roots were constructed. Microarray technique was used to identify differentially expressed genes. A total of 109 unique ESTs were detected. The diversity of the putative functions of all identified genes confirms the complexity of the plant response to drought stress. Keywords: Transcription profiling Two-condition experiment in roots and leaves, control leaves (CL) vs. drought-stressed leaves (DL) and control roots (CR) vs. drought-stressed roots (DR). Biological replicates: 4 control (1-4), drought-stressed (1-4), independently grown and harvested. One swap replicate per array.

2010-06-20 | E-GEOD-18627 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data