Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-MTAB-4306

ABSTRACT: Transcription profiling by high throughput sequencing of rice plants hydroponically treated with Cadmium for 24 hours

TISSUE(S): Root, Shoot

PROVIDER: E-MTAB-4306 | ExpressionAtlas | 2019-01-10

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-MTAB-4306-analysis-methods.tsv	Tabular
	E-MTAB-4306-analytics.tsv	Tabular
	E-MTAB-4306-analytics.tsv.undecorated	Tabular
	E-MTAB-4306-analytics.tsv.undecorated.unrounded	Tabular
	E-MTAB-4306-analytics.tsv.unrounded	Tabular

Items per page:

1 - 5 of 87

Similar Datasets

Expression data of one-week-old rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours

Project description:Expression profiles of one-week-old rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours were monitored by microarray that contains approximately 60,000 rice clones (Affymetrix GeneChip). The probes were prepared from RNAs isolated from rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours, respectively, and those non-treated controls. For hybridization, two biological replicates were used to extract RNAs from different batches of plants.

2012-06-18 | GSE35984 | GEO

Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa

Project description:High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5M-BM-4and 3M-BM-4adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. The libraries containing unique barcodes were combined and subjected to pyrosequencing (454 Life SciencesTM, Roche) [Expression profiling by array] Leaves from rice plants were harvested at two time points after the onset of treatment (30' and 2h) with elicitors of Magnaporthe oryzae 18.1 and used for RNA extraction and hybridization on Affymetrix microarrays. Mock inoculations were performed with sterile water for control experiments. Three biological replicates were analyzed. Each sample represented a pool of approximately 150 rice plants. [High throughput sequencing] 8 samples examined: leaves and roots, treated or not with elicitors at two different time points, 30' and 2h (2x2x2)

2014-01-15 | E-GEOD-30583 | biostudies-arrayexpress

Rice gene global expression during nonhost interaction with Blumeria graminis f. sp. hordei (Bgh)

2012-03-27 | GSE30942 | GEO

Project description:High-throughput sequencing of human osteosarcoma HOS cells by 100 uM capsaicin treated for 24 hours

| PRJNA629456 | ENA

RNA-Seq of Hrip1-treated rice leaves

Project description:Hrip1 was isolated from Alternaria tenuissima and was found to induce systematic acquired resistance in tobacco. In rice plants, it was found to confer immunity against rice blast fungi. To understand the genomic signature of Hrip1-induced immunity, rice seedlings were treated with 30 nm Hrip1 protein and triplicate leaf samples were subjected to sequencing on the BIGSEQ500 platform. Two groups of rice seedlings were grown to the three-leaf stage. The experiment group was treated with 30nm Hrip1 protein while the control plants were treated with Tris-HCl buffer. Triplicate samples from both setups were taken at 6, 12, 24, and 48 hr after treatment. Total RNA was extracted and reverse transcribed in first strand cDNA as input material.

2022-08-21 | GSE211516 | GEO

Extracellular CIRP Induces an Inflammatory Phenotype in Pulmonary Fibroblasts via TLR4

Project description:The wild type (WT) and TLR4 -/- pulmonary fibroblasts were treated with phosphate-buffered saline (PBS), 1 µg/mL recombinant mouse (rm) CIRP, 2 ng/mL rmTGF-ß1 (R&D Systems), or rmCIRP plus rmTGF-ß1. The cell lysates collected at 24 hours were used for high throughput mRNA sequencing.

2021-07-15 | GSE178255 | GEO

Rice gene global expression during nonhost interaction with Blumeria graminis f. sp. hordei (Bgh)

Project description:Powdery mildew is a very common plant disease and only few plants are immune. Host interactions have been identified and characterized for the pathosystems barley-B. graminis f. sp. tritici (Bgt) and wheat-B. graminis f. sp. hordei (Bgh), whereas no data are reported about powdery mildew and nonhost plants, such as rice. On the other hand rice nonhost resistance is widely unexploited and only few expression data are available. To characterize rice response during nonhost interaction with Bgh, a global expression analysis was performed by using the GeneChipM-BM-. Rice Genome Array. To describe rice gene expression profiles during nonhost interaction, 2 week-old rice plantlets were inoculated with Bgh. Treated (inoculated) and control (mock) samples were collected 24 hours post-inoculation for GeneChipM-BM-. Rice Genome Array hybridization. For transcript proM-oM-,M-^Aling experiments with powdery mildew, entire leaves were sampled from rice plantlets 2 weeks old (cv. Nipponbare). Treated and control (mock) rice leaves were collected 24 hours post inoculation. Three biological replicates for inoculated and control plants were extracted and analysed independently with the GeneChipM-BM-. Rice Genome Array.

2012-03-26 | E-GEOD-30942 | biostudies-arrayexpress

Gene expression profiling of the early cadmium response includes abiotic stress signaling pathway in rice

Project description:Plant growth is severely affected by toxic concentrations of the non-essential heavy metal cadmium (Cd). Comprehensive transcriptome analysis by RNA-Seq following cadmium exposure is required to further understand plant responses to Cd and facilitate future systems-based analyses of the underlying regulatory networks. In this study, rice plants were hydroponically treated with 50 ÂµM Cd for 24 hours. In total, ~60,000 transcripts, including transcripts that could not be characterized by microarray-based approaches, were evaluated and ~36,000 transcripts were responsive to Cd exposure. Among multigenic families that may protect cells from generated ROS and reduce Cd toxicity, prominently upregulated antioxidant enzyme genes were identified. Furthermore, 168 different metal ion transporter genes, which might mediate the transport of transition Cd, responded to Cd exposure. qRT-PCR analysis of randomly selected genes indicated that their expression changed obviously after exposure to various heavy metal stresses. The Cd responsive genes included many abiotic stress (drought, high-salinity, low temperature) responsive genes. Based on further investigation into the expression patterns of abiotic stress regulatory genes such as DREB, part of the signal transduction pathway for Cd exposure was determined to cross-talk with abiotic stress signaling pathways. Our results provide useful information for further studies of the molecular mechanisms of plant adaptation to Cd exposure and the improvement of Cd tolerance in crop species.

2014-08-07 | E-MTAB-4306 | biostudies-arrayexpress

Expression data from infected (Xanthomonas oryzae pv. Oryzae (P10)) leaf in japonica rice (cv. Y73)

Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73.

2012-02-27 | GSE36093 | GEO

Shikonin inhibits the malignant progression of triple-negative breast cancer

Project description:To investigate the underlying mechanism of shikonin in TNBC, we performed high-throughput sequencing to screen differentially expressed genes 24 hours after shikonin treatment

2025-08-22 | GSE281168 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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