Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing Facilitates Quantitative Analysis of Wild Type and d5rf mutant Transcriptomes

ABSTRACT: To gain insight into the biological role of D5RF in plants, we conducted a comprehensive survey of global gene expression employing high throughput-RNA sequencing to quantify the variations in transcript abundance between wild-type Columbia-0 (Col-0) and d5rf.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE155112 | GEO | 2020/10/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcript data affected by natural variation or PME17 mutation in Arabidopsis thaliana, infested or not with the aphid Myzus persicae

Project description:Investigation of the ecotype difference between Columbia-0 (Col) and Wassilewskija-0 (WS) on whole gene expression level, of PME17 mutation effect (compared to background WS) and of the aphid infestation effect on Col, WS and pme17 (infested plants compared to non-infested plants).

2019-04-01 | GSE80749 | GEO

Proteomic analysis of fractions of Arabidopsis thaliana proteins captured by immobilized metal affinity chromatography

Project description:Proteins from plant shoot and root tissues were extracted from wild-type Arabidopsis thaliana ecotype Columbia (Col-0). They were enriched on conditioned U(VI)-loaded and U(VI)-free Duolite C467 beads. The enriched proteins were identified and quantified by label-free shotgun proteomics.

2023-02-04 | PXD033354 | Pride

Flower development FRI/FLC

Project description:Arabiposis plants with conbinations of different FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) alleles grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0): fri FLC Columbia with introgressed FRI from Sf-2: FRI FLC Columbia with introgressed FRI and deleted FLC (flc-3): FRI flc Columbia with deleted FLC (flc-3): fri flc Time points: 0, 2, and 4 days after shift to long days Keywords = flowering Keywords: time-course

2003-08-06 | GSE577 | GEO

Flower development

Project description:Wild type and mutanat Arabiposis plants grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0) Landsberg erecta (Ler) leafy-12 (lfy-12, in Col-0) constans-2 (co-2, in Ler) flowering locus T-2 (ft-2, in Ler) Time points: 0, 3, 5, and 7 days after shift to long days Keywords = flowering Keywords: time-course

2003-08-06 | GSE576 | GEO

Transcriptome analysis of Arabidopsis thaliana roots in response to high nickel

Project description:To gain further insights into a larger number of processes potentially altered by high nickel (Ni), we performed a transcriptional profiling of whole roots of Arabidopsis thaliana accession Columbia-0 (Col-0) exposed to 100 µM nickel, a concentration that induces slight chlorosis and intermediate inhibition of root and shoot growth.

2019-10-16 | GSE138859 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of aged (Day10) and young (L4) C. elegans Transcriptomes

Project description:survey on the age-related changes in protein homeostasis machineries of Caenorhabditis elegans

2021-06-04 | GSE176088 | GEO

Arabidopsis Col-0 and cerk1 treated with chitosan or water

Project description:Microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) is the first layer of molecular defense encountered by pathogens when they attempt to infect plants. MTI is dependent on cell surface pattern-recognition receptors (PRR) which act upstream of mitogen-activated protein kinase (MAPK) pathways. Genetic screening and mutant knock-out lines have largely contributed to our knowledge of MTI. However, genetic screening is confined to phenotype-causing mutations and scarcely enables the discovery of redundantly-acting proteins. We sought to discover protein components that contribute in MTI, using a phenotype-independent approach to discern nucleus-localized proteins after MTI induction. We report on the nuclear proteome of Columbia-0 (Col-0) and chitin elicitor receptor kinase 1 (cerk1) mutant plants 15 min after MTI induction. Our approach revealed that MAMP-treated cerk1 plants had many proteins in common with Col-0-treated plants following chitosan treatment. cerk1 plants also manifested several unique proteins that were absent from Col-0 plants when elicited with chitosan indicating that they also perceive chitosan. Detailed analysis of the identified proteins revealed a nuclear accumulation of transcriptional regulators and transcription factors, DNA-modifying enzymes, RNA-binding proteins and ribosomal proteins. No novel MAPKs were found although Receptor for activated C kinase 1, a scaffold protein involved in defense, and a nucleotide binding leucine-rich repeat protein, implicated in resistance to Leptosphaeria maculans, were discovered in the nucleus of chitosan-treated plants and absent from water-treated control plants.

2018-10-26 | PXD003821 | Pride

Roles of proteome dynamics and cytokinin signaling in root-to-hypocotyl ratio changes induced by shading roots of Arabidopsis seedlings

Project description:Seeds of Arabidopsis thaliana ecotype Columbia (Col-0) were surface-sterilized (using 75 % ethanol) and sown on Murashige and Skoog medium (pH 5.7) supplemented with 3 mM morpholinoethane sulfonic acid, solidified with 1% (w/v) agar and stratified at 4 °C for 48 h. Petri dishes were covered by a layer of black stretch shrink wrap film (black foil) and aluminum foil and incubated at 21°C/19°C day/night temperatures, with a 16 h photoperiod (photosynthetic photon fluence rate of 20 μmol m-2 s-1 over the waveband 400-700 nm) for 7 d in an AR-36L growth chamber

2015-02-23 | PXD001612 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and snf[148] ovary Transcriptomes

Project description:Comparison of wild type and tumorous ovaries reveals that tumors inappropriately express a large number of testis genes mRNA profiles of ovaries from 0-24 hour virgin wild type (WT) and 3 day old snf[148] females were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.

2015-02-17 | E-GEOD-65932 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of MicroRNA-148a Inhibited Transcriptomes

Project description:Purpose: MicroRNA-148a regulates the differentiation of dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation. Methods: Monocytes isolated from wild type or microRNA-148a-/- BM were cultured with GM-CSF and IL-4, or not. Cells were collected at day 0 and day 3. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 0.5 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/). Results: Gene ontology analysis showed that obviously changed genes enriched in autoimmune disease related pathways, suggesting miR-148a is important in autoimmune responses. 990 protein-coding genes upregulated in their mRNA abundance in miR-148a-/- monocytes on day 0, and 1036 genes in miR-148a-/- monocytes on day 3. Among them, 136 genes were found upregulation on both day 0 and 3 in miR-148a-/- monocytes.

2019-12-23 | GSE142511 | 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