Name: Arabidopsis SECstroma - Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering
Keywords: Not available

OmicsDI

Browse
Submit Data
Databases
API
Help

Dataset Information

334 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis SECstroma - Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering

ABSTRACT: Native SEC of Arabidopsis chloroplast stroma with BufferA elution, High MWt Fraction1 SDS-PAGE Band1 Tech Rep2, in-gel trypsin digestion LTQ Orbitrap

INSTRUMENT(S): LTQ Orbitrap, instrument model

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Paul Dominic Olinares

PROVIDER: PRD000197 | Pride | 2010-04-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering.

Olinares Paul Dominic B PD Ponnala Lalit L van Wijk Klaas J KJ

Molecular & cellular proteomics : MCP 20100426 7

To characterize MDa-sized macromolecular chloroplast stroma protein assemblies and to extend coverage of the chloroplast stroma proteome, we fractionated soluble chloroplast stroma in the non-denatured state by size exclusion chromatography with a size separation range up to approximately 5 MDa. To maximize protein complex stability and resolution of megadalton complexes, ionic strength and composition were optimized. Subsequent high accuracy tandem mass spectrometry analysis (LTQ-Orbitrap) iden ...[more]

PMID: 20423899

Similar Datasets

Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering.

Project description: Not available

| S-EPMC2938090 | biostudies-literature

Expression profiles of embryo-defective Arabidopsis thaliana mutants increased size exclusion limit1 (ise1) and ise2

Project description:We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified ise1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, while ISE2 encodes a DEVH-type RNA helicase. Here we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function we performed whole genome expression analyses. The most significantly affected class of transcripts in both mutants encodes products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus crosstalk, add PD as a critical player in the plant cell communication network, and thereby illuminate a new signaling pathway, dubbed organelle-nucleus-plasmodesmata signaling (ONPS). Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function. Three biological replicates each of either ise1 or ise2 mutant seeds vs. sister wild-type controls

2011-11-09 | E-GEOD-33558 | biostudies-arrayexpress

Expression profiles of embryo-defective Arabidopsis thaliana mutants increased size exclusion limit1 (ise1) and ise2

2011-11-09 | GSE33558 | GEO

Hierarchical clustering of PDAC cell lines

Project description:Hierarchical clustering of pancreatic cancer cell lines based on differentially regulated genes between mesenchymal and epithelial PDAC cells derived from primary tumours and metastases from KrasG12D-driven mouse models of pancreatic cancer.

2022-11-19 | E-MTAB-8173 | biostudies-arrayexpress

HSP90C interacts with PsbO1 and facilitates its thylakoid distribution from chloroplast stroma in Arabidopsis.

Project description: Not available

| S-EPMC5745004 | biostudies-literature

REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment.

Project description: Not available

| S-EPMC4776492 | biostudies-literature

Genomic Prediction Accuracy Using Haplotypes Defined by Size and Hierarchical Clustering Based on Linkage Disequilibrium.

Project description: Not available

| S-EPMC7067973 | biostudies-literature

Expression data from human pancreatic ductal adenocarcinomas by stroma types

Project description:Pancreatic cancer is characterized by abundant desmoplastic stroma. Despite numerous theoretical and experimental efforts, therapeutic approaches targeting pancreatic cancer stroma have been largely unsuccessful, highlighting the need for more comprehensive assessment of inter- and intratumoral stromal heterogeneity in a large series of clinical tumors. Quantitative computation of FAP-dominant fibroblasts, ACTA2-dominant fibroblasts, and intratumoral collagen in whole-tissue sections from 215 treatment-naïve pancreatic cancers allowed us to identify three distinct stroma types (FAP-dominant fibroblast-rich stroma [F-stroma], ACTA2-dominant fibroblast-rich stroma [A-stroma], and collgen-rich stroma [C-stroma]), which were differentially associated with patient outcomes, molecular characteristics and the immunosuppressive tumor microenvironment. We explored differentially expressed genes between three distinct stroma types (F-stroma, A-stroma, and C-stroma) using frozen samples from 20 patients with pancreatic cancer.

2020-09-03 | GSE157353 | GEO

Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation.

Project description: Not available

| S-EPMC3250172 | biostudies-other

Non-supervised hierarchical clustering of gene expression data

Project description:Despite the frequent detection of circulating tumor antigen-specific T cells, either spontaneously or following active immunization or adoptive transfer, immune-mediated cancer regression occurs only in the minority of patients. One theoretical rate-limiting step is whether effector T cells successfully migrate into metastatic tumor sites. Affymetrix gene expression profiling performed on a series of metastatic melanoma biopsies revealed a major segregation of samples based on the presence or absence of T cell-associated transcripts. The presence of lymphocytes correlated with the expression of defined chemokine genes. A subset of 6 chemokines (CCL2, CCL3, CCL4, CCL5, CXCL9, and CXCL10) was confirmed by protein array and/or quantitative RT-PCR to be preferentially expressed in tumors that contained T cells. Corresponding chemokine receptors were found to be upregulated on human CD8+ effector T cells, and transwell migration assays confirmed the ability of each of these chemokines to promote migration of CD8+ effector cells in vitro. Screening by chemokine protein array identified a subset of melanoma cell lines produced a similar broad array of chemokines. These melanoma cells more effectively recruited human CD8+ effector T cells when implanted as xenografts in NOD/scid mice in vivo. Chemokine blockade with specific antibodies inhibited migration of CD8+ T cells. Our results suggest that lack of critical chemokines in a subset of melanoma metastases may limit the migration of activated T cells, which in turn could limit the effectiveness of anti-tumor immunity. Keywords: Tumor sample microarray

2008-08-30 | GSE12627 | GEO

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