Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

60 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A human integrin-?3 mutation confers major renal developmental defects.

ABSTRACT: Integrin-?3 plays a central role in the interplay of cells, morphogens and ECM, required for proper nephrogenesis, thus adding ITGA3 to the list of CAKUT (congenital anomalies of the kidney and urinary tract)-causing genes. we used renal tissue originally obtained from a patient with an ITGA3 mutation and assessed its gene expression profile as compared to controls

ORGANISM(S): Homo sapiens

SUBMITTER: jasmine jacob

PROVIDER: E-GEOD-54227 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The Wilms' tumor blastema propagating cell is a self-renewing committed epithelial stem cell

Project description:Recently the cancer stem cell (CSC) model has been put forward to describe how a subset of cells within the tumor is responsible for tumor growth and heterogeneity. Wilms' tumor (WT), the most common pediatric renal malignancy, arises from developmentally arrested early renal progenitors. WT NCAM1+ALDH1+ CSCs have been recently isolated and shown to localize to tumor blastema. Herein by generating 'blastema'-only WT xenografts composed solely by cells expressing the SIX2 and NCAM1 embryonic renal stem cell markers, we surprisingly show that sorted ALDH1+ WT CSCs are phenotypically not the earliest renal stem cells. Rather, gene expression and proteomic comparative analysis disclose a more differentiated self-renewing epithelial cell type than bulk of the blastema. Thus, WT CSCs do not represent the transformed counterpart of the most primitive renal stem cell being more differentiated than the presumable WT cell of origin and are likely to de-differentiate to propagate the tumor blastema. We used Wilms tumor Xns, as well as, fetal renal tissue originally obtained from a patients or aborted fetus

2015-12-31 | E-GEOD-57269 | biostudies-arrayexpress

m1A marks translation initiation sites in human and mouse messenger RNA [microarray]

Project description:We developed a novel approach, m1A-seq, for high-resolution mapping of the transcriptome-wide m1A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Using this method we performed immunodepletion of methylated transcipts to assess the average methylation level Immunodepletion of m1A modified transcripts in human compared to the input, allows for estimation of the fraction of methylated transcripts. We compared the expression levels of sup (immunodepleted) and input methylated transcripts to deduce the fraction of m1A methylation.

2016-02-12 | E-GEOD-76057 | biostudies-arrayexpress

Activation of a NCAM1 expressing progenitor cell population in adult human kidney epithelia

Project description:NCAM1+ subpopulation of adult human kidney epithelial cells (hKEpC) can be specifically activated in vitro to stem-like cells that de-differentiate and recapitulate embryogenesis. We used microarrays to detail the global programme of gene expression in the NCAM1+ sub-population in comparison to NCAM1-.

2013-07-23 | E-GEOD-49100 | biostudies-arrayexpress

Identification of human nephron progenitors capable of generation of kidney structures and functional repair of chronic renal disease

Project description:NCAM1+ subpopulation of fetal human kidneyl cells are nephron progenitors We used microarrays to detail the global programme of gene expression in the NCAM1+ sub-population in comparison to total culture.

2013-07-23 | E-GEOD-49101 | biostudies-arrayexpress

Kidney spheroids generate a functional quiescent niche leading to enhanced tubulogenic potency of human kidney-derived cells

Project description:Cell-based approaches utilizing autologous human renal cells require their isolation, expansion in vitro and reintroduction back into the host for renal tissue regeneration. Nevertheless, human kidney epithelial cells (hKEpC) lose their phenotype, dedifferentiate and assume the appearance of fibroblasts after relatively few passages in culture. We hypothesized that growth conditions may influence hKEpC phenotype and function. hKEpC retrieved from human nephrectomy tissue samples showed the ability to reproducibly form kidney-spheres when grown in suspension culture developed in non-adherent conditions. Genetic labeling and time-lapse microscopy indicated, at least in part, the aggregation of hKEpC into 3D-spheroids rather than formation of pure clonally expanded spheres. Characterization of hKEpC spheroids by real-time PCR and FACS analysis showed up-regulation of some renal developmental and 'stemness' markers compared to monolayer and mostly an EpCAM+CD24+CD133+CD44+ spheroid cell phenotype. Oligonucleotide microarrays which were used to identify global transcriptional changes accompanying spheroid formation, showed predominantly up-regulation of cell matrix/cell contact molecules and cellular biogenesis processes and down-regulation of cell cycle, growth and locomotion. Accordingly, hKEpC spheroids proliferated slowly as indicated by low Ki-67 staining, but when grafted in low cell numbers onto the chorioallantoic membrane (CAM) of the chick embryo, they exclusively reconstituted various renal tubular epithelia. Moreover, efficient generation of kidney spheroids was observed after long-term monolayer culture resulting in re-establishment of tubulogenic capacity upon CAM grafting. Thus, generation of a specialized quiescent niche in hKEpC spheroids may provide a functional benefit for kidney-derived cells in vivo. 6 samples, 3 adherent and 3 spheroids samples

2011-12-31 | E-GEOD-28052 | biostudies-arrayexpress

Gene expression profiling of Fast vs. Slow Chinese Hamster Ovary cell lines using Wye3aHamster array

Project description:A 3rd generation Wye3aHamster microarray chip was used to carry out a differential expression microarray study of a panel of 30 slow- and fast-growing production cell lines, identifying a priority list of 240 transcripts (110 Up; 130 Down) that passed a statisical filter (ANOVA p-value <0.05, 1.3 fold-change) when the samples were grouped into fast versus slow and pairwise compared and a minimum Pearson Correlation Coefficent (PCC) of >0.7 when growth rate was used as a continuous variable (i.e. included genes have to satisfy BOTH criteria, not just one). This yielded a list of 240 genes. The 240-member genelist yielded 223 Annotated IDs, 203 of which are Unique and all of which are associated with contributing to a high rate of growth in production CHO cell lines. Prospective samples were isolated from 2 distinct groups of clones (slow growers and fast growers), all chosen from the same project (transfection of product transgene into parent line) generated at Pfizer Inc., Bioprocess R&D, Andover, MA, USA. Each group comprised 5 distinct clones, all of which had comparable Qp characteristics. The clones were passaged for 3 or 4 passages over 3-4 days to stabilise the phenotype and freeze stocks. Samples for array hybridization were generated in batch shake flask culture (60ml working volume) with AS1 medium and without feeds or temperature shift. Samples were collected at a single time point (72hrs - mid/late log) and each clone was grown in triplicate flasks, yielding a total of 30 samples for collection and processing. Two bioprocess-relevant variables, viable cell density (VCD) and viability were measured. From the VCD, the growth rate (h-1) was calculated.

2013-01-01 | E-GEOD-37251 | biostudies-arrayexpress

Gene expression during SMC cord morphogenesis

Project description:SMCs must undergo specialzed patterning during blood vessel stabilization. We used microarray analysis to identify differentially expressed genes as smooth muscle cells were induced to assemble into a network of elongated cords. Two time points (Day 0 and Day 8) and three biological replicates for each, using Affymetrix HGU133A and HGU133B arrays for each sample.

2011-04-17 | E-GEOD-21363 | biostudies-arrayexpress

m1A marks translation initiation sites in human and mouse messenger RNA

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-12 | E-GEOD-76058 | biostudies-arrayexpress

Genotyping of human cancer cell lines

Project description:Multiple genome-wide microarray 500K SNP studies performed to measure the genotype profile of various cancer cell lines

2008-11-17 | E-MTAB-38 | biostudies-arrayexpress

Gene expression profiling of parkinsonian substantia nigra

Project description:Affymetrix HG-Focus array was used to determine a global gene expression profile of clinically and neuropathologically confirmed cases of sporadic Parkinson's disease compared to controls. Major alterations were detected in signal transduction, protein degradation, dopaminergic transmission/metabolism, energy pathways/glycolysis, cell adhesion/cytoskeleton, extracellular matrix components and cell cycle functional classes. Post-mortem human brains were obtained from moderately to severe parkinsonism individuals based on the Hoehn & Yahr criteria. All the subjects were negative for AD pathology according to Braak & Braak. The average age for PD and control is 76.6 and 77.8 years, respectively. The average postmortem delay for PD and control is 26.2 and 19.8 hours, respectively.

2010-03-23 | E-GEOD-20333 | biostudies-arrayexpress

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