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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiling in a VRK1 R358X homozygote patient

ABSTRACT: VRK1 mutations in humans cause a severe neuronal phenotype includung spinal muscular atrophy (SMA) and microcephaly. To study the effect of VRK1 R358X mutation on global gene expression in a homozygote human patient, an expression array was performed using EBV-trasformed B cells from the patient and two healthy controls Gene expression was measured in EBV-transformed B cells from from a VRK1 R358X homozygote and two healthy controls.

ORGANISM(S): Homo sapiens

SUBMITTER: Sharon Zeligson

PROVIDER: E-GEOD-66061 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiling in a VRK1 R358X homozygote patient

Project description:VRK1 mutations in humans cause a severe neuronal phenotype includung spinal muscular atrophy (SMA) and microcephaly. To study the effect of VRK1 R358X mutation on global gene expression in a homozygote human patient, an expression array was performed using EBV-trasformed B cells from the patient and two healthy controls

2015-02-19 | GSE66061 | GEO

Transcriptional analysis of the effect of Alprostadil on NPHP1 URECs

Project description:Micro-array experiment was performed on URECs (Urine-derived Renal Epithelial Cells) from a patient carrying recessive NPHP1 mutation. URECs were treated either with 0.04% of DMSO or 2µM of Alprostadil for 24h.

2022-04-05 | E-MTAB-11582 | biostudies-arrayexpress

Expression data from aortic smooth muscle cells (AoSMC) and myofibroblasts (FB) isolated respectively from the ascending aortas and the aortic valves of bicuspid (BAV) and tricuspid aortic valve (TAV) patients

Project description:AoSMC and FB were cultured and exposed to transforming growth factor beta1 (TGFb1) prior to the exon array analysis The objective was to study the TGFb responsivness, at the gene expression level, in AoSMC and FB form BAV and TAV patients 54 samples in total were generated from biopsies obtained from 23 different individuals. We performed paired analyses to compare the un-treated (c) versus the TGFb1 (t1) treated cells, for each patient

2015-01-15 | E-GEOD-61128 | biostudies-arrayexpress

Identification of IL-21-induced STAT3 dependent genes in human B cells

Project description:IL-21 induces B cell activation, and differentiation into antibody-secreting plasmablasts in vitro. This process is abolished by loss-of function mutations in STAT3 We used microarrays to identify genes that are induced by IL-21 in a STAT3-dependent manner Sort-purified naÃ¯ve B cells from four healthy donors and three patients with AD-HIES due to heterozygous STAT3 mutations were cultured for four days with CD40L in the presence or absence of IL-21 (50ng/ml). After four days, RNA was extracted from the harvested cells and the genetic profile was analysed by microarray.

2014-01-09 | E-GEOD-51587 | biostudies-arrayexpress

Identification of a B cell signature associated with renal transplant Tolerance in humans

Project description:In this study, investigators recruited the largest reported cohort of tolerant kidney transplant recipients who maintained their graft after ceasing to take their immunosuppression drug, and compared this cohort to subjects with stable allograft function while on immunosuppression and healthy non transplated, controls. Using gene expression studies, they identified genetic markers that are strong candidates for predicting kidney transplant candidates who may benefit from minimization or withdrawl of immunosuppression. Microarrays were used to detect expressed gene profiles of whole-blood total RNA from subjects in the tolerant, standard immunotherapy and healthy control participants Total of 19 Tolerant (TOL) participants, 27 Standard Immunotherapy (SI) participants, and 12 Healthy Controls (HC)

2010-06-16 | E-GEOD-22229 | biostudies-arrayexpress

ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE

Project description:Differential gene expression in RNA isolated from stably-transfected EBERs-negative versus EBERs-positive HK1 cell lines We established stable transfection of EBERs in the EBV-negative NPC cell line, HK1,to elucidate the role of the EBERs in NPC pathogenesis. Microarray gene expression profiling was carried out to investigate candidate genes which expression correlates with the expression of the EBERs. Total RNA was extracted from each cell line and processed using GeneChipÂ® Whole Transcript (WT) Sense Target Labelling Assay and then analyzed with GeneChipÂ® Human Gene 1.0 ST Array, with three repeats. Candidate genes differentially expressed between the two transfected HK1 cell lines were identified using GeneSpring GX 10 (Agilent Technologies).

2012-12-31 | E-GEOD-29123 | biostudies-arrayexpress

Human iPSCs derived under feeder free conditions displays an unqiue cell cycle and DNA replication genotype

Project description:Induced pluripotent stem cells (iPSCs) have been generated from various somatic cells under feeder-layer conditions. These feeder-derived iPSCs generated in different labs exhibit greater variability than between different traditional embryo derived hESC lines. For that reason, it is important to develop a standard and defined system for deriving autologous patient stem cells. We have generated iPSCs under feeder-free conditions using Matrigel coated vessels in chemically defined medium, mTeSR1. These feeder-free derived iPSCs are in many ways similar to feeder-derived iPSCs and also to hESCs, with respect to their pluripotent gene expression (OCT4, NANOG, SOX2), protein expression (OCT4, NANOG, SSEA4, TRA160) and differentiation capabilities. We conducted a whole genomic transcript analysis using Affymetrix Human Gene 1.0 ST arrays to elucidate the important differences between traditional feeder-derived iPSCs and feeder-free derived iPSCs. We reveal that feeder-free iPSCs have over-represented terms belonging to DNA replication and cell cycle genes which are lacking in feeder-derived iPSCs. Feeder-free iPSCs are in many aspects more similar to hESCs including; apoptosis, chromatin modification enzymes and mitochondrial energy metabolism. We have also identified potential biomarkers for fully reprogrammed iPSCs (FRZB) and partially reprogrammed iPSCs (POTEG, MX2) based on their expression trends across all cell types. In conclusion, feeder-free derived iPSCs is transcriptomically more similar to hESCs than feeder derived iPSCs, in many biological functions. For each cell sample, 2 or 3 biological replicates were obtained.

2011-06-03 | E-GEOD-21655 | biostudies-arrayexpress

Expression data from multiple sclerosis patients in remission and relapse

Project description:Whole-genome expression of peripheral blood leukocytes was measured in 22 patients and 24 controls using the Human Gene 1.0 ST array by Affymetrix 22 Multiple Sclerosis patients with samples both in remission and relapse (2 samples for each patient; 44 blood samples in total) and 24 healthy controls were included in the study, for a total of 68 samples.

2013-04-01 | E-GEOD-41890 | biostudies-arrayexpress

Proteomics of extracellular vesicles purified by various methods.

Project description:EVs were extracted from EBV-positive lymphoma cells, lymphoma patient sera, and healthy human sera using a variety of techniques.

2022-03-15 | PXD031305 | JPOST Repository

Advanced Study of Aortic Pathology (ASAP)

Project description:BACKGROUND: The vast majority of thoracic aortic aneurysms (TAAs) are observed either together with a bicuspid aortic valve (BAV), a common congenital disorder, or in idiopathic cases such as patients with a normal tricuspid aortic valve (TAV). The main objective of our study was to identify shared and unique gene expression properties underlying the aortic dilation of BAV and TAV patients. METHODS AND RESULTS: Tissue biopsies for RNA and histological analyses were obtained from aorta of non-dilated (<40mm) and dilated (>45mm) aorta of BAV and TAV patients (in total 131 patients). Additional controls were from mammary artery of the same patients (n=88) and aorta from transplant donors (n=13). Gene expression profiles generated using Affymetrix Exon arrays were analyzed from controls and from aorta intima-media and adventitia of patients (in total 345 samples). 606 genes in aortic intima-media were found to be differentially expressed with dilation. Of these, only few (<4%) were differentially expressed in both BAV and TAV patients. Gene set enrichment analysis identified cell adhesion and extracellular region gene ontology sets as common features of TAA in BAV and TAV patients. The set of immune response genes was observed to be particularly overexpressed in aortic media of dilated TAV samples. CONCLUSION: The divergent gene expression profiles indicate fundamental differences in TAA etiology of BAV and TAV patients. Immune response activation solely in the aorta media of TAV patients suggests that inflammation is a causal factor of TAA in this patient group. Biobank of patient material. Each tissue sample is from a different patient as indicated by patient ID.

2016-01-15 | E-GEOD-26155 | biostudies-arrayexpress

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