Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Isogenic patient-derived human iPSCs, wild-type or heterozygous for PIK3CA-E418K

ABSTRACT: The PIK3CA-related overgrowth syndrome (PROS) patient-derived induced pluripotent stem cell (iPSC) lines M98-WT and M98-E418K were obtained from a female, 18-y-old PROS patient by episomal reprogramming of a dermal fibroblast culture with 32% mosaicism for PIK3CA-E418K heterozygosity. All clones used for experimental studies were confirmed transgene-free and expressed high levels of pluripotent stem cell-specific markers, comparable to those of a reference hPSC line. Karyotyping on a single line from each genotype confirmed lack of microscopic genetic rearrangements. The original patient-derived dermal fibroblasts were obtained with full informed consent in accord with the Declaration of Helsinki. The study was approved by The Cambridge South Ethics.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138161 | GEO | 2019/10/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Subcutaneous adipose gene expression from men in the METSIM cohort

Project description:We analyzed the abdominal subcutaneous adipose tissue of 434 male human subjects from the METSIM study, via RNA-sequencing. The METSIM study was approved by the Ethics Committee of the University of Eastern Finland and Kuopio University Hospital in Kuopio, Finland and carried out in accordance with the Helsinki Declaration. Written informed consent was obtained from all participants. Here, we provide the expression values by gene for each subject and relevant covariates. Raw fastq files will be contributed to dbGaP, as they require controlled access.

2019-07-31 | GSE135134 | GEO

Laser capture microdissection and miRNA expression profiling of different tissue morphologies in triple-negative breast cancer

Project description:Triple negative breast cancers (TNBC) are a morphologically and genetically heterogeneous group of breast cancers with uncertain prediction of biological behavior and response to therapy. The aim of our study was to analyze miRNAs expression within areas of TNBCs with different cellular morphology. We performed laser capture microdissection with PALM MicroBeam system from Zeiss and subsequent expression profiling with Affymetrix GeneChip miRNA 4.0 Arrays to identify distinct classes of miRNAs deregulated in respective tissue morphologies. The study was approved by the Ethics Committee of the University Hospital Olomouc and Medical Faculty of Palacky University in compliance with the Helsinki Declaration (Ref No. 111/15). According to the Czech Law (Act. no. 373/11, and its amendment Act no. 202/17), it is not necessary to obtain informed consent in fully anonymised retrospective studies on formalin-fixed paraffin-embedded tissues. At least one tissue block for each patient was retained in the archive to allow future clinical use such as re-evaluation or further studies.

2021-03-04 | GSE162670 | GEO

Transcriptome profiling of 57 LUAD samples and 11 peritumoral normal lung tissues

Project description:RNA was extracted from 57 LUAD patients hospitalized from 2004 to 2010 at the Pasteur Hospital (Departments of Pulmonary Medicine, and Thoracic Surgery, CHU de Nice, France) and 11 normal lung tissue specimens taken from areas at standard distance (3 cm) from the same cohort of patients.The diagnosis of LUAD patients was based on examination of all tumor specimens using the 7th pTNM classification and on the last histological classification of NSCLC. Written informed consent was obtained from participants after explaining the nature of the study, which was approved by the research ethics board of the Nice University hospital and was performed according to the guidelines of the Declaration of Helsinki. The main clinical and pathological data are summarized. Enrollment of patients in our study was conditioned by stringent criteria such as obtained signed consent, availability of resected surgical specimens, good quality RNA and time of follow-up for surviving patients (min 40 months for surviving patients).

2019-09-04 | GSE116959 | GEO

miRNA-seq from white blood cells of responders and non-responders (weight loss) to a hypocaloric mediterranean diet

Project description:The objective of the present study is to identify early miRNAomic biomarkers of response to a hypocaloric mediterranean diet (RESMENA study). The RESMENA study (“REducción del Síndrome Metabólico en Navarra”) is a Spanish, randomized controlled and longitudinal trial over a six-month period that aimed to improve the parameters related with Metabolic Syndrome, including body fat composition, biochemistry, inflammation, or oxidative stress. The study was approved by the Research Ethics Committee of the University of Navarra (ref.065/2009). All the participants (n=96) were Caucasian and gave written informed consent for participation in agreement with the Declaration of Helsinki (www.clinicaltrials.gov; NTC01087086). Participants were categorized into “High Responders” (HR), when weight loss was >8%, and “Low Responders” (LR) when weight loss was <8%. White blood cells were separated from whole blood by centrifugation at 1,100 g at 4ºC for 15 min. Total RNA from WBCs isolated before the nutritional intervention was extracted using TRIzol reagent. miRNAs from white blood cells of 6 LR and 5 HR were sequenced using Illumina’s miRNA-Seq following the standardized protocol.

2019-11-02 | GSE139837 | GEO

Expression profiling in cellular miRNAs of human bone marrow stromal cells

Project description:The aging of bone marrow stromal cells (BMSCs) lead to decreased ability to maintain hematopoiesis. The aim of this study is therefore to determine the age-related change of cellular miRNAs in BMSCs. Human BMSCs of young (yBMSC s, age of donors: 19 and 20 years) and elderly (eBMSC s, age of donors: 68 and 72 years) donors were purchased from Lonza. BM samples were obtained from MM patients (age of donors: 62 and 77 years) in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (mmBMSCs) were isolated using the classical plastic adhesion method. The Cellular miRNA profiling was done using a TaqMan low-density array (ABI), and Studentâ??s t-test was used to determine statistical significance for comparisons between young and old groups using R software.

2017-05-12 | E-GEOD-78866 | biostudies-arrayexpress

Gene Expression Profile of Epiretinal Fibrous Membrane Associated with Proliferative Vitreoretinopathy

Project description:Proliferative vitreoretinopathy (PVR) is a severe vision-threatening disorder characterized by the formation of cicatricial fibrous membranes leading to traction retinal detachment. As the pathophysiology remains unclear, there has been no effective therapeutic approach to date other than vitreoretinal surgery. In order to identify genes associated with the pathogenesis of PVR, we performed gene expression analyses in fibrous membrane in patients with PVR using DNA microarray technology. This study was approved by the Ethics Committee of the Kyushu University Hospital and Fukuoka University Chikushi Hospital, and the surgical specimens were handled in accordance with the ethical standards of the 1989 Declaration of Helsinki. All patients gave informed consent before inclusion in the study. Fibrousl membranes were surgically dissected from the retinal surface with horizontal scissors of patients with PVR undergoing pars plana vitrectomy. Total RNA were extracted from the fibrous membranes with three different PVR patients. RNA from human retina was obtained from Clontech (Palo Alto, CA).

2012-09-21 | E-GEOD-41019 | biostudies-arrayexpress

The gene expression profiles of human bone marrow stromal cells

Project description:Evidence suggests that the bone marrow microenvironment (niches) support hematopoietic stem cells (HSCs). The cell-cell interaction between bone marrow mesenchymal stromal cells (BMSCs) and HSCs plays a crucial role in hematopoiesis. The aging of BMSCs lead to decreased ability to maintain hematopoiesis. We used microarray to determine the age-related change of BMSCs. Human BMSCs of young (yBMSC s, age of donors: 19 and 20 years) and elderly (eBMSC s, age of donors: 68 and 72 years) donors were purchased from Lonza. BM samples were obtained from MM patients (age of donors: 62 and 77 years) in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648). BMSCs derived from MM patients (mmBMSCs) were isolated using the classical plastic adhesion method. Total RNA from each sample (yBMSCs, eBMSCs and mmBMSCs) was processed for hybridization onto GeneChipÂ® human Gene 1.0 ST Array (Affymetrix) according to the manufacturer's protocol and scanned.

2017-05-12 | E-GEOD-78235 | biostudies-arrayexpress

MiRNAs expression in peripheral blood monouclear cells from stable COPD and healthy adults

Project description:To explore which miRNAs were altered in COPD, we performed a microRNA microarray analysis of peripheral blood mononuclear cells from stable COPD patients (n=6) and healthy controls (n=6). Sex, age, BMI and history of cigarette smoke were matched between different groups. Blood samples were obtained from stable COPD patients(n=6) and healthy adults (n=6) from clinical trial (NCT02037828). The study was in compliance with the Declaration of Helsinki and was approved by Peking University Institutional Review Board Office.

2019-02-05 | GSE102915 | GEO

Expression profiling in exosomal miRNAs secreted from human bone marrow stromal cells

Project description:The aging of bone marrow stromal cells (BMSCs) lead to decreased ability to maintain hematopoiesis, however, effects of aging on BMSC-derived exosomes in bone marrow microenvironment remain unclear. The aim of this study is therefore to determine the age-related change of BMSC-derived exosomal miRNAs. Human BMSCs of young (yBMSC s, age of donors: 19 and 20 years) and elderly (eBMSC s, age of donors: 68 and 72 years) donors were purchased from Lonza. BM samples were obtained from MM patients (age of donors: 62 and 77 years) in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (mmBMSCs) were isolated using the classical plastic adhesion method. The exosomes from culture medium of BM-MSCs were isolated by Total Exosome Isolation Reagent (Invitrogen). Exosomal miRNA profiling was done using a TaqMan low-density array (ABI), and Studentâ??s t-test was used to determine statistical significance for comparisons between young and old groups using R software.

2017-05-12 | E-GEOD-78865 | biostudies-arrayexpress

Probiotics as Adjuvant Therapy in the Treatment of Metastatic Colorectal Cancer

Project description:The research will be prospective, randomised, placebo controlled and double-blinded.The research will be carried on with regards to Helsinki Declaration and following the guidelines of Good Clinical Practice.

| 2286775 | ecrin-mdr-crc

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