Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stockholm dataset for prototype muscle age diagnostic

ABSTRACT: Muscle biopsy samples from healthy male subjects at the baseline belonging to either <29y or >59y age range. These samples were used to design a prototype of multi-tissue molecular diagnostic of healthy physiological age, which was then validated in multiple independent studies using gold standard external validation methods

ORGANISM(S): Homo sapiens

PROVIDER: GSE59880 | GEO | 2015/08/05

SECONDARY ACCESSION(S): PRJNA256976

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Stockholm dataset for ageing prototype diagnostic

Project description:Muscle biopsy samples from healthy male subjects at the baseline belonging to either <29y or >59y age range. These samples were used to design a prototype of multi-tissue molecular diagnostic of healthy physiological age. Resting skeletal muscle sample after an overnight fast. related to GSE18583

2015-08-05 | E-GEOD-59880 | biostudies-arrayexpress

Preserving the phosphoproteome of clinical biopsies using a quick freeze collection device

Project description:The current gold standard for collecting and processing cancer biopsies is to flash freeze tumor samples in liquid nitrogen. However, in many clinical settings liquid nitrogen is not readily available, and neither the personnel nor the infrastructure is generally available to rapidly process the tumor samples. As a result, tumors are often subjected to prolonged ischemia and/or chemical fixatives, altering the phosphoproteome such that it may no longer reflect the true in vivo state of the tumor. There is a need for an economical, single-use device that can be stored at room temperature then activated at point of care to rapidly freeze the specimen. Our proof-of-concept quick-freeze prototype device focused on key requirements including cooling performance, device safety, minimizing use error, and the ability to ship via existing cold chain logistics. We have demonstrated that our device can cool a core sample below 0°C in less than 70 seconds, below -8°C in less than 150 seconds, and maintain that sample below 0°C for greater than 70 minutes. To demonstrate feasibility, the performance of our prototype was benchmarked against flash freezing in liquid nitrogen using melanoma-bearing PDX mice as a model system. After subjecting the mice to total body irradiation to elicit a phosphosignaling response in the DNA damage response pathway, tumors were harvested and quadrisected with two parts of the tumor snap frozen in liquid nitrogen, and the remaining two parts rapidly cooled in the prototype quick-freeze biospecimen containers for 1 hour. Phosphoproteins were profiled by LC-MS/MS. The prototype freeze device showed feasibility with bias within acceptable limits and slightly higher variability for a subset of phosphopeptides compared to flash freezing. The prototype device forms the framework for development of a commercial device that will improve tissue biopsy preservation for measurement of important phospho-signaling molecules.

2022-07-18 | PXD029844 | Pride

Serum Protein Risk Stratification Score for Diagnostic Evaluation of Metabolic Dysfunction-Associated Steatohepatitis (MASH)

Project description:Reliable non-invasive tools to diagnose at risk metabolic dysfunction-associated steatohepatitis (MASH) are urgently needed to improve management. We developed a risk stratification score incorporating proteomics-derived serum markers with clinical variables to identify high risk MASH patients (NAFLD Activity Score (NAS) >4 and fibrosis score >2). In this three-phase proteomic study of biopsy-proven metabolic dysfunction-associated steatotic fatty liver disease (MASLD), we first developed a multi-protein predictor for discriminating NAS>4 based on SOMAscan proteomics quantifying 1,305 serum proteins from 57 US patients. Four key predictor proteins were verified by ELISA in the expanded US cohort (N=168), and enhanced by adding clinical variables to create the 9-feature MASH Dx Score which predicted MASH and also high risk MASH (F2+). The MASH Dx Score was validated in two independent, external cohorts from Germany (N=139) and Brazil (N=177). The discovery phase identified a 6-protein classifier that achieved an AUC of 0.93 for identifying MASH. Significant elevation of four proteins (THBS2, GDF15, SELE, IGFBP7) was verified by ELISA in the expanded discovery and independently in the two external cohorts. MASH Dx Score incorporated these proteins with established MASH risk factors (age, BMI, ALT, diabetes, hypertension) to achieve good discrimination between MASH and MASLD without MASH (AUC:0.87- discovery; 0.83- pooled external validation cohorts), with similar performance when evaluating high risk MASH F2-4 (vs. MASH F0-1 and MASLD without MASH). The MASH Dx Score offers the first reliable non-invasive approach combining novel, biologically plausible ELISA-based fibrosis markers and clinical parameters to detect high risk MASH in patient cohorts from the US, Brasil and Europe.

2023-12-22 | GSE251855 | GEO

Homo sapiens

Project description:Stockholm dataset for prototype muscle age diagnostic

| PRJNA256976 | ENA

Gene expression in cutaneous T cell lymphoma (CTCL), dermatitis (D), and healthy subjects (HS)

Project description:FFPE skin biopsy samples from patients with CTCL, dermatitis, or healthy controls were profiled by NanoString gene expression analysis A classifier was constructed that was able to identify mycosis fungoides (MF) samples from dermatitis and healthy controls.

2020-06-16 | GSE143382 | GEO

Methylation studies in plains zebras

Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues of plains zebras (Equus quagga). Both whole blood (96) and remote biopsy (24) samples were obtained from a captive population of zebras maintained in a semi-wild state. After eliminating samples with low confidence for individual identity and age, we retained 76 blood samples and 20 biopsy samples, totaling 96 zebra samples.

2021-11-25 | GSE184223 | GEO

Human Transcriptome Array 2.0 (HTA) from healthy colonic, colorectal adenoma and colorectal cancer tissue

Project description:Whole transcriptome expression levels of healthy colonic, colorectal adenoma and colorectal cancer biopsy samples were analyzed by HTA 2.0 microarrays

2019-09-13 | GSE100179 | GEO

Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development - post-diagnostic HCC blood samples

Project description:Genome wide DNA methylation profiling of blood samples collected from patients after diagnosis with hepatocellular carcinoma (HCC) (cases) vs. blood samples collected from healthy individuals without family history of cancer (controls). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human samples corresponding to cases (post-diagnostic HCC) and controls. Samples included 24 cases and 24 controls. Cases were matched with controls on gender, age, ethnicity, hepatitis C infection, and diabetes. The presence or absence of HCC in our study was determined based on the AASLD criteria.

2022-01-31 | GSE113409 | GEO

Loci-specific differences in blood DNA methylation in HBV-negative populations at risk for hepatocellular carcinoma development - pre-diagnostic HCC blood samples

Project description:Genome wide DNA methylation profiling of blood samples collected from patients prior to diagnosis with hepatocellular carcinoma (HCC) vs. blood samples collected from healthy individuals without family history of cancer. The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human samples corresponding to cases (pre-diagnostic HCC) and controls. Samples included 21 cases and 21 controls. Cases were matched with controls on gender, age, ethnicity, hepatitis C infection, and diabetes. The presence or absence of HCC in our study was determined based on the AASLD criteria.

2022-01-31 | GSE113392 | GEO

SWATH-MS based protein quantification for diagnosis in systemic lupus erythematous

Project description:The gold standard for diagnosing lupus nephritis, one of the common symptoms of systemic lupus erythematosus, is an invasive procedure, a Renal biopsy. To overcome the risk of invasive methods, we constructed a spectral library using biological samples that can be obtained non-invasively and analyzed it using the SWATH-MS method, a quantitative proteomic analysis.

2023-10-24 | PXD040099 | Pride

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