Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A composite immune signature parallels disease progression across T1D subjects (Affymetrix Cohort 0)

ABSTRACT: Technical replicate testing was performed to determine the measurement precision of each analyte in the array-based bioassay. Serum from subjects (n=5) with T1D was used to induce transcription in healthy “reporter” leukocytes. Three independent serum aliquots per subject were thawed and used to stimulate separate wells of reporter cells. Total RNA was isolated from the reporter cell line for gene expression analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE131523 | GEO | 2020/02/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A composite immune signature parallels disease progression across T1D subjects (RNA-Seq Cohort 0 Cell Sorted)

Project description:Technical replicate testing was performed to determine the measurement precision of each analyte. Peripheral blood mononuculear cells were processed and frozen down from blood samples collected from healthy control subjects (n=3) or subjects with Systemic Lupus Erythematosus (n=3). Three separate PBMC aliquots per subject were then independently thawed and sorted by flow into B cell, CD4+ T cell, CD8+ T cell, and monocyte populations. Total RNA was isolated from the sorted cell populations and then RNAseq libraries were prepared.

2020-02-03 | GSE131525 | GEO

A composite immune signature parallels disease progression across T1D subjects (Affymetrix Cohort 2)

Project description:We used an array-based bioassay whereby serum is used to induce transcription in healthy “reporter” leukocytes. Serum samples were obtained from control-arm subjects enrolled in 3 clinical trials evaluating immunotherapies in T1D that were conducted by the Immune Tolerance Network. The included trials evaluated immune-modifying therapy in new-onset T1D, with similar trial timecourses, primary outcomes, and data and sample collection. Total RNA was isolated from the reporter cell line for gene expression analysis.

2020-02-03 | GSE131524 | GEO

A composite immune signature parallels disease progression across T1D subjects (RNA-Seq Cohort 0 WB)

Project description:Technical replicate testing was performed to determine the measurement precision of each analyte. Peripheral blood samples were collected in tempus tubes from a healthy control subject with no family history of autoimmunity (n=1) and from subjects with Type 1 diabetes (n=4). Total RNA was isolated independently from 3 replicate aliquots of the same tempus samples and then globin-reduced. RNAseq libraries were prepared from the globin-reduced RNA.

2020-02-03 | GSE131526 | GEO

A composite immune signature parallels disease progression across T1D subjects (RNA-Seq Cohort 2 Cell Sorted)

Project description:Peripheral blood mononuculear cells were thawed and sorted into B cell, CD4+ T cells, CD8+ T cells, and monocytes. Samples were obtained from control-arm subjects enrolled in 2 clinical trials evaluating immunotherapies in T1D that were conducted by the Immune Tolerance Network. The trials had similar study timepoints, clinical and metabolic measurements, and data and sample collection plans. Total RNA was isolated from the sorted cell populations and then RNAseq libraries were prepared.

2020-02-03 | GSE131527 | GEO

A composite immune signature parallels disease progression across T1D subjects.

Project description:At diagnosis, most people with type 1 diabetes (T1D) produce measurable levels of endogenous insulin, but the rate at which insulin secretion declines is heterogeneous. To explain this heterogeneity, we sought to identify a composite signature predictive of insulin secretion, using a collaborative assay evaluation and analysis pipeline that incorporated multiple cellular and serum measures reflecting β cell health and immune system activity. The ability to predict decline in insulin secretion would be useful for patient stratification for clinical trial enrollment or therapeutic selection. Analytes from 12 qualified assays were measured in shared samples from subjects newly diagnosed with T1D. We developed a computational tool (DIFAcTO, Data Integration Flexible to Account for different Types of data and Outcomes) to identify a composite panel associated with decline in insulin secretion over 2 years following diagnosis. DIFAcTO uses multiple filtering steps to reduce data dimensionality, incorporates error estimation techniques including cross-validation and sensitivity analysis, and is flexible to assay type, clinical outcome, and disease setting. Using this novel analytical tool, we identified a panel of immune markers that, in combination, are highly associated with loss of insulin secretion. The methods used here represent a potentially novel process for identifying combined immune signatures that predict outcomes relevant for complex and heterogeneous diseases like T1D.

| S-EPMC6962023 | biostudies-literature

A composite immune signature parallels disease progression across T1D subjects

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-02-03 | GSE131528 | GEO

HIT T cell versus B cell line proof-of-principle

Project description:We have developed a multi-analyte fluid-phase protein array technology termed high-throughput immunophenotyping using transcription (HIT). This method employs a panel of monoclonal antibodies, each tagged with a unique oligonucleotide sequence that serves as a molecular barcode. After staining a sample, T7 polymerase amplifies the tags which are then hybridized to a DNA microarray for indirect measurement of each analyte. Here we coupled 44 of the tags to aliquots of an IgG1 isotype negative control antibody and the 4 remaining tags we coupled to anti-CD3, anti-CD4, anti-CD19, and anti-CD20 to create a 48-plex HIT cocktail. We then used this cocktail to stain 1 x 10^6 T or B cells and during amplification incorporated either cyanine 3-UTP (Cy3-UTP) or Cy5-UTP. Additionally, we snap froze and thawed an aliquot of the cocktail (FT). Keywords: protein profiling, cell type comparison Two-condition experiment, T cells versus B cells, including dye-swaps and self-self experiments. We also tested an array that had been frozen and thawed.

2010-05-26 | E-GEOD-10761 | biostudies-arrayexpress