Project description:Transcriptome analysis of partially fragmented RNA from EndoC BH1 human beta cells sorted by FACs Global gene expression profiling has shown great promise in identifying altered cell differentiation status from cultured cells. However, FACs sorting cells using internal markers causes the RNA to be partially fragmented. Clariom D pico arrays are able to utilise partially fragmented RNA to provide exon level definition to determine changes in both total gene expression and splicing.

2021-07-28 | GSE173423 | GEO

Exon Level Expression Profiling: a Novel Unbiased Transcriptome Analysis for Body Fluids

Project description:Transcriptome analysis of partially degraded and fragmented RNA samples from body fluids Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals. We analyzed saliva from 18 healthy subjects (7 males, 11 females) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

2008-05-19 | E-GEOD-7760 | biostudies-arrayexpress

Exon Level Expression Profiling: a Novel Unbiased Transcriptome

Project description:Transcriptome analysis of partially degraded and fragmented RNA samples from hiPSCs-derived MNs with Venus or Fos-B + Venus expression by lentivirus infection Fos-B could had a function on axon branching with hiPSCs-derived MNs. However, the grobal profiling under Fos-B expression was not fully elucidated. Thus, we constructed Venus or Fos-B + Venus expression lentivirus and subsequently infected those virus to hiPSCs-derived MNs. Increasing number of axon branching was detected with Fos-B expression MNs, and we demonstrated the pathological confirmation of true exon level expression profiling approach with Fos-B expressed MNs.

2019-08-07 | GSE122010 | GEO

Exon Level Expression Profiling: a Novel Unbiased Transcriptome Analysis for Body Fluids

2008-05-20 | GSE7760 | GEO

Exon Level Expression Profiling: a Novel Unbiased Transcriptome

Project description:Transcriptome analysis of the effect of RECTAS on fibroblast cells derived from a familial dysautonomia patient. We analyzed fibroblast derived from FD patient (3 control (treated with 0.1% DMSO) and 3 treated (treated with 2 M-BM-5M RECTAS)) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

2015-01-31 | E-GEOD-58038 | biostudies-arrayexpress

Exon Level Expression Profiling: a Novel Unbiased Transcriptome

Project description:Transcriptome analysis of usp15 deficient mice RNA metabolism plays an important for regulating protein diversity. USP15, which is a deubiquitinating enzyme, is known to be a responsible gene for developmental disorders and neurodegenerative disorders. Although USP15 is implicated in RNA processing, the downstream targets regulated by USP15 have not been elucidated. Here, we performed exon array screening to identify the target of USP15 using Usp15 deficient mice. We were able to found a lot of candidate genes and several genes are associated with some diseases as described above.

2020-02-18 | GSE145385 | GEO

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