Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A human transcriptome array for high-throughput clinical studies (with a comparison to RNA-seq technology) [expression array]

ABSTRACT: A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts. The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis. The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing. This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data. When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies. Examination exon/gene expression of liver and muscle in quadraplicate using both the array technology and RNA-Seq

ORGANISM(S): Homo sapiens

SUBMITTER: Weihong Xu

PROVIDER: E-GEOD-26072 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A human transcriptome array for high-throughput clinical studies (with a comparison to RNA-seq technology) [RNA-Seq]

Project description:A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts. The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis. The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing. This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data. When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies.

2011-01-27 | GSE26109 | GEO

A human transcriptome array for high-throughput clinical studies (with a comparison to RNA-seq technology) [expression array]

2011-01-27 | GSE26072 | GEO

A human transcriptome array for high-throughput clinical studies (with a comparison to RNA-seq technology) [RNA-Seq]

2011-01-27 | E-GEOD-26109 | biostudies-arrayexpress

Human transcriptome expression analysis of cervical cancer

Project description:Although many protein-coding genes have been identified to be aberrantly expressed in cervical cancer, the mechanisms of development and progression of cervical cancer remain unclear. In recent years, non-coding RNAs, especially including microRNAs and long non-coding RNAs, have been shown to play important regulatory roles in mammalian cell biology. In our study, we investigated the whole genome gene expression level changes by human transcriptome array in tumor tissues and paired adjacent non-tumor tissue of patients with cervical cancer. The functions of different expression microRNAs, long non-coding RNAs and mRNAs were further analyzed in vitro and in vivo using loss-of-function and gain-of-function approaches. A ten chip study using total RNA recovered from five separate cervical cancer tissues and five paired adjacent non-tumor samples.

2014-10-27 | E-GEOD-55940 | biostudies-arrayexpress

Transcriptomic Analysis of PNN- and ESRP1-regulation in Human Corneal Epithelial Cells

Project description:Pnn depletion in developing mouse corneal epithelium led to disrupted alternative splicing of multiple ESRP-regulated epithelial-type exons. In human corneal epithelial cells (HCET), ESRP1 and PNN displayed close localization in and around nuclear speckles and their physical association in protein complexes was identified. In this study, gene expression profiling was performed to identify PNN- and ESRP1-regulated alternative pre-mRNA splicing in human corneal epithelial cells. Immortalized human corneal epithelial cells harboring doxycycline-inducible shRNA against PNN or ESRP1 were created. Whole transcriptome array analysis on ESRP1 or PNN knockdown HCET cells revealed clear alterations in transcript level and splicing pattern of specific subsets of genes with significant overlaps in their candidate targets. Our data suggest that ESRP1 and PNN modulate alternative splicing of a specific subset of exons, but not general splicing events. ESRP1 and PNN may together participate in the regulation of epithelial-specific splicing program in a genome-wide fashion. Parental HCET, shRNA-PNN HCET, and shRNA-ESRP1 HCET cells were cultured for 3 days with/without doxycycline. Total RNA was isolated from four biological replicates of each sample group and then subjected to hGlue3_0 transcriptome array analysis.

2013-01-24 | E-GEOD-41996 | biostudies-arrayexpress

Four-dimensional trapped ion mobility spectrometry lipidomics for high throughput clinical profiling of human blood samples

Project description:Implementation of operational workflows using untargeted high-resolution ion mobility mass spectrometry in clinical lipidomics require reproducible, high-throughput lipid extraction, high-quality lipid annotation, absolute quantification, and cross-validation. We present a high-throughput 4D-PASEF MS platform suitable for clinical plasma lipidomic profiling encompassing automated extraction, accurate lipid annotation, and reproducible quantification. Newly generated 4D-PASEF lipid descriptors (m/z, RT, CCS, MS2) of 200 lipid standards and of 493 lipid signals curated from reference plasma, along with qualification of reproducible features in replicate lipid extracts and dilution analyses enabled highly confident annotation, reaching 100% confidence, of 370 lipids from NIST SRM 1950 plasma and 364 lipids from NIST SRM 1951 serum. 359 plasma lipids were reproducibly quantified using absolute quantification, cross-validated by inter-instrument studies, and supported by inter-laboratory data. The high-throughput 4D-PASEF lipidomics platform was demonstrated by reproducible identification of intra-individual multidien lipidome phenotype in plasma, serum, blood, venous, and finger-prick dried blood spots.

2022-12-07 | ST002402 | MetabolomicsWorkbench

High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

Project description:We present TORNADO-seq —a high-throughput, a high-content drug discovery platform that for the first time uses next-generation sequencing (NGS) based, targeted RNA-seq in organoids monitoring the expression of 206 genes for the evaluation of complex mixtures of cellular phenotypes. TORNADO-seq is a fast, highly-reproducible, time- and cost-effective (5$ per sample including sequencing cost) method that we used to find drugs that enrich for differentiated cell phenotypes in intestinal organoids. These drugs are highly efficacious against cancer compared to wild type organoids and may therefore become promising candidates in CRC treatment. Further, TORNADO-seq facilitated in-depth insight on the mode of action of these drugs.

2021-03-10 | GSE157167 | GEO

Analysis of gene expression in rice mature leaf and cultured cell suspension using Rice SuperSAGE Array1

Project description:We developed a novel platform for genome-wide gene expression analysis in any eukaryotic organism, that we coin SuperSAGE Array. The SuperSAGE Array is a microarray onto which oligonucleotides of 26 nucleotides corresponding to SuperSAGE tag sequences are directly synthesized. A SuperSAGE Array combines the advantages of the highly quantitative SuperSAGE expression analysis with the high-throughput microarray technology. Highly reproducible gene expression profiling by the SuperSAGE Array was demonstrated for a thousand of genes (tags) in rice. Keywords: Tissues, SuperSAGE, 26base oligonucleotide

2006-07-28 | GSE4685 | GEO

UVDE-seq mapping of UV-induced non-CPD lesions

Project description:Here we have used a novel high-throughput sequencing method known as UVDE-seq to map the formation of non-CPD lesions at single nucleotide resolution across the yeast genome in wild-type and rad16 mutant cells, which are deficient in GG-NER.

2020-11-19 | GSE144679 | GEO

Automated sample preparation with SP3 for low-input clinical proteomics

Project description:High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety of sources, including frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format, performing unbiased protein purification and digestion delivering peptides that can be directly analyzed by LCMS. AutoSP3 eliminates hands-on time and minimizes the risk of error, and we show it reduces the protein quantification variability, and improves longitudinal performance and reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low-input samples, reproducibly quantifying 500-1000 proteins from 100-1000 cells (<100 ng protein). Furthermore, we added a LE220-plus focused- ultrasonicator (Covaris Ltd, UK) to our pipeline to include 96-well format lysis of fresh-frozen tissue and cells. Collectively, autoSP3 provides a generic, scalable, and cost-effective pipeline for routine and standardized proteomic sample processing that should enable reproducible proteomics in broad range of clinical and non-clinical applications.

2020-03-27 | PXD015840 | 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