Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evaluating cross-hybridization of murine cDNA to the Affymetrix Human Genome U133 Plus 2.0 chipset

ABSTRACT: Transcriptomic studies of human tumor xenografts are complicated by the presence of murine cellular mRNA. As such, it is useful to know the extent to which mouse mRNA cross-hybridizes to any given array platform. In this study, murine cDNA samples from diverse sources were hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays. In this regard it is possible to identify specific probes that are potential targets of cross-species interference. Array data was generated for 5 different mouse cDNAs and 5 different human cDNAs hybridized to human Affymetrix U133 Plus 2 arrays [3 replicates for each biological sample]. Samples included A) mouse and B) human universal RNA (Strategene, La Jolla, CA), C) B16F10 murine melanoma tumor and D) skin from same model [C57BL/6 mice] E) COLON-26 murine tumor xenograft and F) skin from same model [Balb/C mice] G) NCI-H522 human lung carcinoma xenograft and H) skin from same model (nude mice) I) LOX-IMVI human melanoma xenograft and J) skin from same model (nude mice).

ORGANISM(S): Homo sapiens

SUBMITTER: Stockwin Luke

PROVIDER: S-ECPF-GEOD-49353 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Evaluating cross-hybridization of murine cDNA to the Affymetrix Human Genome U133 Plus 2.0 chipset

2013-07-31 | GSE49353 | GEO

Evaluating cross-hybridization of murine cDNA to the Affymetrix Human Genome U133 Plus 2.0 chipset

Project description:Transcriptomic studies of human tumor xenografts are complicated by the presence of murine cellular mRNA. As such, it is useful to know the extent to which mouse mRNA cross-hybridizes to any given array platform. In this study, murine cDNA samples from diverse sources were hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays. In this regard it is possible to identify specific probes that are potential targets of cross-species interference. Array data was generated for 5 different mouse cDNAs and 5 different human cDNAs hybridized to human Affymetrix U133 Plus 2 arrays [3 replicates for each biological sample]. Samples included A) mouse and B) human universal RNA (Strategene, La Jolla, CA), C) B16F10 murine melanoma tumor and D) skin from same model [C57BL/6 mice] E) COLON-26 murine tumor xenograft and F) skin from same model [Balb/C mice] G) NCI-H522 human lung carcinoma xenograft and H) skin from same model (nude mice) I) LOX-IMVI human melanoma xenograft and J) skin from same model (nude mice).

2013-07-31 | E-GEOD-49353 | biostudies-arrayexpress

Evaluating cross-hybridization of murine cDNA to the Affymetrix Human Genome U133 Plus 2.0 chipset

Project description:Evaluating cross-hybridization of murine cDNA to the Affymetrix Human Genome U133 Plus 2.0 chipset

| PRJNA213716 | ENA

AML genome hybridization to HGU133 Plus 2.0

Project description:CD34-positive and negative fractions were used for genomic DNA preparation, which was hybridized to HGU133 Plus 2.0 arrays. Keywords: Disease state analysis

2007-03-01 | GSE4602 | GEO

Cross-hybridization modeling on Affymetrix exon arrays.

Project description:MotivationMicroarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts.ResultsTo study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion/deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct for cross-hybridization biases of gene-level expression estimates. Comparison with Solexa ultra high-throughput sequencing data demonstrates that correction for cross-hybridization leads to a significant improvement of gene expression estimates.AvailabilityWe provide mappings between human and mouse exon array probes and off-target transcripts and provide software extending the GeneBASE program for generating gene-level expression estimates including the cross-hybridization correction http://biogibbs.stanford.edu/~kkapur/GeneBase/.

| S-EPMC2639301 | biostudies-literature

AML mRNA hybridization to HGU133 Plus 2.0

Project description:CD34-positive fractions were used for mRNA preparation, which was hybridized to HGU 133 Plus 2.0 arrays. Keywords: Disease state analysis

2007-05-01 | GSE4608 | GEO

Gene expression profiles of gliomas with Affymetrix Human Genome U133 Plus 2.0 Array

Project description:Correlate the gene expression profiles with the most relevant patterns of chromosome abnormalities (cytogenetic subgroups of gliomas) and the histopathology.

2013-01-05 | GSE43289 | GEO

Microenvironment Cell Populations Affymetrix 133 Plus 2.0 series

Project description:Human tissues harbour a wide array of cellular populations, often including both immune and lymphoid cell populations, endothelial cells and fibroblasts. The goal of this study was to identify transcriptomic markers of these cell populations, in order to quantify their abundances using transcriptomic data. The present super-series is composed of a large number of transcriptomic profiles of these cell populations. These profiles were obtained from public repositories, normalized using the fRMA R package (which allows a consistent normalization of profiles across public series), and consistently annotated. This series corresponds to Affymetrix 133 Plus 2.0 profiles. Sample's annotation is available as supplementary material.

2016-09-02 | GSE86362 | GEO

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array.

Project description:One of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. We believe that this is largely the result of poor gene identification. We re-identified the probesets on the Affymetrix U133 plus 2.0 GeneChip array. This identification was based on the sequence of the probes and the sequence of the human genome. Using the BLAST program, we matched probes with documented and postulated human transcripts. This resulted in the redefinition of approximately 37% of the probes on the U133 plus 2.0 array. This updated identification specifically points out where the identification is complicated by cross-hybridization from splice variants or closely related genes. More than 5000 probesets detect multiple transcripts and therefore the exact protein affected cannot be readily concluded from the performance of one probeset alone. This makes naming difficult and impacts any downstream analysis such as associating gene ontologies, mapping affected pathways or simply validating expression changes. We have now automated the sequence-based identification and can more appropriately annotate any array where the sequence on each spot is known.

| S-EPMC549426 | biostudies-literature

Comparison between cell lines from 9 different cancer tissue (NCI-60) (Affymetrix U133 Plus 2.0)

Project description:Comparison between cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel. Cell lines from 9 different cancer tissue of origin types

| S-ECPF-GEOD-32474 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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