Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human Stratagene Universal RNA on Affymetrix U133 Plus 2.0 and U133 A Chips

ABSTRACT: Stratagene universal human RNA hybridized to both U133 Plus 2.0 and U133 A arrays. Experiment Overall Design: Stratagene universal human RNA was processed using 5 aliquots of 2 ug each. The samples were hybridized to both 133 Plus 2.0 and 133 A arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Sean Yoder

PROVIDER: E-GEOD-3061 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression.

Zhang LanMin L Yoder Sean J SJ Enkemann Steven A SA

BMC genomics 20060615

<h4>Background</h4>There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization.<h4>Results</h4>We demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to pr ...[more]

PMID: 16776839

Similar Datasets

Stratagene Universal Human RNA Hybridized to Affymetrix U133 Plus 2.0 and U133 A Chips

Project description:Stratagene universal human RNA hybridized to both U133 Plus 2.0 and U133 A arrays. Keywords: Affymetrix platform comparison

2006-07-25 | GSE3061 | GEO

Wilms tumor versus Stratagene Universal Reference

Project description:Gene expression comparison of Wilms tumor RNA versus Stratagene Universal reference RNA Keywords: repeat sample

2004-12-31 | GSE1158 | GEO

Homo sapiens

Project description:Stratagene Universal Human RNA Hybridized to Affymetrix U133 Plus 2.0 and U133 A Chips

| PRJNA93149 | ENA

Transcription profiling of human Wilms tumor versus stratagene universal reference

Project description:Gene expression comparison of Wilms tumor RNA versus Stratagene Universal reference RNA

2008-06-11 | E-GEOD-1158 | biostudies-arrayexpress

Background analysis using yeast RNA on the U133 plus 2.0 array

Project description:We used yeast RNA to estimate background binding for each probe on the human U133 plus 2.0 array.

2011-01-01 | GSE22974 | GEO

Rhesus Macaque gene expression data obtained using Rhesus Macaque Array or Human Genome U133 Plus 2.0 Array

Project description:The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. The primary goal of this study was to compare the performances of Rhesus Macaque Genome Array and Human Genome U133 Plus 2.0 Array with respect to the detection of differential expressions when rhesus macaque RNA extracts were labeled and hybridized. The secondary goal of this study was to investigate the effect of mismatch position on signal strength in Affymetrix GeneChips by examining naturally occurring mismatches between rhesus macaque transcripts and human probes from Human Genome U133 Plus 2.0 Array. Keywords: cross hybridization

2008-06-15 | GSE9531 | GEO

Hypoxic MDA-MB-231 U133 Plus 2.0 array

Project description:MiR-544 was inhibited by either a miR-544 antagomir or compound 1 under hypoxic conditions in MDA-MB-231 cells U133 Plus 2.0 microarray was utilized to examine the specificity of 1 for miR-544.

2014-12-23 | GSE64435 | GEO

Affymetrix U133 Plus 2.0 Arrays Hybridized With Varying Amounts of Starting Material

2006-07-25 | GSE3062 | GEO

Transcription profiling of Stratagene univeral human reference RNA using different amounts of RNA to investigate array variability

Project description:Affymetrix U133 Plus 2.0 arrays were hybridized with varying amounts of starting material to determine whether different measurements of gene expression were observed. Experiment Overall Design: 1 ug, 2, ug, 5, and 10 ug of Stratagene universal human reference RNA was used to setup a series of reactions which were subsequently hybridized to Affymetrix U133 Plus 2.0 arrays. 1 ug samples were performed in triplicate and the entire experiement was repeated. BACKGROUND: There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization. RESULTS: We demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to probes designed for the U133 Plus 2.0 arrays the values obtained from an experimental hybridization can be quite different. Nearly half of the probesets in common between the two array types can produce slightly different values from the same sample. Nearly 70% of the individual probes in these probesets produced array specific differences. CONCLUSION: The context of the probe may also contribute some bias to the final measured value of gene expression. At a minimum, this should add an extra level of caution when considering the direct comparison of experiments performed in two microarray formats. More importantly, this suggests that it may not be possible to know which value is the most accurate representation of a biological sample when comparing two formats.

2007-10-27 | E-GEOD-3062 | biostudies-arrayexpress

caArray_EXP-608: TCGA (Laml): Analysis of RNA Expression Array Data for Acute Myeloid Leukemia Using Affymetrix HG-U133 Plus 2.0 (WUSTL)

Project description:TCGA Analysis of RNA Expression Array Data for Acute Myeloid Leukemia Using Affymetrix HG-U133 Plus 2.0

2015-05-14 | GSE68833 | GEO