Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of Affymetrix and NuGEN amplification methods for HTA 2.0 microarray

ABSTRACT: Comparison of total RNA-seq and Affymetrix GeneChip(R) Human Transcriptome Array 2.0 analysis methods and Affymetrix GeneChip® WT PLUS Reagent and NuGEN Ovation® PICO WTA System V2 amplification methods for the detection of significant differentially expressed genes isolated from whole blood and brain RNA samples Affymetrix and NuGEN amplification methods are compared to determine which is most efficient, cost effective, and accurate in the detection of differentialy expressed transcript clusters on the HTA 2.0 microarray The optimum amplification microarray data is compared to total RNA-seq analysis of the same samples to determine which is the most efficient, cost effective, and accurate method of detecting differentially expressed genes

ORGANISM(S): Homo sapiens

PROVIDER: GSE120327 | GEO | 2020/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Comparison of Affymetrix and NuGEN amplification methods for HTA 2.0 microarray

Project description:Comparison of Affymetrix and NuGEN amplification methods for HTA 2.0 microarray

| PRJNA492492 | ENA

Relative spatial heterogeneity revealed by transcriptional profiling of multi-region high-grade glioma samples

Project description:Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array profiling of 20 primary, multi-region high-grade glioma samples.

2015-12-31 | GSE62802 | GEO

Expression data for 4 colon tumor (Duke's stage II) /matching mucosa tissue pairs

Project description:Analysis of expression changes between colon tumors (Duke's stage II) and matching colon mucosa tissues using Affymetrix GeneChip® Human Gene 2.0 ST arrays.

2013-12-31 | GSE47074 | GEO

Comparison of the transcriptomic profiles of two human glioma cell lines, U87 and Glio6.

Project description:Using Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array, we compared the gene expression profiles between the glioma cell lines U87 and Glio6, cultured at 3% of oxygene.

2018-07-01 | GSE58646 | GEO

Lymphatic endothelial cells comparison gene array data

Project description:GeneChip® Mouse Gene 2.0 ST Array for C57BL/6 mouse skin dermal primary lymphatic endothelial cells (Ms LEC) and mouse lymphatic endothelial cell line SVEC4-10 GeneChip® Human Gene 2.0 ST Array for human primary lymphatic endothelial cells (Hu LEC) Total RNA from lymphatic cell line SVEC4-10 were used for GeneChip® Mouse Gene 2.0 ST Array.

2016-07-20 | GSE84551 | GEO

Molecular regulation of acute kidney injury (mRNA)

Project description:18 zero-hour and 18 selected post-transplant (Tx) biopsy samples from 18 kidney allografts (8 acute kidney injury (AKI), 10 PBx - protocol biopsies - controls) were analyzed by using the Affymetrix GeneChip® Human Gene 2.0 ST Array.

2015-01-15 | GSE53769 | GEO

Hormonal Regulation of MicroRNA Expression in Rat Adrenal Gland

Project description:To determine miRNA profiles in rat adrenals from animals treated with vehicle, ACTH, 17α-ethinyl estradiol (17α-E2) or dexamethasone (DEX). miRNA expression profiling was performed using Affymetrix® GeneChip® miRNA 2.0 Arrays. Together with qRT-PCR, several adrenal miRNAs have been identified, whose expression is subject to regulation by one or more than one hormone.

2014-05-16 | GSE47131 | GEO

miRNA expression in breast cancer cell lines

Project description:We analyzed the miRNA expression in 6 breast cancer cell lines from young (HCC1500, HCC1937) and old (MCF-7, MDA-MB-231, HCC1806 and MDA-MB-468) patients with breast cancer using the GeneChip® miRNA 2.0 Array (Affymetrix, Santa Clara, CA, USA).

2020-04-16 | GSE121396 | GEO

zhang-affy-mouse-175010

Project description:In our original grant we proposed to use the NR3B-null mouse model to study the role of NR3B subunit in motor neuron function. We have now successfully generated NR3B null mice. Interestingly, NR3B-null mice invariably die at age P4-P8. Our preliminary examination indicates that the motor strength of these mice is severely impaired prior to death. As we continue to explore the cause of death in NR3B null mice, we propose to conduct gene profiling experiments to search for transcription changes in the brain related to ablation of the NR3B gene. We have previously used the UCLA array facility provided by the NINDS/NIMH Microarray Consortium to identify genes that show abnormal expression patterns in these mice using whole brain samples. Now, we would like to use the same approach to analyze pure motor neuron samples obtained by Laser Capture Microdisection (LCM). As these samples are of small size we need to use RNA amplification method. We would like to compare probes from two amplification methods to see which one gives the best result. We will collect the cDNA probe obtained by RNA-based single primer isothermal amplification developed by Nugen, Inc. and the aRNA probe obtained from T7-based RNA amplification. Both the hybridization intensity and the percentage of the present call of these two types of probe will be analyzed. The cDNA probe obtained by RNA-based single primer isothermal amplification developed by Nugen, Inc. may have some advantage over the aRNA probe obtained from T7-based RNA amplification. Two samples will be processed by either RNA-based single primer isothermal amplification developed by Nugen or T7-based RNA amplification to obtain cDNA or aRNA probes, respectively. For each sample we will use 600 motor neurons obtained by LCM. Both types of probe will be labeled by biotin and hybridize to Affymetrix GeneChip Mouse Genome 430 2.0 Array. Data analysis will be performed by array facility. Keywords: dose response

2006-06-09 | GSE5036 | GEO

Transcriptome profiling by array after Kit Nugen Ovation

Project description:Affymetrix GeneChipÂ® Human Transcriptome Array 2.0

| EGAD00010001273 | EGA