Affymetrix gene chip u133plus 2.0 array

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Affymetrix Gene Chip U133Plus 2.0 Array is a high-density microarray designed for whole-genome expression analysis. It contains over 54,000 probe sets representing more than 47,000 transcripts and variants, which enables comprehensive transcriptome coverage. The array is compatible with a wide range of sample types and provides reliable and reproducible gene expression data.

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Lab products found in correlation

Fl ovation cdna biotin module v2, by Tecan (2 mentions) Rnaeasy micro kit, by Qiagen (2 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions) Genechip scanner 3000, by Thermo Fisher Scientific (1 mentions) Fluidics station 450, by Thermo Fisher Scientific (1 mentions)

4 protocols using affymetrix gene chip u133plus 2.0 array

Transcriptome Analysis of Microarray Experiments

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RNA was extracted using Qiagen RNAeasy® Micro Kit, following the manufacturer's
instructions. After RNA extraction, all quantitation and microarray experiments were performed at
the UCLA Department of Pathology Clinical Microarray Core Laboratory. RNA integrity was analyzed
using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA purity and
concentration was determined using a Nanodrop 8000 (Nanodrop Products, Wilmington, DE). Microarray
targets were generated using FL-Ovation cDNA Biotin Module V2 (NuGen Technologies, San Carlos, CA)
and then hybridized to the Affymetrix Gene Chip U133Plus 2.0 Array (Affymetrix, Santa Clara, CA),
all according to the manufacturer's instructions. The arrays were washed and stained with
streptavidin phycoerythrin in Affymetrix GeneChip protocol, and then scanned using an Affymetrix
GeneChip Scanner 3000.

Liu H., Cadaneanu R.M., Lai K., Zhang B., Huo L., An D.S., Li X., Lewis M.S, & Garraway I.P. (2015). Differential Gene Expression Profiling of Functionally and Developmentally Distinct Human Prostate Epithelial Populations. The Prostate, 75(7), 764-776.

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Transcriptomic Analysis of HepG2 Cells Treated with US597

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HepG2 cells were cultured in medium containing 5 μM US597 for 24 h, and cells incubated in medium without US597 acted as a control. Total RNA was extracted from HepG2 cells (2 × 10⁶) using TRIzol reagent (Invitrogen) and mRNA microarray analyses using Affymetrix GeneChip U133plus2.0 Array (Affymetrix, Santa Clara, CA) were performed according to manufacturer's instructions. Microarrays were scanned by using Affymetrix^® GeneChip Command Console (AGCC) which installed in GeneChip^® Scanner 3000. The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek^® Genomics Suite 6.6. Pathway analysis of the genes obtained from the Natural Language Processing (NLP) analysis. Values presented are log2 RMA signal intensity.

Xiang L., Chi T., Tang Q., Yang X., Ou M., Chen X., Yu X., Chen J., Ho R.J., Shao J, & Jia L. (2015). A pentacyclic triterpene natural product, ursolic acid and its prodrug US597 inhibit targets within cell adhesion pathway and prevent cancer metastasis. Oncotarget, 6(11), 9295-9312.

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RNA Extraction and Microarray Analysis Protocol

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RNA was extracted from fractionated cells using Qiagen RNAeasy^® Micro Kit (Qiagen, Valencia, CA, USA), following the manufacturer’s instructions. After RNA extraction, all quantitation and microarray experiments were performed at the UCLA Department of Pathology Clinical Microarray Core Laboratory as previously described using Affymetrix Gene Chip U133Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA) [6 (link)]. The Partek Genomics Suite Version 6.4 (Partek, St Louis, MO, USA) was employed and conducted using Partek default settings. RNA was extracted from FC, TIC, BC, and LC fractions as previously described[6 (link)]. A comparison of TIC versus BC and LC differentially expressed genes (n = 853) were selected at ≥ 2-fold difference. In order to evaluate the impact of FC, analysis of these 853 genes was performed using data from the pooled FC population (FC and TIC versus BC and LC). The list of the top 60 significantly enriched genes is shown in S1 Table. ANOVA analysis and t-test were used in order to identify differentially expressed genes with P<0.05.

Liu S., Cadaneanu R.M., Zhang B., Huo L., Lai K., Li X., Galet C., Grogan T.R., Elashoff D., Freedland S.J., Rettig M., Aronson W.J., Knudsen B.S., Lewis M.S, & Garraway I.P. (2016). Keratin 13 Is Enriched in Prostate Tubule-Initiating Cells and May Identify Primary Prostate Tumors that Metastasize to the Bone. PLoS ONE, 11(10), e0163232.

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Amplified FFPE RNA Microarray Analysis

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Microarray targets were prepared by using the NuGEN WT-Ovation formalin-fixed and paraffinembedded RNA Amplification System V2. This system offers the most efficient cDNA amplification powered by Ribo-SPIA technology and is ideal for global gene expression analysis with the small amount of degraded RNA derived from formalinfixed and paraffin-embedded samples. Fifty nanograms of the total RNA were used for the first-strand synthesis. After the second-strand cDNA synthesis, the double-stranded cDNA was purified using Agencourt RNAClean beads provided with the WT-Ovation kit, followed by SPIA cDNA Amplification. Five micrograms of amplified cDNA were fragmented and labeled by using NuGEN's FL-Ovation cDNA Biotin Module V2 according to the instructions (NuGEN Technologies, San Carlos, CA, USA) and then hybridized to the Affymetrix GeneChip U133 plus 2.0 array (Affymetrix, Santa Clara, CA, USA) according to the manufacturers' instructions. The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 by using the Affymetrix GeneChip protocol and scanned by using an Affymetrix GeneChip Scanner 3000.

Ra S.H., Su A., Li X., Zhou J., Cochran A.J., Kulkarni R.P, & Binder S.W. (2015). Keratoacanthoma and squamous cell carcinoma are distinct from a molecular perspective. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 28(6).

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