High density microarrays

Manufactured by Thermo Fisher Scientific

High-density microarrays are a type of laboratory equipment used for the analysis of gene expression, DNA sequencing, and other genomic studies. They consist of a solid surface, typically a glass slide or silicon chip, that has been coated with a large number of small, discrete DNA or RNA sequences, known as probes. These probes are designed to hybridize with and detect specific target molecules in a sample, allowing researchers to study the expression levels of thousands of genes simultaneously.

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Lab products found in correlation

Oncomine database, by Thermo Fisher Scientific (1 mentions) Hg u133a, by Thermo Fisher Scientific (1 mentions)

2 protocols using high density microarrays

Genome-wide SNP Association with Alzheimer's Disease

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Single nucleotide polymorphisms (SNPs) in genome-wide association with AD risk were nominated from the literature. Three AD genome-wide association studies (GWAS) together examining >70,000 AD subjects and >380,000 controls were used to identify candidate SNPs [16 (link), 24 (link), 25 (link)]. SNPs reaching genome-wide significance (p < 5 × 10⁻⁸) in at least two of these three major GWAS were included in our study. Twenty independent loci reached criteria for inclusion.
For the Penn cases, SNP genotype was determined by Illumina Global Screening Arrays (GSA), or TaqMan SNP Genotyping Assays, as previously described [7 (link)]. In some cases, proxy SNPs (D’>0.8 in the EUR reference population from 1000 Genomes Project Phase 3 [41 ]) were substituted, as indicated in the text. For the NACC cases, SNP genotyping was completed by the Alzheimer’s Disease Genetic Consortium (ADGC) via Illumina or Affymetrix high-density microarrays, as previously described [33 (link)].

Dai D.L., Tropea T.F., Robinson J.L., Suh E., Hurtig H., Weintraub D., Van Deerlin V., Lee E.B., Trojanowski J.Q, & Chen-Plotkin A.S. (2020). ADNC-RS, a clinical-genetic risk score, predicts Alzheimer’s pathology in autopsy-confirmed Parkinson’s Disease and Dementia with Lewy Bodies. Acta neuropathologica, 140(4), 449-461.

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Comparative Analysis of p54nrb Expression in Cancers

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To analyze the expressional level of p54nrb gene in cervical tumors, colon carcinoma, and melanoma, expressional levels were compared to control samples by using Oncomine database (Thermo Fisher Scientific). In the study by Scotto et al RNA isolated from 29 cervical carcinoma cases (20 primary tumors enriched for tumor cells by microdissection and 9 cell lines) and 20 microdisssected normal cervical squamous epithelial cells were used for expression studies. [23 (link)]. RNA expressional levels were detected by employing Affymetrix high density microarrays. The array data are available from the NCBI Gene Expression Omnibus using series accession number GSE7803. In the study of Notterman et al gene expression of 18 colon adenocarcinoma and 18 paired normal tissue was measured by using the Human 6500 GeneChip Set (Affymetrix, Santa Clara, CA USA) as previously described [24 (link)]. In the study bz Talantov et al the RNA was isolated from 7 normal skin and 45 cutaneous melanoma samples as previously described [25 (link)]. The microarray scanning was performed with high-densitiy oligonucleotide microarrays (HG_U133A, Affymetrix).

Eichler M., Distler U., Nasrullah U., Krishnan A., Kaulich M., Husnjak K., Eberhardt W., Rajalingam K., Tenzer S., Pfeilschifter J, & Imre G. (2022). The caspase-2 substrate p54nrb exhibits a multifaceted role in tumor cell death susceptibility via gene regulatory functions. Cell Death & Disease, 13(4), 386.

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