Whole human genome oligo microarray 4x44k

Manufactured by Agilent Technologies

Sourced in Germany

The Whole Human Genome Oligo Microarray (4x44K) is a laboratory equipment product designed for gene expression analysis. It contains over 44,000 60-mer oligonucleotide probes that represent the entire human genome.

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Lab products found in correlation

Agilent feature extraction software, by Agilent Technologies (2 mentions) Agilent array platform, by Agilent Technologies (1 mentions) Quick amp labeling protocol, by Agilent Technologies (1 mentions) Agilent scanner g2505c, by Agilent Technologies (1 mentions) Genespring gx v11, by Agilent Technologies (1 mentions) Genespring gx11, by Agilent Technologies (1 mentions) Allprep dna rna mini kit, by Qiagen (1 mentions) Mtesr1, by STEMCELL (1 mentions) One color microarray based gene expression analysis protocol, by Agilent Technologies (1 mentions)

5 protocols using whole human genome oligo microarray 4x44k

Human Gene Expression Microarray Protocol

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Infected cell samples were pelleted and frozen. Samples were sent to Arraystar (Rockville, MD) for RNA extraction and microarray analysis with the Agilent Human 4 x 44K gene expression array. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, the Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.

McClure R.S., Wendler J.P., Adkins J.N., Swanstrom J., Baric R., Kaiser B.L., Oxford K.L., Waters K.M, & McDermott J.E. (2019). Unified feature association networks through integration of transcriptomic and proteomic data. PLoS Computational Biology, 15(9), e1007241.

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TNF-induced Gene Expression in Monocytes

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Gene expression data of long term TNF incubated primary human monocytes were obtained from a data set published earlier [7 (link)], in which the Whole Human Genome Oligo Microarray 4x44K (Agilent, Ratingen, Germany; gene expression omnibus series accession number GSE45371) was used.

Welz B., Bikker R., Junemann J., Christmann M., Neumann K., Weber M., Hoffmeister L., Preuß K., Pich A., Huber R, & Brand K. (2019). Proteome and Phosphoproteome Analysis in TNF Long Term-Exposed Primary Human Monocytes. International Journal of Molecular Sciences, 20(5), 1241.

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Fenofibrate Regulated Transcriptome Analysis

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The total RNA was extracted by TRIzol after harvesting cells treated with fenofibrate. The Whole Human Genome Oligo Microarray (4x44K, Agilent Technologies) was done by KangChen Biotechnology. The data extracted from Agilent Feature Extraction software (version 11.0.1.1) were quantile normalized and analyzed by the GeneSpring GX v11.5.1 software package (Agilent Technologies). The fold change filtering identified differentially expressed genes. Pathway and gene ontology (GO) analysis were applied to identify the roles of these differentially expressed genes playing in biological pathways or GO terms. The microarray data was accessible through Gene Expression Omnibus (GEO) [22 (link)] series accession number GSE49965 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49965).

Li T., Zhang Q., Zhang J., Yang G., Shao Z., Luo J., Fan M., Ni C., Wu Z, & Hu X. (2014). Fenofibrate induces apoptosis of triple-negative breast cancer cells via activation of NF-κB pathway. BMC Cancer, 14, 96.

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Profiling Hepatocellular Carcinoma Cell Lines

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Using the AllPrep DNA/RNA Mini Kit (Qiagen), total RNA was prepared from a hepatocellular carcinoma cell line (HuH-7) and uncultured human adult hepatocytes (obtained from the Health Science Research Resources Bank) as well as clones AFB1-1, NGC1-1, and NGC1-2 that were cultured on the MEFs (5 X 10⁴ cells/cm²) with mTeSR1 (StemCell Technologies) medium in gelatin-coated 100-mm dishes before long-term serial passage. The microarray study was carried out using a Whole Human Genome Oligo Microarray 4X44K (Agilent). The analysis was performed by Bio Matrix Research according to Agilent technical protocols. Data from these experiments and the GEO database for hESCs (hES_ES01, GSM194392; hES_BG03, GSM194391; hES_H9, GSM194390) and hiPSCs (201B7, GSM241846) established from human adult fibroblasts (fibroblast, GSM242095) were analyzed with GeneSpring GX 11.5 software (Agilent). The microarray data reported in this paper are available on the Gene Expression Omnibus under accession number GSE63844.

Ishikawa T., Kobayashi M., Yanagi S., Kato C., Takashima R., Kobayashi E., Hagiwara K, & Ochiya T. (2015). Human Induced Hepatic Lineage-Oriented Stem Cells: Autonomous Specification of Human iPS Cells toward Hepatocyte-Like Cells without Any Exogenous Differentiation Factors. PLoS ONE, 10(4), e0123193.

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Transcriptomic Analysis of ESC-CECs and LSCs

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The total RNAs of ESC-CECs and human LSCs were extracted by TRIzol after the cells were harvested. The Whole Human Genome Oligo Microarray (4x44K, Agilent Technologies, Santa Clara, CA) analysis was performed by Kangchen Biotechnology (Shanghai, China). Briefly, RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Agilent Feature Extraction software was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package. Differentially expressed (DE) genes between the two samples were identified through Fold Change filtering. Gene ontology (GO) analysis was performed in the standard enrichment computation method. The GO categories were derived from Gene Ontology and included three structured networks: biological process (BP), cellular component (CC), and molecular function (MF). The microarray data was available through the GEO database with accession number GSE70152.

Wang Z., Zhou Q., Duan H., Wang Y., Dong M, & Shi W. (2016). Immunological Properties of Corneal Epithelial-Like Cells Derived from Human Embryonic Stem Cells. PLoS ONE, 11(3), e0150731.

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