Agilent whole mouse genome 4 44 multiplex format oligo arrays

Manufactured by Agilent Technologies

Sourced in United States

The Agilent Whole Mouse Genome 4×44 multiplex format oligo arrays are high-density microarray products designed for whole-genome expression analysis of mouse samples. The arrays provide comprehensive coverage of the mouse transcriptome, enabling researchers to measure the expression levels of thousands of mouse genes simultaneously.

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Lab products found in correlation

Agilent feature extraction software v9, by Agilent Technologies (1 mentions) Agilent feature extraction software, by Agilent Technologies (1 mentions) Ingenuity pathway analysis software, by Qiagen (1 mentions) Agilent scanner, by Agilent Technologies (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Trizol reagent, by Thermo Fisher Scientific (1 mentions) Rnalater stabilization solution, by Thermo Fisher Scientific (1 mentions) Ingenuity pathway analysis software ipa, by Qiagen (1 mentions) Rneasy kit, by Qiagen (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

Agilent arrays (7 citations) Whole Genome Oligo Array (6 citations) Agilent Whole Mouse Genome arrays (4 citations)

5 protocols using agilent whole mouse genome 4 44 multiplex format oligo arrays

Microarray Analysis of Mouse Genome

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Microarray analysis was performed by NIEHS molecular genomics core laboratory using the Agilent Whole Mouse Genome 4×44 multiplex format oligo arrays (014868) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500 ng of total RNA, Cy3 labeled cRNA was produced according to the manufacturer’s protocol. For each sample, 1.65 μg of Cy3 labeled cRNAs were fragmented and hybridized for 17 h in a rotating hybridization oven. Slides were washed and then scanned with an Agilent Scanner. Data were obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using the Rosetta Resolver system (version 7.2). In order to identify differentially expressed probes, ANOVA was used to determine if there was a statistical difference between the means of groups. The analysis was performed with setting parameters of at least 2-fold difference and significance at p < 0.01. Data were deposited in Gene Expression Omnibus (GSE138443).

Arao Y., Hamilton K.J., Grimm S.A, & Korach K.S. (2020). The genomic regulatory elements for estrogen receptor alpha transactivation-function-1 regulated genes. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 34(12), 16003-16021.

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Colon Gene Expression Microarray in GR Mouse Models

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Gene expression microarrays from colon samples from C57BL/6 mice GR^flox and GR^iKO +/− DSS mouse models (GR^floxCtol n = 4; GR^iKO Ctol n = 4; GR^flox DSS n = 3; GR^iKO DSS n = 3) were conducted using Agilent whole mouse genome 4 × 44 multiplex format oligo arrays (014868) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500 ng of total RNA, Cy3-labeled cRNA was produced according to the manufacturer’s protocol. For each sample, 1.65 mg of Cy3-labeled cRNA was fragmented and hybridized for 17 h in a rotating hybridization oven. Slides were washed and then scanned with an Agilent scanner. Data was obtained using the Agilent feature extraction Software (Version 12.0), using the 1-color defaults for all parameters. The Agilent feature extraction software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using Omicsoft Array Studio Software (Version 7.0). The Gene Expression Omnibus accession number of this dataset is GSE146048 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146048), last accessed on 20 December 2021.

Landskron G., Dubois-Camacho K., Orellana-Serradell O., De la Fuente M., Parada-Venegas D., Bitrán M., Diaz-Jimenez D., Tang S., Cidlowski J.A., Li X., Molina H., Gonzalez C.M., Simian D., Lubascher J., Pola V., Montecino M., Blokzijl T., Faber K.N., González M.J., Quera R, & Hermoso M.A. (2022). Regulation of the Intestinal Extra-Adrenal Steroidogenic Pathway Component LRH-1 by Glucocorticoids in Ulcerative Colitis. Cells, 11(12), 1905.

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Transcriptomic Analysis of Metabolic Tissues

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mRNA from adipose, liver, and muscle was purified using Trizol reagent and RNeasy mini kit using WT fed, WT fasted, KI fed, and KI fasted groups (n=4). Gene expression analysis was conducted using Agilent Whole Mouse Genome 4×44 multiplex format oligo arrays (014868) (Agilent Technologies) following the Agilent 1-color microarray-based gene expression analysis protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol. For each sample, 1.65 µg of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven. Slides were washed and then scanned with an Agilent Scanner. Data were obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using OmicSoft Array Studio (Version 9.0) software. Gene expression comparisons among obtained data sets were performed with Ingenuity Pathway Analysis software (Qiagen). Threshold for gene expression changes were set to > 5-fold and P <0.05 and >2-fold and P<0.05.

Sueyoshi T., Sakuma T., Shindo S., Fashe M., Kanayama T., Ray M., Moore R, & Negishi M. (2019). A phosphorylation-deficient mutant of retinoid X receptor α at Thr167 alters fasting response and energy metabolism in mice. Laboratory investigation; a journal of technical methods and pathology, 99(10), 1470-1483.

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Transcriptomic profiling of prostate cancer

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Harvested prostates were immediately treated with RNAlater stabilization solution (Thermo Fisher Scientific), RNAs from which were collected and purified using Trizol reagent (Thermo Fisher Scientific) and RNeasy mini kit (QIAGEN, Valencia, CA, USA). Gene expression analysis was conducted using Agilent Whole Mouse Genome 4 × 44 multiplex format oligo arrays (014868) (Agilent Technologies, Palo Alto, CA, USA) as described previously [6 (link)]. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. Genes were considered differentially expressed if they showed a fold-change of at least 2.0 with a p-value<0.05 tested by an ANOVA and Benjamini-Hochberg multiple test correction performed using OmicSoft Array Studio software (Version 10). Ingenuity Pathway Analysis software (IPA, Qiagen) was utilized to search the Canonical pathway. The pathways with Z-score >2 and <−2 were considered significantly activated and repressed pathways, respectively. Gene set enrichment analysis (GSEA, version 4.0.3) was performed to analyze gene expression signatures, focusing on the hallmark gene sets (H) or regulatory gene sets (C3) from Molecular Signature Database (MSigDB, v7.1).

Yokobori K, & Negishi M. (2022). Ser815 Phosphorylation stabilizes the androgen receptor homodimer and stimulates ER-stress induced cell death. Biochemical and biophysical research communications, 639, 54-61.

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Comprehensive Liver Transcriptome Analysis

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Extracted RNAs obtained from livers using Trizol (Invitrogen, Carlsbad, CA) were purified with QIAGEN RNeasy kit (QIAGEN, Hilden, Germany) according to a manufacture's protocol. Gene expression analysis was conducted using Agilent Whole Mouse Genome 4×44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA) following the Agilent 1-color microarray-based gene expression analysis protocol as reported previously [23] (link). In order to identify differentially expressed probes, analysis of variance (ANOVA) was used to determine if there was a statistical difference between the means of groups. Gene tags were identified as PB responsive genes if p-value was smaller than 0.05. To investigate functional characteristics as well as upstream regulators of specific gene lists, we used Ingenuity Pathway Analysis (IPA, Ingenuity Systems; www.ingenuity.com). cDNAs obtained from non-treated animals fasted for 24 h were also investigated by microarray analysis as described above. GEO accession number for our data is GSE56557.

Ohno M., Kanayama T., Moore R., Ray M, & Negishi M. (2014). The Roles of Co-Chaperone CCRP/DNAJC7 in Cyp2b10 Gene Activation and Steatosis Development in Mouse Livers. PLoS ONE, 9(12), e115663.

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