The macrophages of WT and EP2−/− mice collected from the peritoneal cavity 3 days after intraperitoneal injection with 3% thioglycollate (BD Biosciences) were hybridized to a Mouse Oligo Microarray (Agilent), according to the manufacturer's procedure, and the arrays were scanned with a Microarray Scanner System (Agilent). All data were analyzed by GeneSpring GX software (Agilent), and gene ontology analysis was conducted using DAVID software. The macrophages from the WT mice served as the baseline for quantile normalization and median polish probe summarization. The expression levels in the first quantile were filtered out to remove noise, and genes that were not detected in at least 2 of the 3 biological replicates were further removed from additional analyses. Genes were defined as differentially expressed if they had a fold change of at least ±2 combined with the Student t test (P<0.05), with the Benjamini‐Hochberg adjustment for false discovery rate.
Mouse oligo microarray
Manufactured by Agilent Technologies
The Mouse Oligo Microarray is a laboratory equipment product designed for gene expression analysis in mouse samples. It provides a platform for the simultaneous measurement of thousands of mouse genes. The microarray contains pre-designed oligonucleotide probes that target specific mouse transcripts, enabling researchers to study gene expression patterns and profiles in mouse models.
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Lab products found in correlation
Genespring gx software, by Agilent Technologies (3 mentions)
Microarray scanner system, by Agilent Technologies (2 mentions)
Thioglycollate, by BD (1 mentions)
G2565ba microarray scanner system, by Agilent Technologies (1 mentions)
Stabilization and drying solution, by Agilent Technologies (1 mentions)
Dna microarray scanner, by Agilent Technologies (1 mentions)
4 protocols using mouse oligo microarray
1
Differential Gene Expression in WT and EP2-/- Macrophages
2
Mouse Oligo Microarray Analysis of Cardiomyocyte Reprogramming
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Samples from different reprogramming time points were hybridized to a Mouse Oligo Microarray (Agilent) following the manufacturer's procedure, and arrays were scanned with Microarray Scanner System (Agilent). All 23 CEL files were analyzed by GeneSpring GX software (Agilent) with quantile normalization and median polish probe summarization using D0 as a baseline. The expression levels in the first quantile were filtered out to remove noise, and the gene that was not detected in at least two of the three biological replicates was further removed for additional analysis. Genes were defined as differentially expressed if they had fold changes of at least ± 2 combined with the Student's t‐test (P < 0.05) with the Benjamini–Hochberg adjustment for false discovery rate (FDR). Gene Ontology analysis was conducted using DAVID software (Huang et al, 2009 ). Besides two replicates for reprogramming day 6 of NC, the biological replicates were three for different time points during cardiomyocyte (CM) or non‐cardiomyocyte (NC) reprogramming. The accession number for microarray data is E‐MTAB‐5295.
3
Profiling Transcriptome Changes in Hybrid Cells
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Total RNA from ES cells, cancer cells, hybrid cells and differentiated hybrid cells (D7 and D14) were labeled with Cy5. Samples were hybridized to a Mouse Oligo Microarray (G4121B; Agilent, Shanghai, China) according to the manufacturer's protocol. Arrays were scanned with a G2565BA Microarray Scanner System (Agilent). Data were analyzed using GeneSpring GX software (Agilent). Microarray data have been deposited in the Gene Expression Omnibus database (GSE30965).
4
Agilent Mouse Oligo Microarray Protocol
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The Agilent Mouse Oligo Microarray is comprised of 22,575 (60-mer) oligonucleotide probes representing 20,000 mouse genes and transcripts in the mouse genome. Probe labeling and hybridization were carried out following the manufacturer‘s specified protocols. Briefly, amplification and labeling of 5 μg of total RNA were performed using Cy5 for healthy control skin sample RNA and Cy3 for newborn subcutaneous tumor sample RNA. Hybridization was performed for 16 hrs at 60°C and arrays were scanned on an Agilent DNA microarray scanner. Following the manufacturer's protocol, Agilent's Stabilization and Drying Solution (#5185-5979) was used to protect against the ozone-induced degradation of cyanine dyes on microarray slides during hybridization and processing steps. Images were analyzed and data were extracted, background was subtracted and normalized using the standard procedures of Agilent Feature Extraction Software A.7.5.1. Arrays were analyzed. Linear & LOWESS, the default normalization method in the Agilent Feature Extraction Software A.7.5.1, were applied for normalizing Agilent microarrays. The method performs a linear normalization across the entire range of data, followed by a non-linear normalization (LOWESS) to the linearized data set.
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