The GSE40156 dataset (12 (link)) was downloaded from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/ ) to determine and investigate the candidate DEGs that potentially contribute to the progression of ATLOs. Samples of the ApoE−/− and wild-type (WT) aorta, ATLO, plaque, adventitia, blood, spleen and renal lymph node were included in the present study. Additionally, the raw data and annotation files were collected with reference to the GPL1261 (Affymetrix Mouse Genome 430 2.0 Array; Affymetrix; Thermo Fisher Scientific, Inc., Waltham, MA, USA) and GPL8321 platforms for downstream analysis (Affymetrix Mouse Genome 430A 2.0 Array; Affymetrix; Thermo Fisher Scientific, Inc.).
Affymetrix mouse genome 430 2.0 array
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Affymetrix Mouse Genome 430 2.0 Array is a microarray platform designed to analyze the expression of over 39,000 transcripts and variants from the mouse genome. It provides a comprehensive coverage of the mouse transcriptome and enables researchers to study gene expression profiles in mouse samples.
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Lab products found in correlation
Genechip command console, by Thermo Fisher Scientific (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Affymetrix human genome u133a array, by Thermo Fisher Scientific (1 mentions)
Genechip 3 ivt express kit, by Thermo Fisher Scientific (1 mentions)
Rnalater, by Thermo Fisher Scientific (1 mentions)
Rneasy mini kit, by Qiagen (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Qiazol lysis reagent, by Qiagen (1 mentions)
Rnase free dnase, by Qiagen (1 mentions)
Genechip ivt labeling kit, by Thermo Fisher Scientific (1 mentions)
Transcriptome analysis console software, by Thermo Fisher Scientific (1 mentions)
Expression console, by Thermo Fisher Scientific (1 mentions)
Genechip scanner 3000 7g, by Thermo Fisher Scientific (1 mentions)
Genechip fluidics station 450, by Thermo Fisher Scientific (1 mentions)
Genechip hybridization oven 640, by Thermo Fisher Scientific (1 mentions)
Nugen ovation rna amplification system v2, by Tecan (1 mentions)
Rneasy micro kit, by Qiagen (1 mentions)
Nucleospin rna plus, by Macherey-Nagel (1 mentions)
Genechip 3 ivt plus reagent kit, by Thermo Fisher Scientific (1 mentions)
Sybr qpcr mix, by Toyobo (1 mentions)
12 protocols using affymetrix mouse genome 430 2.0 array
1
Investigating Candidate Genes in Aortic Tertiary Lymphoid Organs
2
Transcriptional Study of Mouse Ischemic Tolerance
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Microarray assays were performed based on a previous transcriptional study of mouse ischemic tolerance in transient middle cerebral artery occlusion (tMCAO) stroke model, which included 224 samples with 6 experimental conditions (19 (link),20 (link)). In the present study, we investigated CIRI in mice suffering 45-min tMCAO or sham surgical procedure at 3 and 24 h after reperfusion (n=4/treatment/time), respectively (Table I ). The original CEL files of the 45-min tMCAO group (n=8, I3 and I24 groups) and relevant sham surgery group (n=8, S3 and S24 groups) were downloaded from the National Center of Biotechnology Information Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/ ) via the accession number GSE32529, which was based on the platform of the GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array (Thermo Fisher Scientific, Inc.). Experimental analysis confirmed infarcts in tMCAO mice at 3 or 24 h after reperfusion, but not in sham-operated mice (19 (link)). It should be noted that we performed a bioinformatics study based on the public microarray data, and no mice were used for experimental analysis in the present study.
3
Transcriptomic Analysis of Muscle Atrophy
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Total RNA was extracted from the GAST muscles of male control and fmARKO mice (n = 4 per group) and analyzed using Affymetrix mouse genome 430 2.0 array (Thermo Fisher Scientific). Probes with an absolute twofold change and a corrected P value of <0.05 were considered significantly different. GO analysis was performed by DNA Chip Research Inc.
4
Differential Gene Expression in Diabetic Mouse Hearts
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The gene expression profile of GSE32078 was obtained from the study of Vijaya et al (4 (link)), which was deposited in Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/ ) of National Center of Biotechnology Information (NCBI). A total of 12 samples were available, including three embryonic heart tissue samples at E13.5 and three embryonic heart tissue samples at E15.5 from streptozotocin-induced diabetic Swiss albino mice (8–10 weeks), as well as their respective controls from normal mice. The day when a copulation plug was observed was counted as E0.5. Raw data were collected with the Affymetrix Mouse Genome 430 2.0 Array (Affymetrix, CA, USA). All raw data files were pretreated by RMA method in Affy package (17 (link)).
5
Comprehensive Mouse Tissue Transcriptome
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mRNA expression profiles from the GSE9954 data series were downloaded from the GEO database (16 (link)). The GSE9954 data series (Affymetrix Mouse Genome 430 2.0 Array; Affymetrix, Inc., Santa Clara, CA, USA) included the profiles of 58 wild-type tissue samples obtained from 10–12-week-old C57BL/6 male mice, including 3 epididymal adipose, 3 liver, 3 diaphragm, 3 salivary gland, 3 spleen, 4 muscle, 3 brain, 3 lung, 3 kidney, 3 adrenal gland, 4 bone marrow, 5 pituitary gland, 3 seminal vesicle, 3 thymus, 3 testis, 3 heart, 3 small intestine and 3 eye tissue samples.
6
Transcriptome Analysis of Mouse Genes
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cDNA was synthesized from 2 μg of purified total RNA, and then biotinylated aRNA was transcribed with T7 RNA polymerase. The aRNA quality was assessed with an Agilent 2100 Bioanalyzer, which showed sufficiently long viability for the purpose of our experiments. The aRNA was fragmented and hybridized to an Affymetrix Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA) that contained probes for approximately 14,000 mouse genes. After hybridization at 45 °C for 16 h, the array was washed and stained with phycoerythrin. Fluorescence signals were scanned with the Affymetrix GeneChip System. The Affymetrix GeneChip Command Console (AGCC) software was used to reduce the array images to the intensity values for each probe (CEL files).
7
Differential Gene Expression Analysis of HIBD
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The HIBD microarrays, GSE2161 and GSE11686, were retrieved from the National Center for Biotechnology information (NCBI). The data of the microarrays were downloaded from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo ). GSE2161 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2161 ) included four HIBD samples and four normal samples with annotation probe [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array (GPL1261). GSE11686 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = GSE11686) included 6 HIBD samples and 10 normal samples with annotation probe [HG-U133A] Affymetrix Human Genome U133A Array (GPL96). The “limma” package (http://www.bioconductor.org/packages/release/bioc/html/limma.html ) in the R Language Programming based on Bioconductor was used to select important differentially expressed genes through Empirical Bayes [14 ]. At last, the differentially expressed genes were annotated using the “annotate” package (http://www.bioconductor.org/packages/release/bioc/html/annotate.html ). Differentially expressed mRNAs were judged by the threshold of p< 0.05 and |Log2FoldChange| >1.5.
8
Comparative Transcriptomics of Spinal Cord Injury
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We downloaded two SCI datasets (GSE5296, GSE47681) from the NCBI Gene Expression Omnibus (GEO) (Clough and Barrett, 2016 (link)). These two datasets were gene expression arrays generated using GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, United States) (Barrett et al., 2013 (link)). We selected 18 samples with SCI and 12 sham samples from the GSE5296 dataset. Similarly, we selected 17 spinal cord tissue samples from the GSE47681 dataset (Wu et al., 2013 (link)), including 13 samples with SCI and 4 sham spinal cord tissue samples.
9
Testicular RNA Expression Profiling
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After euthanasia of prepubertal males, their testes were dissected, immersed in RNAlater (Ambion, Austin, TX), and stored at −20°C. Total RNA from the whole testis was extracted using QIAzol Lysis Reagent and an RNeasy Mini kit (Qiagen. Valencia, CA). DNase digestion of the purified RNA with RNase-free DNase (Qiagen) was performed according to the manufacturer's protocol. RNA quality was checked with an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and only RNA samples with >9 RNA integrity number were used in experiments. Biotinylated amplified RNA was generated from 100 ng total RNA using an Affymetrix GeneChip 3′IVT Express Kit, and then hybridized to an Affymetrix Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA) following the manufacturer's instructions. For each strain or genotype, three distinct mice were tested separately. For the B6-Chr1MSM/B6XTMSM strain, a total of eight mice were tested, because they showed variable expression profiles.
10
Affymetrix Microarray Gene Expression Analysis
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Microarray was conducted in Capital Bio Corporation (Beijing, China) using Affymetrix GeneChip, which was authorized by Affymetrix, Inc. (Santa Clara, CA, USA). In microarray experiments, 100ng of total RNA was used for cDNA synthesis. Biotin-tagged cRNA was produced using the GeneChip IVT Labeling Kit (Affymetrix). Subsequently, 15μg fragmented cRNA, Control Oligo B2 and eukaryotic hybridization controls was hybridized to Affymetrix Mouse Genome 430 2.0 Array at 45°C for 16 h in Affymetrix GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA). The GeneChip arrays were then washed and stained with streptavidin phycoerythrinonan with Affymetrix GeneChip FluidicsStation 450, followed by scanning with Affymetrix GeneChip Scanner 3000 7G. Data were analyzed using Affymetrix Expression Console and Transcriptome Analysis Console software. Gene array was run in triplicate, and the significance for each gene was determined by one-way ANOVA. 1.5-fold change value was defined as genes with different expression.
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