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Mouse gene 2.0 st microarray

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The Mouse Gene 2.0 ST microarray is a lab equipment product designed for gene expression analysis in mice. It provides a comprehensive coverage of the mouse transcriptome, enabling researchers to study gene expression patterns and profiles. The core function of this microarray is to facilitate the measurement and analysis of gene expression levels in mouse samples.

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Genechip wt terminal labeling kit, by Thermo Fisher Scientific (2 mentions) Wt ovation pico rna amplification system, by Tecan (1 mentions) Genechip scanner 3000 7g system, by Thermo Fisher Scientific (1 mentions) Transcriptome analysis console software, by Thermo Fisher Scientific (1 mentions) Expression console software, by Thermo Fisher Scientific (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Rneasy micro kit, by Qiagen (1 mentions) Ingenuity pathway analysis software, by Qiagen (1 mentions) Agilent rna nano labchips, by Agilent Technologies (1 mentions) Genechip scanner 3000, by Thermo Fisher Scientific (1 mentions) Rneasy kit, by Qiagen (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Bioanalyzer, by Agilent Technologies (1 mentions) Mouse promoter 1.0r array, by Thermo Fisher Scientific (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions)

9 protocols using mouse gene 2.0 st microarray

1

Microarray Analysis of Purified Thy1+ LSK Cells

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RNA for microarray was extracted from FACS purified Thy1+LSK cells using the RNeasy Micro kit (QIAGEN). RNA quantity and quality was assessed using a 2100 Bioanalyzer (Agilent). For global gene expression analysis, isolated RNA was amplified using the WT Ovation Pico RNA amplification system (Nugen). After labeling with the GeneChip WT terminal labeling kit (Affymetrix), labeled cRNA of each individual sample was hybridized to an Affymetrix Mouse Gene 2.0ST microarray (Affymetrix), stained and scanned by GeneChip Scanner 3000 7 G system (Affymetrix) according to standard protocols. Raw data were normalized using Expression Console Software (Affymetrix) and analyzed using Transcriptome Analysis Console Software (Affymetrix). Unannotated and sex-specific genes varying among samples were removed for analysis. Gene set enrichment analysis was performed using the gene set enrichment analysis tool (GSEA; Broad Institute).
Stanley R.F., Piszczatowski R.T., Bartholdy B., Mitchell K., McKimpson W.M., Narayanagari S., Walter D., Todorova T.I., Hirsch C., Makishima H., Will B., McMahon C., Gritsman K., Maciejewski J.P., Kitsis R.N, & Steidl U. (2017). A myeloid tumor suppressor role for NOL3. The Journal of Experimental Medicine, 214(3), 753-771.
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2

Microarray Analysis of Gene Expression

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J o u r n a l P r e -p r o o f confirmed on Agilent RNA Nano LabChips (Agilent Technologies). The sense cDNA was prepared from 300 ng of total RNA using the Ambion WT Expression Kit. The sense strand cDNA was fragmented and biotinylated using the Affymetrix GeneChip WT Terminal Labeling Kit (PN 900671). According to the manufacturer's instructions, labeled sense cDNA was hybridized to the Affymetrix Mouse Gene 2.0 ST microarray and with the GeneChip Hybridization, Wash, and Stain Kit. Genechips were scanned with the Affymetrix GeneChip Scanner 3000. Background correction and normalization were done using RMA (Robust Multichip Average) algorithm (Irizarry et al., 2003) and a filtering process was performed to eliminate low expression probe sets. R/Bioconductor (Gentleman et al, 2006) was used for preprocessing and statistical analysis. LIMMA (Linear Models for Microarray Data) (Smyth, 2004 (link)) method was used first to find out the probe sets that showed significant differential expression between experimental conditions, selecting genes as significant using p-value<0.01 as threshold.
False Discovery Rate (FDR) method was also use to correct for multiple hypotheses testing and finally the Ingenuity Pathway Analysis software (Ingenuity Systems, www.ingenuity.com) was used to check altered metabolic pathways between groups.
Pérez-González M., Mendioroz M., Badesso S., Sucunza D., Roldan M., Espelosín M., Ursua S., Luján R., Cuadrado-Tejedor M, & Garcia-Osta A. (2020). PLA2G4E, a candidate gene for resilience in Alzheimer´s disease and a new target for dementia treatment. Progress in neurobiology, 191.
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3

Analyzing Slam1 Expression in BMDC Coculture

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3 × 105 non-adherent BMDCs from wild-type C57BL6,
Card9−/− and MyD88−/− mice
were cocultured with 3 × 105B. dermatitidis vaccine yeast or medium alone in a 24-well
plate for 24 hours. Total RNA from the BMDC cultures described above was
purified using the Qiagen RNeasy kit (Cat. # 74106) according to the
manufacturer’s protocol. Genomic DNA was removed using Turbo DNase
(Ambion Cat.#AM2238). Following DNase treatment, the RNA was cleaned up using
Qiagen RNeasy columns according to the manufacturer’s protocol. RNA was
reverse transcribed and Slam1 expression analyzed by Affymetrix mouse gene 2.0
ST microarray at the Biotech Center at UW-Madison and RT-PCR. The n-fold change
of gene expression for yeast stimulation vs. non-stimulation was calculated
using the comparative CT method (16 (link)).
Kohn E.M., dos Santos Dias L., Dobson H.E., He X., Wang H., Klein B.S, & Wüthrich M. (2022). SLAMF1 is dispensable for vaccine induced T cell development but required for resistance to fungal infection. Journal of immunology (Baltimore, Md. : 1950), 208(6), 1417-1423.
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4

Bac 1.2F5 Cells: RNA Isolation and Microarray

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For analysis of gene expression of Bac 1.2F5 cells, RNA was isolated using a Qiagen RNeasy mini kit. The RNA was quality controlled using an Agilent Bioanalyzer and then provided to the Einstein Genomics Core. The core performed labeling, hybridization, scanning, and RNA normalization using an Affymetrix Mouse Gene 2.0 ST microarray. The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE185443.
Sharma V.P., Tang B., Wang Y., Duran C.L., Karagiannis G.S., Xue E.A., Entenberg D., Borriello L., Coste A., Eddy R.J., Kim G., Ye X., Jones J.G., Grunblatt E., Agi N., Roy S., Bandyopadhyaya G., Adler E., Surve C.R., Esposito D., Goswami S., Segall J.E., Guo W., Condeelis J.S., Wakefield L.M, & Oktay M.H. (2021). Live tumor imaging shows macrophage induction and TMEM-mediated enrichment of cancer stem cells during metastatic dissemination. Nature Communications, 12, 7300.
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5

Gamma-irradiated RNA Profiling Using Microarrays

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Gamma-irradiated and non-irradiated RNA samples were amplified and hybridized using an Affymetrix Mouse Gene 2.0 ST microarray (Affymetrix, Santa Clara, CA, USA) according to manufacturer instructions. After scanning the arrays, differentially expressed probe sets were selected based on 2-fold changes relative to the control. DEGs were analyzed using a heatmap and grouped into early, medium-, and late-response genes based on the time post-IR exposure.
Bai H. (2021). "An Early Excessive Release of Cytokines by Ionizing Radiation Exposure in Macrophages Accentuates Inflammatory Disorders". Biomedical Journal of Scientific & Technical Research, 38(4).
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6

Microarray Analysis of Gene Methylation and Expression

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The potential mechanism was investigated in detail using Affymetrix microarrays analysis. In brief, the methylation of genes promoter were analyzed using Affymetrix Mouse Promoter 1.0R Array. Gene expression was analyzed by the Affymetrix Mouse Gene 2.0 ST microarrays. Microarray experiments and data analyses were carried out at the Gminix company (Shanghai, China) as reported previously [23 (link)]. Some genes were selected according to the highest fold change and verified with methylation-specific PCR (MSP) and real-time PCR.
Liu Y., Liu W.B., Liu K.J., Ao L., Zhong J.L., Cao J, & Liu J.Y. (2015). Effect of 50 Hz Extremely Low-Frequency Electromagnetic Fields on the DNA Methylation and DNA Methyltransferases in Mouse Spermatocyte-Derived Cell Line GC-2. BioMed Research International, 2015, 237183.
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7

Transcriptional Profiling of mNSC Subtypes

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RNA was extracted from three independently generated pools of mNSC expressing one of eGFP, MYBtr, MYB-QKI5, MYB-QKI6 or QKItr. Gene expression profiles were assayed using Affymetrix Mouse Gene 2.0 ST microarrays (Affymetrix, Santa Clara, CA). CEL files were RMA normalized24 . Comparative marker selection analysis25 was performed in GenePattern using default settings. Genes with p-value <0.05 and q-value <0.35 were considered significant. GSEA was performed using the C2 (CP) gene sets (MSigDB). Genesets with nominal p-values <0.05 were considered significant. The MYB-QKI signature was defined using the ClassNeighbours module of GenePattern (default settings).
Bandopadhayay P., Ramkissoon L.A., Jain P., Bergthold G., Wala J., Zeid R., Schumacher S.E., Urbanski L., O’Rourke R., Gibson W.J., Pelton K., Ramkissoon S.H., Han H.J., Zhu Y., Choudhari N., Silva A., Boucher K., Henn R.E., Kang Y.J., Knoff D., Paolella B.R., Gladden-Young A., Varlet P., Pages M., Horowitz P.M., Federation A., Malkin H., Tracy A., Seepo S., Ducar M., Hummelen P.V., Santi M., Buccoliero A.M., Scagnet M., Bowers D.C., Giannini C., Puget S., Hawkins C., Tabori U., Klekner A., Bognar L., Burger P.C., Eberhart C., Rodriguez F.J., Hill D.A., Mueller S., Haas-Kogan D.A., Phillips J.J., Santagata S., Stiles C.D., Bradner J.E., Jabado N., Goren A., Grill J., Ligon A.H., Goumnerova L., Waanders A.J., Storm P.B., Kieran M.W., Ligon K.L., Beroukhim R, & Resnick A.C. (2016). MYB-QKI rearrangements in Angiocentric Glioma drive tumorigenicity through a tripartite mechanism. Nature genetics, 48(3), 273-282.
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8

Microarray Analysis of Ubf Knockout

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RNA for expression microarray analysis was extracted by the acid phenol/guanidinium thiocyanate method [76] (link), and subsequently purified using the RNeasy Plus Mini kit (QIAGEN). Expression analysis was carried out using Affymetrix Mouse Gene 2.0 ST microarrays by the Genome Québec Innovation Centre (Montréal). Data analysis was performed using the Affymetrix Power tools version 1.14.4 and R (www.r-project.org) version 2.14.0. Firstly, data were normalized using RMA-sketch. Ubfwt/wt/Er-cre+/+ normalized gene expression was then subtracted from the corresponding Ubffl/fl/Er-cre+/+ timepoint before all the expressions were placed relative to time T0. We required a gene to be detected in at least one time point using a cutoff of 0.001 on the detection p-values obtained from the DABG algorithm (Affymetrix Power tools) to be used in the analysis.
Hamdane N., Stefanovsky V.Y., Tremblay M.G., Németh A., Paquet E., Lessard F., Sanij E., Hannan R, & Moss T. (2014). Conditional Inactivation of Upstream Binding Factor Reveals Its Epigenetic Functions and the Existence of a Somatic Nucleolar Precursor Body. PLoS Genetics, 10(8), e1004505.
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9

Transcriptional Profiling of mNSC Subtypes

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RNA was extracted from three independently generated pools of mNSC expressing one of eGFP, MYBtr, MYB-QKI5, MYB-QKI6 or QKItr. Gene expression profiles were assayed using Affymetrix Mouse Gene 2.0 ST microarrays (Affymetrix, Santa Clara, CA). CEL files were RMA normalized24 . Comparative marker selection analysis25 was performed in GenePattern using default settings. Genes with p-value <0.05 and q-value <0.35 were considered significant. GSEA was performed using the C2 (CP) gene sets (MSigDB). Genesets with nominal p-values <0.05 were considered significant. The MYB-QKI signature was defined using the ClassNeighbours module of GenePattern (default settings).
Bandopadhayay P., Ramkissoon L.A., Jain P., Bergthold G., Wala J., Zeid R., Schumacher S.E., Urbanski L., O’Rourke R., Gibson W.J., Pelton K., Ramkissoon S.H., Han H.J., Zhu Y., Choudhari N., Silva A., Boucher K., Henn R.E., Kang Y.J., Knoff D., Paolella B.R., Gladden-Young A., Varlet P., Pages M., Horowitz P.M., Federation A., Malkin H., Tracy A., Seepo S., Ducar M., Hummelen P.V., Santi M., Buccoliero A.M., Scagnet M., Bowers D.C., Giannini C., Puget S., Hawkins C., Tabori U., Klekner A., Bognar L., Burger P.C., Eberhart C., Rodriguez F.J., Hill D.A., Mueller S., Haas-Kogan D.A., Phillips J.J., Santagata S., Stiles C.D., Bradner J.E., Jabado N., Goren A., Grill J., Ligon A.H., Goumnerova L., Waanders A.J., Storm P.B., Kieran M.W., Ligon K.L., Beroukhim R, & Resnick A.C. (2016). MYB-QKI rearrangements in Angiocentric Glioma drive tumorigenicity through a tripartite mechanism. Nature genetics, 48(3), 273-282.
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