Sureprint g3 mouse ge 8 60k microarray kit

Manufactured by Agilent Technologies

Sourced in United States

The SurePrint G3 Mouse GE 8×60K Microarray Kit is a high-density microarray platform for gene expression profiling in mice. It features 60,000 probes that cover the majority of the mouse genome. The kit provides a comprehensive and accurate tool for analyzing gene expression patterns in mouse samples.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

SurePrint G3 Mouse GE 8 × 60K (2 citations) SurePrint G3 mouse GE microarray kit (2 citations) Mouse GE 8×60K Microarray Kit (2 citations)

8 protocols using sureprint g3 mouse ge 8 60k microarray kit

Gene Expression Microarray Analysis

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Gene expression microarray studies were carried out with the SurePrint G3 Mouse GE 8×60K Microarray Kit (Agilent Technologies, product number G4852A). Microarray data were deposited in the NCBI’s Gene Expression Omnibus (GEO accession number GSE83554). Microarrays were background corrected, normalized and statistically analysed with limma [54 (link)] with moderated t-test for significance of the factors (sex and experimental group) and the interaction between sex and treatments for both day 14 and day 28 samples. P-values were corrected for multiple comparisons with the Benjamini-Hochberg method. Genes were tested for enrichment in functional associations using the R package tmod [55 ] with the CERNO test with Benjamini-Hochberg correction. Detailed R scripts used in the analysis are available upon request.

Beigier-Bompadre M., Montagna G.N., Kühl A.A., Lozza L., Weiner J I.I.I., Kupz A., Vogelzang A., Mollenkopf H.J., Löwe D., Bandermann S., Dorhoi A., Brinkmann V., Matuschewski K, & Kaufmann S.H. (2017). Mycobacterium tuberculosis infection modulates adipose tissue biology. PLoS Pathogens, 13(10), e1006676.

+ Open protocol

+ Expand

Microarray Transcriptional Profiling of Mouse Colon

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was isolated using the protocol described above. RNA integrity was verified using a Bioanalyser 2100 with RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA, USA). Transcriptional profiling was performed on mouse colon samples using the SurePrint G3 Mouse GE 8 × 60 K Microarray kit (design ID: 028005, Agilent Technologies). Cyanine-3 (Cy3)-labeled cRNAs were prepared with 100 ng of total RNA using a One-Color Low Input Quick Amp Labeling kit (Agilent Technologies), following the recommended protocol. The specific activities and cRNA yields were determined by using a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/μg of cRNA) were fragmented at 60 °C for 30 min and hybridized to the microarrays for 17 h at 65 °C in a rotating hybridization oven (Agilent Technologies). After hybridization, the microarrays were washed and then immediately dried. After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies) at a resolution of 3 μm and a dynamic range of 20 bits. The resulting TIFF images were analyzed using the Feature Extraction Software v10.7.3.1 (Agilent Technologies) according to the GE1_107_Sep09 protocol. The microarray data were submitted to GEO under accession number GSE67577.

Lamas B., Richard M.L., Leducq V., Pham H.P., Michel M.L., Da Costa G., Bridonneau C., Jegou S., Hoffmann T.W., Natividad J.M., Brot L., Taleb S., Couturier-Maillard A., Nion-Larmurier I., Merabtene F., Seksik P., Bourrier A., Cosnes J., Ryffel B., Beaugerie L., Launay J.M., Langella P., Xavier R.J, & Sokol H. (2016). CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nature medicine, 22(6), 598-605.

+ Open protocol

+ Expand

Transcriptional Profiling of Mouse Colon

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was isolated using the protocol described above. RNA integrity was verified using a Bioanalyser2100 with RNA6000 Nano chips (Agilent Technologies). Transcriptional profiling was performed on mouse colon samples using the SurePrint G3 Mouse GE8 × 60 K Microarray kit (design ID: 028005, Agilent Technologies). Cyanine-3 (Cy3)-labeled cRNAs were prepared with 100 ng of total RNA using a One-Color Low Input Quick Amp Labeling kit (Agilent Technologies). The specific activities and cRNA yields were determined by using a NanoDrop ND-1000 (Thermo Fisher Scientific). For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/μg of cRNA) was fragmented at 60 °C for 30 min and hybridized to the microarrays for 17 h at 65 °C in a rotating hybridization oven (Agilent Technologies). After hybridization, the microarrays were washed and then immediately dried. After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies) at a resolution of 3 μm and a dynamic range of 20 bits. The resulting TIFF images were analyzed using the Feature Extraction Software v10.7.3.1 (Agilent Technologies) according to the GE1_107_Sep09 protocol. The microarray data were submitted to GEO under accession number.

Danne C., Lamas B., Lavelle A., Michel M.L., Da Costa G., Pham H.P., Lefevre A., Bridonneau C., Bredon M., Planchais J., Straube M., Emond P., Langella P, & Sokol H. (2024). Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9−/− mice to colitis. Microbiome, 12, 76.

+ Open protocol

+ Expand

Microarray analysis of mRNA expression

Check if the same lab product or an alternative is used in the 5 most similar protocols

mRNA expression in YTN2, YTN3, YTN5, and YTN16 cell lines was evaluated by microarray. Total RNA was isolated using an AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers’ protocols. Gene expression was evaluated using SurePrint G3 Mouse GE 8 × 60K Microarray Kit (Agilent Technologies, Santa Clara, CA, USA). Datasets were normalized using the Subio Platform (Subio Inc., Kagoshima, Japan) as follows: (i) signals were aligned at the 75th percentile; (ii) weak signals <4.0 were replaced with the value 4.0; (iii) fold changes to mean values were converted to log₂. Probes were excluded if their values were 0 for all samples.

Yamamoto M., Nomura S., Hosoi A., Nagaoka K., Iino T., Yasuda T., Saito T., Matsushita H., Uchida E., Seto Y., Goldenring J.R., Kakimi K., Tatematsu M, & Tsukamoto T. (2018). Established gastric cancer cell lines transplantable into C57BL/6 mice show fibroblast growth factor receptor 4 promotion of tumor growth. Cancer Science, 109(5), 1480-1492.

+ Open protocol

+ Expand

Profiling Tumor Cell Transcriptomes

Check if the same lab product or an alternative is used in the 5 most similar protocols

Total RNA was isolated from YTN2 and YTN16 tumor cells. Gene expressions of tumor cell lines were evaluated using SurePrint G3 Mouse GE 8×60K Microarray Kit (Agilent Technologies, Santa Clara, California, USA). Fold changes to mean values were converted to log₂. Raw data were deposited to GEO database (accession number GSE153231).

Nagaoka K., Shirai M., Taniguchi K., Hosoi A., Sun C., Kobayashi Y., Maejima K., Fujita M., Nakagawa H., Nomura S, & Kakimi K. (2020). Deep immunophenotyping at the single-cell level identifies a combination of anti-IL-17 and checkpoint blockade as an effective treatment in a preclinical model of data-guided personalized immunotherapy. Journal for Immunotherapy of Cancer, 8(2), e001358.

+ Open protocol

+ Expand

Gene Expression Analysis of Liver Tissues

Check if the same lab product or an alternative is used in the 5 most similar protocols

Gene expression profiles of tumors and adjacent non-tumor liver tissues from 3 HF- and 5 HFHC-fed mice (same samples as for exome sequencing) were analyzed using the SurePrint G3 Mouse GE 8 × 60 K Microarray Kit (Agilent Technologies, Palo Alto, CA), which contained 39,430 Entrez Gene RNAs. In brief, RNA was extracted using Qiazol reagent (Qiagen, Valencia, CA). The cDNA probes were prepared from 5 μg of total RNA labeled with Cy5-dUTP (red) or Cy3-dUTP (green) by reverse transcription (Amersham Biosciences, Piscataway, NJ). Two labeled cDNAs were competitively hybridized to the microarray. Signal intensities were analyzed using a SureScan microarray scanner (Agilent Technologies). Array data were presented as log base 2 ratio of the Cy5/Cy3 signals. Gene expression patterns between HF and HFHC groups were compared using unsupervised hierarchical clustering.

Liang J.Q., Teoh N., Xu L., Pok S., Li X., Chu E.S., Chiu J., Dong L., Arfianti E., Haigh W.G., Yeh M.M., Ioannou G.N., Sung J.J., Farrell G, & Yu J. (2018). Dietary cholesterol promotes steatohepatitis related hepatocellular carcinoma through dysregulated metabolism and calcium signaling. Nature Communications, 9, 4490.

+ Open protocol

+ Expand

Microarray Analysis of AAI-Induced Liver Gene Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols

The microarray data are available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101530. For microarray hybridization, total liver RNA was isolated from four groups of animals, AAI- or corn oil-treated female and male C57BL/6 wild type mice, using RNeasy Mini Kits (Qiagen Inc., Valencia, CA, USA). In each group, pooled RNA was prepared by mixing the same amount total RNA from 5 mice. The microarray hybridization was performed by Welgene Biotech, Co., Ltd. (Taipei, Taiwan) using SurePrint G3 Mouse GE 8 × 60 K Microarray kit (Agilent Technologies, CA, USA). Genes that were significantly up- or downregulated by more than 2-fold were subjected to GO enrichment analysis using the cluster Profiler software. Normalized intensities were transformed to gene expression log₂ ratios between the control and AAI treatment groups. The genes with log₂ ratio ≥ 1 or ≤ −1 and p-value < 0.05 were collected for further analysis. The analyses of gene expression patterns, canonical pathways and directional predictions were generated through the use of Ingenuity Pathway Analysis (IPA^®, QIAGEN Inc., https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/).

Chang M.M., Lin C.N., Fang C.C., Chen M., Liang P.I., Li W.M., Yeh B.W., Cheng H.C., Huang B.M., Wu W.J, & Chen Y.M. (2018). Glycine N-methyltransferase inhibits aristolochic acid nephropathy by increasing CYP3A44 and decreasing NQO1 expression in female mouse hepatocytes. Scientific Reports, 8, 6960.

+ Open protocol

+ Expand

Hepatic Gene Expression Profiling in NASH

Check if the same lab product or an alternative is used in the 5 most similar protocols

Cyanine 3 (Cy3)-labeled complementary RNA (cRNA) was synthesized from 150 ng of liver total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer's instructions. The synthesized Cy3-labeled cRNA was hybridized with a microarray slide (SurePrint G3 Mouse GE 8×60 K Microarray Kit; Agilent Technologies) at 65°C for 17 h. After hybridization, the slides were washed with the Gene Expression Wash Pack (Agilent Technologies). Cy3 fluorescence signals were detected with a SureScan Microarray Scanner (Agilent Technologies). Fluorescent images were quantified using Feature Extraction software (Agilent Technologies). GeneSpring 14.5 software (Agilent Technologies) was used for normalization and expression analysis. Genes showing an expression level fold change >1.5 or higher were analyzed by comparing the control and NASH groups. Function prediction was performed using Ingenuity Pathway Analysis (IPA) (Qiagen).

Matsumoto K., Kato Y., Hayashi M., Miura R., Monzen S, & Chiba M. (2022). Hepatic gene expression and functional changes associated with nonalcoholic steatohepatitis. Molecular Medicine Reports, 26(5), 325.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!