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sample preparation and microarray hybridization protocols  (Arraystar inc)

 
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    Structured Review

    Arraystar inc sample preparation and microarray hybridization protocols
    Sample Preparation And Microarray Hybridization Protocols, supplied by Arraystar inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/microarray+protocols/microarray+hybridization/pm39695693-64-4-13
    Average 90 stars, based on 1 article reviews
    sample preparation and microarray hybridization protocols - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Sample Prep:

    Article Title: Circular RNA circPHLPP2 promotes tumor growth and anti-PD-1 resistance through binding ILF3 to regulate IL36γ transcription in colorectal cancer.
    Article Snippet: .. All sample preparation and microarray hybridization were performed according to the protocols of Arraystar (Rockville, MD, USA). .. Briefly, circRNAs were enriched by removing linear RNAs with Rnase R. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA with a random priming method (Arraystar Super RNA Labeling Kit).

    Article Title: Circular RNA circTATDN3 promotes the Warburg effect and proliferation in colorectal cancer.
    Article Snippet: As one of the key metabolic enzymes in the glycolytic pathway, lactate dehydrogenase A (LDHA) might be linked to tumor proliferation by driving the Warburg effect.. Circular RNAs (circRNAs) are widely implicated in tumor progression.. Here, we report that circTATDN3, a circular RNA that interacts with LDHA, plays a critical role in proliferation and energy metabolism in CRC.

    Article Title: METTL3-m6A methylation inhibits the proliferation and viability of type II alveolar epithelial cells in acute lung injury by enhancing the stability and translation efficiency of Pten mRNA.
    Article Snippet: The total RNA of each sample was quantified by the NanoDrop ND-1000 spectrophotometer, and the integrity of RNA was evaluated by the Bioanalyzer 2100 or Mops electrophoresis. .. Following Arraystar’s standard protocol, sample preparation and microarray hybridization were executed. ..

    Article Title: CircXPO6 promotes breast cancer progression through competitively inhibiting the ubiquitination degradation of c-Myc.
    Article Snippet: The number of breast cancer (BC) patients is increasing year by year, which is severely endangering to human life and health. c-Myc is a transcription factor, studies have shown that it is a very significant factor in tumor progression, but how it is regulated in BC is still not well understood.. Here, we used the RIP microarray sequencing to confirm circXPO6, which had a high affinity with c-Myc and highly expressed in triple-negative breast cancer (TNBC) tissues and cells.. CircXPO6 overexpression promoted tumor growth in vivo and in vitro.

    Article Title: m6A demethylase Fto inhibited macrophage activation and glycolysis in diabetic nephropathy via m6A/Npas2/Hif‐1α axis
    Article Snippet: .. The sample preparation and microarray hybridization were conducted following the standard protocols provided by Arraystar. .. Acquired array images were analyzed using Agilent Feature Extraction software.

    Article Title: METTL16 promotes corneal nerve regeneration in diabetic corneal neuropathy.
    Article Snippet: As a leading ocular disorder caused by diabetes mellitus, diabetic corneal neuropathy (DCN) is characterized by decreased corneal sensation, ocular irritation, delayed corneal wound healing and corneal neuropathic pain.. Several researchers including us previously evidenced that DCN is regulated by several transcriptional and/or epigenetic factors.. However, the role of N6-methyladenosine (m6A) modification, the most common internal modification in eukaryotic RNAs, in the pathogenesis of DCN remains largely unexplored.

    Article Title: m6A demethylase Fto inhibited macrophage activation and glycolysis in diabetic nephropathy via m6A/Npas2/Hif‐1α axis
    Article Snippet: .. The sample preparation and microarray hybridization were conducted following the standard protocols provided by Arraystar. .. Acquired array images were analyzed using Agilent Feature Extraction software.

    Microarray:

    Article Title: Circular RNA circPHLPP2 promotes tumor growth and anti-PD-1 resistance through binding ILF3 to regulate IL36γ transcription in colorectal cancer.
    Article Snippet: .. All sample preparation and microarray hybridization were performed according to the protocols of Arraystar (Rockville, MD, USA). .. Briefly, circRNAs were enriched by removing linear RNAs with Rnase R. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA with a random priming method (Arraystar Super RNA Labeling Kit).

    Article Title: Circular RNA circTATDN3 promotes the Warburg effect and proliferation in colorectal cancer.
    Article Snippet: As one of the key metabolic enzymes in the glycolytic pathway, lactate dehydrogenase A (LDHA) might be linked to tumor proliferation by driving the Warburg effect.. Circular RNAs (circRNAs) are widely implicated in tumor progression.. Here, we report that circTATDN3, a circular RNA that interacts with LDHA, plays a critical role in proliferation and energy metabolism in CRC.

    Article Title: METTL3-m6A methylation inhibits the proliferation and viability of type II alveolar epithelial cells in acute lung injury by enhancing the stability and translation efficiency of Pten mRNA.
    Article Snippet: The total RNA of each sample was quantified by the NanoDrop ND-1000 spectrophotometer, and the integrity of RNA was evaluated by the Bioanalyzer 2100 or Mops electrophoresis. .. Following Arraystar’s standard protocol, sample preparation and microarray hybridization were executed. ..

    Article Title: CircXPO6 promotes breast cancer progression through competitively inhibiting the ubiquitination degradation of c-Myc.
    Article Snippet: The number of breast cancer (BC) patients is increasing year by year, which is severely endangering to human life and health. c-Myc is a transcription factor, studies have shown that it is a very significant factor in tumor progression, but how it is regulated in BC is still not well understood.. Here, we used the RIP microarray sequencing to confirm circXPO6, which had a high affinity with c-Myc and highly expressed in triple-negative breast cancer (TNBC) tissues and cells.. CircXPO6 overexpression promoted tumor growth in vivo and in vitro.

    Article Title: m6A demethylase Fto inhibited macrophage activation and glycolysis in diabetic nephropathy via m6A/Npas2/Hif‐1α axis
    Article Snippet: .. The sample preparation and microarray hybridization were conducted following the standard protocols provided by Arraystar. .. Acquired array images were analyzed using Agilent Feature Extraction software.

    Article Title: METTL16 promotes corneal nerve regeneration in diabetic corneal neuropathy.
    Article Snippet: As a leading ocular disorder caused by diabetes mellitus, diabetic corneal neuropathy (DCN) is characterized by decreased corneal sensation, ocular irritation, delayed corneal wound healing and corneal neuropathic pain.. Several researchers including us previously evidenced that DCN is regulated by several transcriptional and/or epigenetic factors.. However, the role of N6-methyladenosine (m6A) modification, the most common internal modification in eukaryotic RNAs, in the pathogenesis of DCN remains largely unexplored.

    Article Title: m6A demethylase Fto inhibited macrophage activation and glycolysis in diabetic nephropathy via m6A/Npas2/Hif‐1α axis
    Article Snippet: .. The sample preparation and microarray hybridization were conducted following the standard protocols provided by Arraystar. .. Acquired array images were analyzed using Agilent Feature Extraction software.

    Hybridization:

    Article Title: Circular RNA circPHLPP2 promotes tumor growth and anti-PD-1 resistance through binding ILF3 to regulate IL36γ transcription in colorectal cancer.
    Article Snippet: .. All sample preparation and microarray hybridization were performed according to the protocols of Arraystar (Rockville, MD, USA). .. Briefly, circRNAs were enriched by removing linear RNAs with Rnase R. The enriched circRNAs were then amplified and transcribed into fluorescent cRNA with a random priming method (Arraystar Super RNA Labeling Kit).

    Article Title: Circular RNA circTATDN3 promotes the Warburg effect and proliferation in colorectal cancer.
    Article Snippet: As one of the key metabolic enzymes in the glycolytic pathway, lactate dehydrogenase A (LDHA) might be linked to tumor proliferation by driving the Warburg effect.. Circular RNAs (circRNAs) are widely implicated in tumor progression.. Here, we report that circTATDN3, a circular RNA that interacts with LDHA, plays a critical role in proliferation and energy metabolism in CRC.

    Article Title: METTL3-m6A methylation inhibits the proliferation and viability of type II alveolar epithelial cells in acute lung injury by enhancing the stability and translation efficiency of Pten mRNA.
    Article Snippet: The total RNA of each sample was quantified by the NanoDrop ND-1000 spectrophotometer, and the integrity of RNA was evaluated by the Bioanalyzer 2100 or Mops electrophoresis. .. Following Arraystar’s standard protocol, sample preparation and microarray hybridization were executed. ..

    Article Title: CircXPO6 promotes breast cancer progression through competitively inhibiting the ubiquitination degradation of c-Myc.
    Article Snippet: The number of breast cancer (BC) patients is increasing year by year, which is severely endangering to human life and health. c-Myc is a transcription factor, studies have shown that it is a very significant factor in tumor progression, but how it is regulated in BC is still not well understood.. Here, we used the RIP microarray sequencing to confirm circXPO6, which had a high affinity with c-Myc and highly expressed in triple-negative breast cancer (TNBC) tissues and cells.. CircXPO6 overexpression promoted tumor growth in vivo and in vitro.

    Article Title: m6A demethylase Fto inhibited macrophage activation and glycolysis in diabetic nephropathy via m6A/Npas2/Hif‐1α axis
    Article Snippet: .. The sample preparation and microarray hybridization were conducted following the standard protocols provided by Arraystar. .. Acquired array images were analyzed using Agilent Feature Extraction software.

    Article Title: METTL16 promotes corneal nerve regeneration in diabetic corneal neuropathy.
    Article Snippet: As a leading ocular disorder caused by diabetes mellitus, diabetic corneal neuropathy (DCN) is characterized by decreased corneal sensation, ocular irritation, delayed corneal wound healing and corneal neuropathic pain.. Several researchers including us previously evidenced that DCN is regulated by several transcriptional and/or epigenetic factors.. However, the role of N6-methyladenosine (m6A) modification, the most common internal modification in eukaryotic RNAs, in the pathogenesis of DCN remains largely unexplored.

    Article Title: m6A demethylase Fto inhibited macrophage activation and glycolysis in diabetic nephropathy via m6A/Npas2/Hif‐1α axis
    Article Snippet: .. The sample preparation and microarray hybridization were conducted following the standard protocols provided by Arraystar. .. Acquired array images were analyzed using Agilent Feature Extraction software.



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    Significant genes of each signature were represented according to their gene function and specific role in the cell, localization and type of interaction between them. Node border color refers to cell localization, node shape to general function and node color to specific function in the cell. Edge color refers to physical interactions, biochemical interactions or to both; when not specified, a functional interaction is assumed. Upstream arrow (red) means up-regulation versus the other categories, and downstream arrow (blue) means down-regulation versus the other categories. <t>Microarray</t> data values represented here are shown in and .
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    <t>Microarray</t> analysis of hUCB-MSCs from the normal and preeclampsia groups. (a) The scatter plot and MA plot show the DEGs between N3 and P3 cells. In the scatter plot, the median line indicates no difference in signal intensity between the two groups. The upper gray line indicates a twofold higher signal intensity, and the lower gray line indicates a twofold lower signal intensity for hUCB-MSCs from the preeclampsia group as compared to the normal group. In the MA plot, the median line represents N signal/P signal = 1. The upper gray line represents N signal/P signal = 2, and the lower gray line represents N signal/P signal = 0.5. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: hUCB-MSCs at passage 3, preeclampsia. (b, c) Hierarchical cluster analysis of differentially expressed genes (DEGs) between N3 and P3 cells. Red represents upregulated gene clusters, and green represents downregulated gene clusters. The panels show genes up- or downregulated twofold (b) or fourfold (c) in P3 (versus N3) cells. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: early hUCB-MSCs at passage 3, preeclampsia.
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    Image Search Results


    Comparison of mRNA expression in seven candidate genes between TPCH test (n = 30, microarray) and training set (n = 62 qRT-PCR data), with two public microarray datasets of lung tissue samples (Spira et al , , n = 34; and Golpon et al , n = 10) . Fold change represents mean expression ratio of moderate versus mild emphysema (TPCH training set), severe/mild emphysema versus normal (Spira et al ), or severe emphysema versus normal samples (Golpon et al ). The absence of a bar indicates the gene was not represented on the microarray platform.

    Journal: Respiratory Research

    Article Title: Expression profiling identifies genes involved in emphysema severity

    doi: 10.1186/1465-9921-10-81

    Figure Lengend Snippet: Comparison of mRNA expression in seven candidate genes between TPCH test (n = 30, microarray) and training set (n = 62 qRT-PCR data), with two public microarray datasets of lung tissue samples (Spira et al , , n = 34; and Golpon et al , n = 10) . Fold change represents mean expression ratio of moderate versus mild emphysema (TPCH training set), severe/mild emphysema versus normal (Spira et al ), or severe emphysema versus normal samples (Golpon et al ). The absence of a bar indicates the gene was not represented on the microarray platform.

    Article Snippet: Lung and universal reference RNA (Stratagene, La Jolla, CA, USA) was reverse transcribed, labeled with Cy5 and Cy3 (Amersham/GE Healthcare, Buckinghamshire, England) respectively and co-hybridized onto a 22K Operon V2.1 Human Genome Oligo Microarray chip http://www.operon.com containing 21,329 70 mer probes representing ~14,200 named transcripts printed by the British Columbia Gene Array Facility http://www.microarray.prostatecentre.com .

    Techniques: Expressing, Microarray, Quantitative RT-PCR

    Significant genes of each signature were represented according to their gene function and specific role in the cell, localization and type of interaction between them. Node border color refers to cell localization, node shape to general function and node color to specific function in the cell. Edge color refers to physical interactions, biochemical interactions or to both; when not specified, a functional interaction is assumed. Upstream arrow (red) means up-regulation versus the other categories, and downstream arrow (blue) means down-regulation versus the other categories. Microarray data values represented here are shown in and .

    Journal: PLoS ONE

    Article Title: Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development

    doi: 10.1371/journal.pone.0062135

    Figure Lengend Snippet: Significant genes of each signature were represented according to their gene function and specific role in the cell, localization and type of interaction between them. Node border color refers to cell localization, node shape to general function and node color to specific function in the cell. Edge color refers to physical interactions, biochemical interactions or to both; when not specified, a functional interaction is assumed. Upstream arrow (red) means up-regulation versus the other categories, and downstream arrow (blue) means down-regulation versus the other categories. Microarray data values represented here are shown in and .

    Article Snippet: Following ‘One-Color Microarray-Based Gene Expression Analysis’ protocol Version 5.7 (Agilent p/n G4140-90040), 3 µg of labelled cRNA was hybridised with the Whole Human Genome Oligo Microarray Kit (Agilent p/n G2519F-014850) containing 41,000+ unique human genes and transcripts.

    Techniques: Functional Assay, Microarray

    Microarray analysis of hUCB-MSCs from the normal and preeclampsia groups. (a) The scatter plot and MA plot show the DEGs between N3 and P3 cells. In the scatter plot, the median line indicates no difference in signal intensity between the two groups. The upper gray line indicates a twofold higher signal intensity, and the lower gray line indicates a twofold lower signal intensity for hUCB-MSCs from the preeclampsia group as compared to the normal group. In the MA plot, the median line represents N signal/P signal = 1. The upper gray line represents N signal/P signal = 2, and the lower gray line represents N signal/P signal = 0.5. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: hUCB-MSCs at passage 3, preeclampsia. (b, c) Hierarchical cluster analysis of differentially expressed genes (DEGs) between N3 and P3 cells. Red represents upregulated gene clusters, and green represents downregulated gene clusters. The panels show genes up- or downregulated twofold (b) or fourfold (c) in P3 (versus N3) cells. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: early hUCB-MSCs at passage 3, preeclampsia.

    Journal: Stem Cells International

    Article Title: Comparative Analysis of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells between Preeclampsia and Normal Pregnant Women

    doi: 10.1155/2020/8403192

    Figure Lengend Snippet: Microarray analysis of hUCB-MSCs from the normal and preeclampsia groups. (a) The scatter plot and MA plot show the DEGs between N3 and P3 cells. In the scatter plot, the median line indicates no difference in signal intensity between the two groups. The upper gray line indicates a twofold higher signal intensity, and the lower gray line indicates a twofold lower signal intensity for hUCB-MSCs from the preeclampsia group as compared to the normal group. In the MA plot, the median line represents N signal/P signal = 1. The upper gray line represents N signal/P signal = 2, and the lower gray line represents N signal/P signal = 0.5. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: hUCB-MSCs at passage 3, preeclampsia. (b, c) Hierarchical cluster analysis of differentially expressed genes (DEGs) between N3 and P3 cells. Red represents upregulated gene clusters, and green represents downregulated gene clusters. The panels show genes up- or downregulated twofold (b) or fourfold (c) in P3 (versus N3) cells. N3: hUCB-MSCs at passage 3, normal pregnancy; P3: early hUCB-MSCs at passage 3, preeclampsia.

    Article Snippet: The standard protocol used for sample preparation and microarray processing is available from Agilent Technologies.

    Techniques: Microarray

    Network analysis of senescence-related differentially expressed genes (DEGs). Genes represented by a large circle are senescence-related differentially expressed genes (DEGs) obtained from microarray analysis. Red ones are genes related with senescence as well as cell aging. FDR: false discovery rate.

    Journal: Stem Cells International

    Article Title: Comparative Analysis of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells between Preeclampsia and Normal Pregnant Women

    doi: 10.1155/2020/8403192

    Figure Lengend Snippet: Network analysis of senescence-related differentially expressed genes (DEGs). Genes represented by a large circle are senescence-related differentially expressed genes (DEGs) obtained from microarray analysis. Red ones are genes related with senescence as well as cell aging. FDR: false discovery rate.

    Article Snippet: The standard protocol used for sample preparation and microarray processing is available from Agilent Technologies.

    Techniques: Microarray