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labeling of total rna, microarray processing data analysis, and normalization  (OakLabs Inc)

 
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    Structured Review

    OakLabs Inc labeling of total rna, microarray processing data analysis, and normalization
    Labeling Of Total Rna, Microarray Processing Data Analysis, And Normalization, supplied by OakLabs 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/rna+microarray+data/microarray+analysis/pmc10921668-76-3-13
    Average 90 stars, based on 1 article reviews
    labeling of total rna, microarray processing data analysis, and normalization - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Purification:

    Article Title: Genome-wide strategies reveal target genes of Npas4l associated with vascular development in zebrafish.
    Article Snippet: .. After purification with RNA Clean and Concentrator kit (Zymo Research), the microarray analysis was performed by Oaklabs (Hennigsdorf, Germany). .. A 8 × 60 K zebrafish expression array (XS -5090; Agilent 60-mer SurePrint technology) analysis was performed according to manufacturer's protocol.

    Article Title: Transcriptomic and Proteomic Analysis of Clear Cell Foci (CCF) in the Human Non-Cirrhotic Liver Identifies Several Differentially Expressed Genes and Proteins with Functions in Cancer Cell Biology and Glycogen Metabolism
    Article Snippet: RNA was quantified using a Nanodrop 8000 (Thermo Scientific, Waltham, MA, USA) and RNA quality was assessed using a Bioanalyzer (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA) (Supplementary Table S1). .. Processing of purified RNA for microarray analysis and the microarray analysis were carried out at OakLabs (Hennigsdorf, Germany) according to their standard procedures. .. Briefly, RNA concentrations were between 17 and 66 ng/μL in volumes of 30 or 40 μL H2O with integrity numbers (RIN, Bioanalyzer, Agilent Technologies, USA) between 6.3 and 7.9 (Supplementary Table S1).

    Article Title: Transcriptomic and Proteomic analysis of clear cell foci (CCF) in the human non-cirrhotic liver identifies several differentially expressed genes and proteins with functions in cancer cell biology and glycogen metabolism
    Article Snippet: .. Processing of purified RNA for microarray analysis and microarray analysis was carried out at OakLabs (Hennigsdorf, Germany) according to their standard procedures. ..

    Article Title: The molecular and physiological consequences of cold plasma treatment in murine skin and its barrier function.
    Article Snippet: .. After purification, the Cy3-573 cRNA was fragmented and hybridized on the microarray chip using the Gene 574 Expression Hybridization Kit (customized 8x60K microarray chip; OakLabs, Berlin, 575 Germany) 17 h at 65 °C. .. The chips were then washed using the Gene Expression Wash 576 Buffer Kit (all from Agilent, Waldbronn, Germany), dried, and scanned using an Agilent 577 SureScan device.

    Microarray:

    Article Title: Genome-wide strategies reveal target genes of Npas4l associated with vascular development in zebrafish.
    Article Snippet: .. After purification with RNA Clean and Concentrator kit (Zymo Research), the microarray analysis was performed by Oaklabs (Hennigsdorf, Germany). .. A 8 × 60 K zebrafish expression array (XS -5090; Agilent 60-mer SurePrint technology) analysis was performed according to manufacturer's protocol.

    Article Title: Transcriptomic and Proteomic Analysis of Clear Cell Foci (CCF) in the Human Non-Cirrhotic Liver Identifies Several Differentially Expressed Genes and Proteins with Functions in Cancer Cell Biology and Glycogen Metabolism
    Article Snippet: RNA was quantified using a Nanodrop 8000 (Thermo Scientific, Waltham, MA, USA) and RNA quality was assessed using a Bioanalyzer (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA, USA) (Supplementary Table S1). .. Processing of purified RNA for microarray analysis and the microarray analysis were carried out at OakLabs (Hennigsdorf, Germany) according to their standard procedures. .. Briefly, RNA concentrations were between 17 and 66 ng/μL in volumes of 30 or 40 μL H2O with integrity numbers (RIN, Bioanalyzer, Agilent Technologies, USA) between 6.3 and 7.9 (Supplementary Table S1).

    Article Title: Transcriptomic and Proteomic analysis of clear cell foci (CCF) in the human non-cirrhotic liver identifies several differentially expressed genes and proteins with functions in cancer cell biology and glycogen metabolism
    Article Snippet: .. Processing of purified RNA for microarray analysis and microarray analysis was carried out at OakLabs (Hennigsdorf, Germany) according to their standard procedures. ..

    Article Title: A regeneration-triggered metabolic adaptation is necessary for cell identity transitions and cell cycle re-entry to support blastema formation and bone regeneration
    Article Snippet: .. Samples were maintained at –80 °C until sent to OakLabs GmbH (Henningsdorf, Germany) for cDNA generation, microarray chip set up and data analysis. .. To compare the transcriptome profiles of mature OB in homeostasis to OB during dedifferentiation, a genome- wide gene expression profiling was set up using the 8x60 K ArrayXS Zebrafish platform by Agilent and performed by OakLabs GmbH (Henningsdorf, Germany).

    Article Title: Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativa L.).
    Article Snippet: Iron toxicity frequently affects lowland rice and leads to oxidative stress via the Fenton reaction.. Tolerance mechanisms were investigated in contrasting genotypes: the intolerant IR29 and the tolerant recombinant inbred line FL483.. Seedlings were exposed to 1000mgL ferrous iron, and the regulation of genes involved in three hypothetical tolerance mechanisms was investigated (I) Iron uptake, partitioning and storage.

    Article Title: Modulation of early gene expression responses to water deprivation stress by the E3 ubiquitin ligase ATL80: implications for retrograde signaling interplay
    Article Snippet: RNA was isolated from frozen seedlings using a RNeasy plant mini kit (Qiagen; Hilden, Germany). .. Labeling of total RNA, microarray processing data analysis, and normalization was performed by Oaklabs GmbH (Hennigsdorf, Germany). .. An ArrayXS Arabidopsis v2 (XS-5010) microarray in the Agilent 8 × 60 K format representing 30,541 Arabidopsis genes was used.

    Article Title: The molecular and physiological consequences of cold plasma treatment in murine skin and its barrier function.
    Article Snippet: .. After purification, the Cy3-573 cRNA was fragmented and hybridized on the microarray chip using the Gene 574 Expression Hybridization Kit (customized 8x60K microarray chip; OakLabs, Berlin, 575 Germany) 17 h at 65 °C. .. The chips were then washed using the Gene Expression Wash 576 Buffer Kit (all from Agilent, Waldbronn, Germany), dried, and scanned using an Agilent 577 SureScan device.

    Article Title: Molecular basis for neofunctionalization of duplicated E3 ubiquitin ligases underlying adaptation to drought tolerance in Arabidopsis thaliana.
    Article Snippet: This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record.. Please cite this article as doi: 10.1111/TPJ.14938 This article is protected by copyright.. All rights reserved

    Hybridization:

    Article Title: Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativa L.).
    Article Snippet: Iron toxicity frequently affects lowland rice and leads to oxidative stress via the Fenton reaction.. Tolerance mechanisms were investigated in contrasting genotypes: the intolerant IR29 and the tolerant recombinant inbred line FL483.. Seedlings were exposed to 1000mgL ferrous iron, and the regulation of genes involved in three hypothetical tolerance mechanisms was investigated (I) Iron uptake, partitioning and storage.

    Article Title: The molecular and physiological consequences of cold plasma treatment in murine skin and its barrier function.
    Article Snippet: .. After purification, the Cy3-573 cRNA was fragmented and hybridized on the microarray chip using the Gene 574 Expression Hybridization Kit (customized 8x60K microarray chip; OakLabs, Berlin, 575 Germany) 17 h at 65 °C. .. The chips were then washed using the Gene Expression Wash 576 Buffer Kit (all from Agilent, Waldbronn, Germany), dried, and scanned using an Agilent 577 SureScan device.

    Labeling:

    Article Title: Modulation of early gene expression responses to water deprivation stress by the E3 ubiquitin ligase ATL80: implications for retrograde signaling interplay
    Article Snippet: RNA was isolated from frozen seedlings using a RNeasy plant mini kit (Qiagen; Hilden, Germany). .. Labeling of total RNA, microarray processing data analysis, and normalization was performed by Oaklabs GmbH (Hennigsdorf, Germany). .. An ArrayXS Arabidopsis v2 (XS-5010) microarray in the Agilent 8 × 60 K format representing 30,541 Arabidopsis genes was used.

    Expressing:

    Article Title: The molecular and physiological consequences of cold plasma treatment in murine skin and its barrier function.
    Article Snippet: .. After purification, the Cy3-573 cRNA was fragmented and hybridized on the microarray chip using the Gene 574 Expression Hybridization Kit (customized 8x60K microarray chip; OakLabs, Berlin, 575 Germany) 17 h at 65 °C. .. The chips were then washed using the Gene Expression Wash 576 Buffer Kit (all from Agilent, Waldbronn, Germany), dried, and scanned using an Agilent 577 SureScan device.



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    FIGURE 3 Upregulation of IL4I1 infers an unfavorable prognosis for glioma. (A) Representative images (left) and quantification (right) showing IL4I1 staining of normal brain tissues (n = 16) and glioma tissues (n = 37) with the anti-IL4I1 antibody, with scale bars 100 µm (up) and 20 µm (down). (B–D) Kaplan– Meier analysis for OS based on three glioma datasets <t>(CGGA,</t> Rembrandt, and GSE16011). (E–G) ROC curves of OS in CGGA, Rembrandt, and GSE16011 datasets. (H, I) Univariate and multivariate analyses of OS based on CGGA-glioma datasets. ****p < 0.0001.
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    Image Search Results


    Protein candidates proposed as potential prognostic markers for high and low risk of tumour recurrence in CRC-II patients.

    Journal: BJC Reports

    Article Title: Protein prognostic biomarkers in stage II colorectal cancer: implications for post-operative management

    doi: 10.1038/s44276-024-00043-z

    Figure Lengend Snippet: Protein candidates proposed as potential prognostic markers for high and low risk of tumour recurrence in CRC-II patients.

    Article Snippet: Candidate selection can be made via informatics approaches [ , ], DNA/RNA microarray data analyses [ ], protein involvement in key biochemical processes [ ], being differentially expressed through mass spectrometry (MS) analysis [ ], Olink proteomics assays [ ] or SomaLogic assays [ ] or as a diagnostic or prognostic marker for other tumour types [ ].

    Techniques: Biomarker Discovery, Expressing, Marker, Reverse Transcription Polymerase Chain Reaction, Microarray, Over Expression

    FIGURE 3 Upregulation of IL4I1 infers an unfavorable prognosis for glioma. (A) Representative images (left) and quantification (right) showing IL4I1 staining of normal brain tissues (n = 16) and glioma tissues (n = 37) with the anti-IL4I1 antibody, with scale bars 100 µm (up) and 20 µm (down). (B–D) Kaplan– Meier analysis for OS based on three glioma datasets (CGGA, Rembrandt, and GSE16011). (E–G) ROC curves of OS in CGGA, Rembrandt, and GSE16011 datasets. (H, I) Univariate and multivariate analyses of OS based on CGGA-glioma datasets. ****p < 0.0001.

    Journal: Frontiers in immunology

    Article Title: IL4I1 in M2-like macrophage promotes glioma progression and is a promising target for immunotherapy.

    doi: 10.3389/fimmu.2023.1338244

    Figure Lengend Snippet: FIGURE 3 Upregulation of IL4I1 infers an unfavorable prognosis for glioma. (A) Representative images (left) and quantification (right) showing IL4I1 staining of normal brain tissues (n = 16) and glioma tissues (n = 37) with the anti-IL4I1 antibody, with scale bars 100 µm (up) and 20 µm (down). (B–D) Kaplan– Meier analysis for OS based on three glioma datasets (CGGA, Rembrandt, and GSE16011). (E–G) ROC curves of OS in CGGA, Rembrandt, and GSE16011 datasets. (H, I) Univariate and multivariate analyses of OS based on CGGA-glioma datasets. ****p < 0.0001.

    Article Snippet: Dataset Data type WHO grade II WHO grade III WHO grade IV CGGA RNA-seq 291 334 388 Rembrandt Microarray 98 85 130 GSE16011 Microarray 24 85 159 frontiersin.org (1:2000, 60143-1-Ig, Proteintech), CD163 (1:1,000, ab182422, Abcam), CD86 (1:1,000, ab239075, Abcam), and beta-tubulin (1:2000, DF7967, Affinity) overnight.

    Techniques: Staining

    FIGURE 4 Heightened IL4I1 expression is correlated with the malignant phenotype of gliomas. (A–D) IL4I1 shows a significant increase in GBM (WHO IV) in TCGA, Rembrandt, GSE16011, and CGGA datasets. Additionally, box plots visualizing the associations between IL4I1 and various clinical characteristics based on the CGGA dataset. Specifically: (E) Age. (F) Status. (G) Histology. (H, I) High expression of IL4I1 in IDH wild-type and 1p/19q non-codel gliomas.

    Journal: Frontiers in immunology

    Article Title: IL4I1 in M2-like macrophage promotes glioma progression and is a promising target for immunotherapy.

    doi: 10.3389/fimmu.2023.1338244

    Figure Lengend Snippet: FIGURE 4 Heightened IL4I1 expression is correlated with the malignant phenotype of gliomas. (A–D) IL4I1 shows a significant increase in GBM (WHO IV) in TCGA, Rembrandt, GSE16011, and CGGA datasets. Additionally, box plots visualizing the associations between IL4I1 and various clinical characteristics based on the CGGA dataset. Specifically: (E) Age. (F) Status. (G) Histology. (H, I) High expression of IL4I1 in IDH wild-type and 1p/19q non-codel gliomas.

    Article Snippet: Dataset Data type WHO grade II WHO grade III WHO grade IV CGGA RNA-seq 291 334 388 Rembrandt Microarray 98 85 130 GSE16011 Microarray 24 85 159 frontiersin.org (1:2000, 60143-1-Ig, Proteintech), CD163 (1:1,000, ab182422, Abcam), CD86 (1:1,000, ab239075, Abcam), and beta-tubulin (1:2000, DF7967, Affinity) overnight.

    Techniques: Expressing

    FIGURE 6 IL4I1 is expressed in M2-like macrophages in glioma. (A) Summary of IL4I1 expression in 12 distinct single-cell datasets from glioma patients. (B) Association between IL4I1 and macrophages on XCELL, TIMER, and EPIC algorithms. (C) Association between IL4I1 expression and markers of M1 and M2 macrophages in CGGA and TCGA databases. Color depth and digital scale represent the strength of association. (D) Representative colocalization images from IF staining between IL4I1 and CD206 in clinical glioma specimens. DAPI (blue), IL4I1 (red) and CD206 (green). Scale bar: 20 mm. (E) Measurement of protein and mRNA expression levels for markers (CD11B, CD204, CD86, CD206, and CD163) of THP-1, M0, M1, and M2 macrophages using WB and RT-qPCR. (F) Assessment of IL4I1 expression in various macrophage subtypes (M0, M1, and M2) and glioma cells (U87, LN229, and U251). (G) Representative IF pictures of the difference of IL4I1 among M0, M1, and M2 macrophages, U87, and LN229 cells with DAPI (blue) and IL4I1 (red). *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.

    Journal: Frontiers in immunology

    Article Title: IL4I1 in M2-like macrophage promotes glioma progression and is a promising target for immunotherapy.

    doi: 10.3389/fimmu.2023.1338244

    Figure Lengend Snippet: FIGURE 6 IL4I1 is expressed in M2-like macrophages in glioma. (A) Summary of IL4I1 expression in 12 distinct single-cell datasets from glioma patients. (B) Association between IL4I1 and macrophages on XCELL, TIMER, and EPIC algorithms. (C) Association between IL4I1 expression and markers of M1 and M2 macrophages in CGGA and TCGA databases. Color depth and digital scale represent the strength of association. (D) Representative colocalization images from IF staining between IL4I1 and CD206 in clinical glioma specimens. DAPI (blue), IL4I1 (red) and CD206 (green). Scale bar: 20 mm. (E) Measurement of protein and mRNA expression levels for markers (CD11B, CD204, CD86, CD206, and CD163) of THP-1, M0, M1, and M2 macrophages using WB and RT-qPCR. (F) Assessment of IL4I1 expression in various macrophage subtypes (M0, M1, and M2) and glioma cells (U87, LN229, and U251). (G) Representative IF pictures of the difference of IL4I1 among M0, M1, and M2 macrophages, U87, and LN229 cells with DAPI (blue) and IL4I1 (red). *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.

    Article Snippet: Dataset Data type WHO grade II WHO grade III WHO grade IV CGGA RNA-seq 291 334 388 Rembrandt Microarray 98 85 130 GSE16011 Microarray 24 85 159 frontiersin.org (1:2000, 60143-1-Ig, Proteintech), CD163 (1:1,000, ab182422, Abcam), CD86 (1:1,000, ab239075, Abcam), and beta-tubulin (1:2000, DF7967, Affinity) overnight.

    Techniques: Expressing, Staining, Quantitative RT-PCR