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combimatrix array  (CombiMatrix)

 
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    CombiMatrix combimatrix array
    Combimatrix Array, supplied by CombiMatrix, 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/combimatrix+arrays/combimatrix+microarray/pm37071416-875-11-11
    Average 90 stars, based on 1 article reviews
    combimatrix array - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Hybridization:

    Article Title: Protocol for Gene Expression Profiling Using DNA Microarrays in Neisseria gonorrhoeae
    Article Snippet: .. CombiMatrix Arrays: Hybridization and Data Collection Our laboratory focuses on iron regulation in the human pathogen N. gonorrhoeae . ..

    Article Title: Mass Spectrometry Facility Montana State University, Bozeman
    Article Snippet: .. The Functional Genomics Core houses mini-fluorometers and nanodrop spectrometers; Affymetrix and slide array hybridization, scanning, and analysis equipment; and CombiMatrix arrays. .. Microdissection is provided via a Zeiss fluorescence-equipped microscope, PALM LMPC, and optical tweezers.

    Article Title: Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
    Article Snippet: .. Platforms varied both in overall signal intensity and number of probes called “present.” The former property is affected by a combination of labeling chemistry, input RNA concentration, and hybridization efficiency, with Combimatrix arrays producing the brightest signal. .. However, the low numbers of “present” calls (127, 85, 105) on this platform are similar to those produced by the low-intensity Invitrogen arrays (49, 103, 100), underscoring the importance of distinguishing between the two metrics.

    Article Title: Diagnosis of Sexually Transmitted Diseases
    Article Snippet: .. CombiMatrix Arrays: Hybridization and Data Collection Fig. 3. .. Biotinylated cDNA from N. gonorrhoeae FA1090 grown in CDM in iron minus conditions was hybridized to a 12K CombiMatrix ElectraSenseTM CustomArray.

    Article Title: Protocol for Gene Expression Profiling Using DNA Microarrays in Neisseria gonorrhoeae
    Article Snippet: .. CombiMatrix Arrays: Hybridization and Data Collection N. gonorrhoeae FA1090 CombiMatrix 12K ElectraSenseTM Custom Array. .. 12K ElectraSenseTM Hybridization Chamber (CombiMatrix).

    Labeling:

    Article Title: Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays
    Article Snippet: .. Fluorescently labeled cDNA was hybridized to CombiMatrix arrays as previously described[ ]. ..

    Article Title: Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
    Article Snippet: .. Platforms varied both in overall signal intensity and number of probes called “present.” The former property is affected by a combination of labeling chemistry, input RNA concentration, and hybridization efficiency, with Combimatrix arrays producing the brightest signal. .. However, the low numbers of “present” calls (127, 85, 105) on this platform are similar to those produced by the low-intensity Invitrogen arrays (49, 103, 100), underscoring the importance of distinguishing between the two metrics.

    Functional Assay:

    Article Title: Mass Spectrometry Facility Montana State University, Bozeman
    Article Snippet: .. The Functional Genomics Core houses mini-fluorometers and nanodrop spectrometers; Affymetrix and slide array hybridization, scanning, and analysis equipment; and CombiMatrix arrays. .. Microdissection is provided via a Zeiss fluorescence-equipped microscope, PALM LMPC, and optical tweezers.

    Sequencing:

    Article Title: Ability of Bifidobacterium breve To Grow on Different Types of Milk: Exploring the Metabolism of Milk through Genome Analysis
    Article Snippet: .. To determine if B. breve 4L functionally and distinctly responds to different types of milks, we performed transcriptional profiling studies using CombiMatrix arrays (CombiMatrix, Mukilteo, WA) based on the genome sequence of B. breve DSM20213 (NCBI source {"type":"entrez-nucleotide","attrs":{"text":"NZ_ACCG00000000","term_id":"268308874","term_text":"NZ_ACCG00000000"}} NZ_ACCG00000000 ). .. Oligos were synthesized in 18 replicates on a 2x40K CombiMatrix array.

    Concentration Assay:

    Article Title: Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
    Article Snippet: .. Platforms varied both in overall signal intensity and number of probes called “present.” The former property is affected by a combination of labeling chemistry, input RNA concentration, and hybridization efficiency, with Combimatrix arrays producing the brightest signal. .. However, the low numbers of “present” calls (127, 85, 105) on this platform are similar to those produced by the low-intensity Invitrogen arrays (49, 103, 100), underscoring the importance of distinguishing between the two metrics.



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    Architecture of the RiceATM platform. Step 1: Eight agronomic traits are represented in the RiceATM web server. The user can select an interesting trait and identify the associated miRNAs. Step 2: After selecting the agronomic trait, the user must fill in the ‘High cumulative percentage’ and “Low cumulative percentage” fields to identify the high- and low-quantity groups. The miRNA expression data on these two groups are selected for analysis. Step 3: In the microarray data pretreatment step, the user can select quantile normalization and data adjustment to normalize the microarray data. Step 4: To identify the miRNAs associated with the agronomic trait in the two groups of cultivars, RiceATM supports Student’s t -tests or ANOVAs. Step 5: Finally, the user can select the miRanda or psRNATarget algorithm to predict the target genes of the associated miRNAs.

    Journal: Database: The Journal of Biological Databases and Curation

    Article Title: RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

    doi: 10.1093/database/baw151

    Figure Lengend Snippet: Architecture of the RiceATM platform. Step 1: Eight agronomic traits are represented in the RiceATM web server. The user can select an interesting trait and identify the associated miRNAs. Step 2: After selecting the agronomic trait, the user must fill in the ‘High cumulative percentage’ and “Low cumulative percentage” fields to identify the high- and low-quantity groups. The miRNA expression data on these two groups are selected for analysis. Step 3: In the microarray data pretreatment step, the user can select quantile normalization and data adjustment to normalize the microarray data. Step 4: To identify the miRNAs associated with the agronomic trait in the two groups of cultivars, RiceATM supports Student’s t -tests or ANOVAs. Step 5: Finally, the user can select the miRanda or psRNATarget algorithm to predict the target genes of the associated miRNAs.

    Article Snippet: The mature miRNA sequences and six control probes (four positive and two negative) were used to produce the customized rice miRNA microarray (Combimatrix Custom Array 4 × 2 K, CA, USA).

    Techniques: Expressing, Microarray

    Example of browsing the RiceATM platform. (A) Eight agronomic traits affecting yield are represented in RiceATM, including the heading date, plant height, panicle number, panicle length, panicle weight, spikelet number, seed-set %, and 1000-seed weight. Here, we select ‘Heading Date’ as a demonstration. (B) RiceATM includes 187 rice cultivars: 155 japonica and 32 indica. The user can select total (japonica plus indica), japonica or indica cultivars to analyse by checking the ‘Variety’ box. In this example, we select the k-means clustering algorithm to select the high and low heading date groups for the total cultivars. (C) In the data pretreatment step, we use quantile normalization and then clip the minimum value at 800 to normalize the microarray data. (D) Differentially expressed miRNAs are evaluated by ANOVA and then subjected to target gene prediction by the psRNATarget algorithm. Thus, RiceATM shows the regulatory miRNA network. Large orange circles, miRNAs with high expression in the high-quantity group; large green circles, miRNAs with high expression in the low-quantity group; small blue circles, targeted mRNAs.

    Journal: Database: The Journal of Biological Databases and Curation

    Article Title: RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

    doi: 10.1093/database/baw151

    Figure Lengend Snippet: Example of browsing the RiceATM platform. (A) Eight agronomic traits affecting yield are represented in RiceATM, including the heading date, plant height, panicle number, panicle length, panicle weight, spikelet number, seed-set %, and 1000-seed weight. Here, we select ‘Heading Date’ as a demonstration. (B) RiceATM includes 187 rice cultivars: 155 japonica and 32 indica. The user can select total (japonica plus indica), japonica or indica cultivars to analyse by checking the ‘Variety’ box. In this example, we select the k-means clustering algorithm to select the high and low heading date groups for the total cultivars. (C) In the data pretreatment step, we use quantile normalization and then clip the minimum value at 800 to normalize the microarray data. (D) Differentially expressed miRNAs are evaluated by ANOVA and then subjected to target gene prediction by the psRNATarget algorithm. Thus, RiceATM shows the regulatory miRNA network. Large orange circles, miRNAs with high expression in the high-quantity group; large green circles, miRNAs with high expression in the low-quantity group; small blue circles, targeted mRNAs.

    Article Snippet: The mature miRNA sequences and six control probes (four positive and two negative) were used to produce the customized rice miRNA microarray (Combimatrix Custom Array 4 × 2 K, CA, USA).

    Techniques: Microarray, Expressing

    Expression trend of candidate miRNAs in the early and late heading date groups of rice cultivars. Four miRNA derived from RiceATM analysis and associated with heading date were subjected to a real-time PCR assay. Early, early heading date group, n = 4; Late, late heading date group, n = 4. Actin served as the internal control. (A) miR172d-3p; (B) miR818c; (C) miR820c and (D) miR399f. * P < 0.05, compared with the early group.

    Journal: Database: The Journal of Biological Databases and Curation

    Article Title: RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression

    doi: 10.1093/database/baw151

    Figure Lengend Snippet: Expression trend of candidate miRNAs in the early and late heading date groups of rice cultivars. Four miRNA derived from RiceATM analysis and associated with heading date were subjected to a real-time PCR assay. Early, early heading date group, n = 4; Late, late heading date group, n = 4. Actin served as the internal control. (A) miR172d-3p; (B) miR818c; (C) miR820c and (D) miR399f. * P < 0.05, compared with the early group.

    Article Snippet: The mature miRNA sequences and six control probes (four positive and two negative) were used to produce the customized rice miRNA microarray (Combimatrix Custom Array 4 × 2 K, CA, USA).

    Techniques: Expressing, Derivative Assay, Real-time Polymerase Chain Reaction, Control