2100 bioanalyzer Agilent Technologies Search Results


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  • 99
    Agilent technologies 2100 bioanalyser system
    Depicts the integrity of RNA isolated at 30 °C from different Coffea arabica tissues (mature and immature leaf, fruit, root) and from leaves belonging to 3 different coffee species, Coffea arabica, C. canephora and C. eugenoides . The isolated RNA were analysed by electrophoretic separation using 2% agarose gel ( A ) and the Agilent <t>2100</t> <t>bioanalyser</t> system with the RNA 6000 Nano ™ kits ( B ). The total RNA fraction contained ribosomal RNA, mRNA and small RNA had a RIN value ranging between 7.5 and 8.5.
    2100 Bioanalyser System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 93 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 93 article reviews
    Price from $9.99 to $1999.99
    2100 bioanalyser system - by Bioz Stars, 2019-08
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    99
    Agilent technologies bioanalyzer 2100 instrument
    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent <t>Bioanalyzer</t> 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.
    Bioanalyzer 2100 Instrument, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 7255 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioanalyzer 2100 instrument/product/Agilent technologies
    Average 99 stars, based on 7255 article reviews
    Price from $9.99 to $1999.99
    bioanalyzer 2100 instrument - by Bioz Stars, 2019-08
    99/100 stars
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    99
    Agilent technologies dna chips
    Specificity of the locked nucleic acid (LNA) probes for the detection of miR and pre-miR using in situ hybridization. Using 2.5 pmol of locked nucleic acid (LNA) probes prelabelled with digoxigenin, we determined in situ hybridization patterns of scramble miR (A; negative control), U6 small nuclear <t>RNA</t> (B; positive control), let-7b (C), mir-365 (D), pre-let-7b (E) and pre-mir-302a (F) probes (lane 1). In the second lane, Digoxigenin-labeled probes were competed with excessive amount (25 pmol ie 10× more) of unlabeled probes. Most of the signal observed in the panels of the first lane are absent from the panels in the second lane. Scale bars = 10 µm. Images are not scaled to the same intensity range. Positive in situ hybridization signals showed were normalized by scramble <t>mirna</t> signal intensity (negative control).
    Dna Chips, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 496 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna chips/product/Agilent technologies
    Average 99 stars, based on 496 article reviews
    Price from $9.99 to $1999.99
    dna chips - by Bioz Stars, 2019-08
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    Image Search Results


    Depicts the integrity of RNA isolated at 30 °C from different Coffea arabica tissues (mature and immature leaf, fruit, root) and from leaves belonging to 3 different coffee species, Coffea arabica, C. canephora and C. eugenoides . The isolated RNA were analysed by electrophoretic separation using 2% agarose gel ( A ) and the Agilent 2100 bioanalyser system with the RNA 6000 Nano ™ kits ( B ). The total RNA fraction contained ribosomal RNA, mRNA and small RNA had a RIN value ranging between 7.5 and 8.5.

    Journal: Scientific Reports

    Article Title: A single-step method for RNA isolation from tropical crops in the field

    doi: 10.1038/srep38368

    Figure Lengend Snippet: Depicts the integrity of RNA isolated at 30 °C from different Coffea arabica tissues (mature and immature leaf, fruit, root) and from leaves belonging to 3 different coffee species, Coffea arabica, C. canephora and C. eugenoides . The isolated RNA were analysed by electrophoretic separation using 2% agarose gel ( A ) and the Agilent 2100 bioanalyser system with the RNA 6000 Nano ™ kits ( B ). The total RNA fraction contained ribosomal RNA, mRNA and small RNA had a RIN value ranging between 7.5 and 8.5.

    Article Snippet: The Agilent 2100 bioanalyser system confirmed the absence of genomic DNA in the RNA samples.

    Techniques: Isolation, Agarose Gel Electrophoresis

    Comparison of the effectiveness of RNAzol RT (RNA extraction in field) and TRIzol Reagent or spin-columns kit (RNA extraction in laboratory with recommended cold conditions) to isolate total RNA. ( A ) Electrophoretic separation using 2% agarose gel of RNA extracted from the same four samples using the three methods. ( B ) Electropherogram and Electrophoresis of representative sample of RNA analysed with the Agilent 2100 bioanalyser system with the RNA 6000 Nano ™ kits. The white arrow shows genomic DNA contaminants.

    Journal: Scientific Reports

    Article Title: A single-step method for RNA isolation from tropical crops in the field

    doi: 10.1038/srep38368

    Figure Lengend Snippet: Comparison of the effectiveness of RNAzol RT (RNA extraction in field) and TRIzol Reagent or spin-columns kit (RNA extraction in laboratory with recommended cold conditions) to isolate total RNA. ( A ) Electrophoretic separation using 2% agarose gel of RNA extracted from the same four samples using the three methods. ( B ) Electropherogram and Electrophoresis of representative sample of RNA analysed with the Agilent 2100 bioanalyser system with the RNA 6000 Nano ™ kits. The white arrow shows genomic DNA contaminants.

    Article Snippet: The Agilent 2100 bioanalyser system confirmed the absence of genomic DNA in the RNA samples.

    Techniques: RNA Extraction, Agarose Gel Electrophoresis, Electrophoresis

    Depicts the integrity of RNA isolated at 30 °C from leaf tissue samples from Coffea arabica, Manihot esculenta, Oryza sativa and Zea mais . ( A ) The left-hand side of the figure shows the electrophoresis analysis by agarose gel. ( B ) The right-hand side of the figure shows the Agilent 2100 bioanalyser electrophoresis for each sample. The total RNA fraction had a RIN value ranging between 8 and 9.

    Journal: Scientific Reports

    Article Title: A single-step method for RNA isolation from tropical crops in the field

    doi: 10.1038/srep38368

    Figure Lengend Snippet: Depicts the integrity of RNA isolated at 30 °C from leaf tissue samples from Coffea arabica, Manihot esculenta, Oryza sativa and Zea mais . ( A ) The left-hand side of the figure shows the electrophoresis analysis by agarose gel. ( B ) The right-hand side of the figure shows the Agilent 2100 bioanalyser electrophoresis for each sample. The total RNA fraction had a RIN value ranging between 8 and 9.

    Article Snippet: The Agilent 2100 bioanalyser system confirmed the absence of genomic DNA in the RNA samples.

    Techniques: Isolation, Electrophoresis, Agarose Gel Electrophoresis

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Concentrated maternal cfDNA was analyzed by Agilent Bioanalyzer 2100 instrument and Agilent DNA High Sensitivity Kit following manufacturer’s recommended protocol.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Concentrated maternal cfDNA was analyzed by Agilent Bioanalyzer 2100 instrument and Agilent DNA High Sensitivity Kit following manufacturer’s recommended protocol.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Concentrated maternal cfDNA was analyzed by Agilent Bioanalyzer 2100 instrument and Agilent DNA High Sensitivity Kit following manufacturer’s recommended protocol.

    Techniques:

    Quality and quantity of biomacromolecular fractions isolated from the representative LAO-enriched microbial community sample using either the NA-, QA- and TR-based method (following prior metabolite extractions) or using the reference methods (no metabolite extractions were carried out before the respective extractions). ( a and b ) Representative Agilent Bioanalyzer 2100 electropherograms of the total RNA and small RNA fractions, respectively. ( c ) Agarose gel image highlighting representative genomic DNA fractions obtained (Mean amount ( n =3) loaded in μg±s.d., from right to left; NA: 0.35±0.17; QA: 0.35±0.08; TR: 0.83±0.85; RM: 0.08±0.04) and ( d ) SDS-PAGE image of representative protein fractions (Mean amount ( n =3) loaded in μg±s.d., from right to left; NA, first elution: 3.20±0.19; QA: 5.44±1.06; TR: 3.88±0.30; RM: 4.62±0.09). The arrow and the box represent the dominant gel band which was submitted to tryptic digestion and MALDI-ToF/ToF analysis. ( e ) Biomacromolecular yield obtained for the small RNA, □ total and large RNA, DNA and protein (first elution) fractions ( n =5, error bars represent s.d.). FU, fluorescent unit; L, ladder; M, marker; NA, NA-based method; Norm., normalized; nt, nucleotides; RM, reference methods; TR, TR-based method; QA, QA-based method.

    Journal: The ISME Journal

    Article Title: A biomolecular isolation framework for eco-systems biology

    doi: 10.1038/ismej.2012.72

    Figure Lengend Snippet: Quality and quantity of biomacromolecular fractions isolated from the representative LAO-enriched microbial community sample using either the NA-, QA- and TR-based method (following prior metabolite extractions) or using the reference methods (no metabolite extractions were carried out before the respective extractions). ( a and b ) Representative Agilent Bioanalyzer 2100 electropherograms of the total RNA and small RNA fractions, respectively. ( c ) Agarose gel image highlighting representative genomic DNA fractions obtained (Mean amount ( n =3) loaded in μg±s.d., from right to left; NA: 0.35±0.17; QA: 0.35±0.08; TR: 0.83±0.85; RM: 0.08±0.04) and ( d ) SDS-PAGE image of representative protein fractions (Mean amount ( n =3) loaded in μg±s.d., from right to left; NA, first elution: 3.20±0.19; QA: 5.44±1.06; TR: 3.88±0.30; RM: 4.62±0.09). The arrow and the box represent the dominant gel band which was submitted to tryptic digestion and MALDI-ToF/ToF analysis. ( e ) Biomacromolecular yield obtained for the small RNA, □ total and large RNA, DNA and protein (first elution) fractions ( n =5, error bars represent s.d.). FU, fluorescent unit; L, ladder; M, marker; NA, NA-based method; Norm., normalized; nt, nucleotides; RM, reference methods; TR, TR-based method; QA, QA-based method.

    Article Snippet: The Agilent Bioanalyzer 2100 electropherograms ( ) show distinct peaks between 100 and 4500 nt representing the total RNA fractions obtained using the different methods.

    Techniques: Isolation, Agarose Gel Electrophoresis, SDS Page, Marker

    Application of the developed biomolecular isolation methodology to a LAO-enriched microbial community ( n =3), river water filtrate ( n =3) and human feces ( n =3). ( a – c ) Left-hand panels represent LAO-enriched microbial communities, middle panels represent river water filtrate and right-hand panels represent human feces. ( a ) Representative GC–MS total ion chromatograms of polar and non-polar metabolite fractions. Representative Agilent Bioanalyzer 2100 electropherograms of the ( b ) total RNA fractions and ( c ) small RNA fractions. ( d ) Agarose gel electrophoresis image of the genomic DNA fractions (Mean amount loaded in μg±s.d., right to left; LAO: 0.63±0.28; river water: 0.35±0.03; feces: 0.61±0.26) for each of the three technical replicates considered. ( e ) SDS-PAGE image of protein fractions, first elution (Mean amount loaded in μg±s.d., right to left; LAO: 1.19±0.40; river water: 1.70±0.63; feces: 1.19±1.21) for each of the three technical replicates considered. L, ladder; RT, retention time.

    Journal: The ISME Journal

    Article Title: A biomolecular isolation framework for eco-systems biology

    doi: 10.1038/ismej.2012.72

    Figure Lengend Snippet: Application of the developed biomolecular isolation methodology to a LAO-enriched microbial community ( n =3), river water filtrate ( n =3) and human feces ( n =3). ( a – c ) Left-hand panels represent LAO-enriched microbial communities, middle panels represent river water filtrate and right-hand panels represent human feces. ( a ) Representative GC–MS total ion chromatograms of polar and non-polar metabolite fractions. Representative Agilent Bioanalyzer 2100 electropherograms of the ( b ) total RNA fractions and ( c ) small RNA fractions. ( d ) Agarose gel electrophoresis image of the genomic DNA fractions (Mean amount loaded in μg±s.d., right to left; LAO: 0.63±0.28; river water: 0.35±0.03; feces: 0.61±0.26) for each of the three technical replicates considered. ( e ) SDS-PAGE image of protein fractions, first elution (Mean amount loaded in μg±s.d., right to left; LAO: 1.19±0.40; river water: 1.70±0.63; feces: 1.19±1.21) for each of the three technical replicates considered. L, ladder; RT, retention time.

    Article Snippet: The Agilent Bioanalyzer 2100 electropherograms ( ) show distinct peaks between 100 and 4500 nt representing the total RNA fractions obtained using the different methods.

    Techniques: Isolation, Gas Chromatography, Mass Spectrometry, Agarose Gel Electrophoresis, Electrophoresis, SDS Page

    Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of fixation and postfixation processing on total cellular RNA: gel-simulated image (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Lane L: RNA ladder. Lane 1: Native non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of fixation and postfixation processing on total cellular RNA: gel-simulated image (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Lane L: RNA ladder. Lane 1: Native non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of buffer composition on postfixation processing of an RNA 50mer: gel-simulated image (Agilent 2100 Bioanalyzer). Lane L: RNA ladder. Lane 1: Native RNA 50mer. Lane 2: RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Excess formaldehyde

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of buffer composition on postfixation processing of an RNA 50mer: gel-simulated image (Agilent 2100 Bioanalyzer). Lane L: RNA ladder. Lane 1: Native RNA 50mer. Lane 2: RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Excess formaldehyde

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Postformaldehyde fixation processing of an RNA 50mer. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours and then heated at 70°C for 30 minutes, where indicated, in the following

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Postformaldehyde fixation processing of an RNA 50mer. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours and then heated at 70°C for 30 minutes, where indicated, in the following

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of fixation and postfixation processing on total HeLa RNA. Electropherograms (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. FU denotes fluorescence units. A: Non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of fixation and postfixation processing on total HeLa RNA. Electropherograms (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. FU denotes fluorescence units. A: Non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques: Fluorescence

    Analysis of tear proteins obtained by running aliquots from the same samples in parallel. Tear samples (one to eight) were runned through the 2100 Bioanalyzer (upper part of the figure, Protein 230 kit, gel-like view), and the 1D SDS–PAGE (lower part of the figure). The corresponding molecular weight in kDa is reported on the left of the ladder L : and of the prestained protein standard S : The same profiles were obtained for each sample in the two analytical methods.

    Journal: Molecular Vision

    Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins

    doi:

    Figure Lengend Snippet: Analysis of tear proteins obtained by running aliquots from the same samples in parallel. Tear samples (one to eight) were runned through the 2100 Bioanalyzer (upper part of the figure, Protein 230 kit, gel-like view), and the 1D SDS–PAGE (lower part of the figure). The corresponding molecular weight in kDa is reported on the left of the ladder L : and of the prestained protein standard S : The same profiles were obtained for each sample in the two analytical methods.

    Article Snippet: Calculation of measurement noise for Agilent 2100 Bioanalyzer applied to detecting tear proteins exhibited a high degree of precision and accuracy in terms of reproducibility ( and ) and repeatability ( ) .

    Techniques: SDS Page, Molecular Weight

    Inter-practitioner (Techn1 and Techn2) measurement variability (reproducibility) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed by Techn1 (y-axis) and by Techn 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed by two different laboratory technicians (Techn 1 and Techn 2), is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained by Techn 1 and Techn 2. The y-axis indicates the difference in measurement between the two technicians. The mean difference of the technicians is 0.01, with an upper specification limit of 0.23 and a lower specification limit of 0.20. C : The concordance correlation coefficients calculated for the two technicians are shown; all values demonstrated the high reproducibility of the Bioanalyzer method.

    Journal: Molecular Vision

    Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins

    doi:

    Figure Lengend Snippet: Inter-practitioner (Techn1 and Techn2) measurement variability (reproducibility) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed by Techn1 (y-axis) and by Techn 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed by two different laboratory technicians (Techn 1 and Techn 2), is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained by Techn 1 and Techn 2. The y-axis indicates the difference in measurement between the two technicians. The mean difference of the technicians is 0.01, with an upper specification limit of 0.23 and a lower specification limit of 0.20. C : The concordance correlation coefficients calculated for the two technicians are shown; all values demonstrated the high reproducibility of the Bioanalyzer method.

    Article Snippet: Calculation of measurement noise for Agilent 2100 Bioanalyzer applied to detecting tear proteins exhibited a high degree of precision and accuracy in terms of reproducibility ( and ) and repeatability ( ) .

    Techniques:

    Degree of agreement between measurements conducted on replicate specimens. The same tear samples were runned with two methods: monodimensional sodium dodecyl sulfate-polyacrylamide lectrophoresis (1D SDS–PAGE) electrophoresis and the 2100 Agilent Bioanalyzer (Protein 230 kit). A : The measurements obtained with 1D-SDS–PAGE electrophoresis (y-axis) and the 2100 Agilent Bioanalyzer (x-axis) are graphed. B : The Bland–Altman plot for various samples of tears analyzed for lysozyme content, performed with the two methods, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained with 1D SDS–PAGE electrophoresis and the 2100 Agilent Bioanalyzer. The y-axis indicates the difference in measurement between the two methods. The mean difference is 0.08, with an upper specification limit of 0.28 and a lower specification limit of 0.43. C : The concordance correlation coefficients calculated for the two methods are shown; all values demonstrated high correlation between the two methods.

    Journal: Molecular Vision

    Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins

    doi:

    Figure Lengend Snippet: Degree of agreement between measurements conducted on replicate specimens. The same tear samples were runned with two methods: monodimensional sodium dodecyl sulfate-polyacrylamide lectrophoresis (1D SDS–PAGE) electrophoresis and the 2100 Agilent Bioanalyzer (Protein 230 kit). A : The measurements obtained with 1D-SDS–PAGE electrophoresis (y-axis) and the 2100 Agilent Bioanalyzer (x-axis) are graphed. B : The Bland–Altman plot for various samples of tears analyzed for lysozyme content, performed with the two methods, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained with 1D SDS–PAGE electrophoresis and the 2100 Agilent Bioanalyzer. The y-axis indicates the difference in measurement between the two methods. The mean difference is 0.08, with an upper specification limit of 0.28 and a lower specification limit of 0.43. C : The concordance correlation coefficients calculated for the two methods are shown; all values demonstrated high correlation between the two methods.

    Article Snippet: Calculation of measurement noise for Agilent 2100 Bioanalyzer applied to detecting tear proteins exhibited a high degree of precision and accuracy in terms of reproducibility ( and ) and repeatability ( ) .

    Techniques: SDS Page, Electrophoresis

    Inter-session (session 1 and session 2) measurement variability (repeatability) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed during session 1 (y-axis) and session 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed in two sessions, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained in session 1 and session 2. The y-axis indicates the difference in measurement between the two sessions. The mean difference of both sessions is 0.04, with an upper specification limit of 0.24 and a lower specification limit of 0.16. C : The concordance correlation coefficients calculated for the two sessions are shown; all values demonstrated the high repeatability of the Bioanalyzer method.

    Journal: Molecular Vision

    Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins

    doi:

    Figure Lengend Snippet: Inter-session (session 1 and session 2) measurement variability (repeatability) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed during session 1 (y-axis) and session 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed in two sessions, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained in session 1 and session 2. The y-axis indicates the difference in measurement between the two sessions. The mean difference of both sessions is 0.04, with an upper specification limit of 0.24 and a lower specification limit of 0.16. C : The concordance correlation coefficients calculated for the two sessions are shown; all values demonstrated the high repeatability of the Bioanalyzer method.

    Article Snippet: Calculation of measurement noise for Agilent 2100 Bioanalyzer applied to detecting tear proteins exhibited a high degree of precision and accuracy in terms of reproducibility ( and ) and repeatability ( ) .

    Techniques:

    Transcriptional changes of cir gene expression during the course of infection . For RFLP analyses of expression changes of the cir genes during the course of infection, blood of female NMRI mice infected with 100 pRBCs were passaged on days 7, 14 and 21 days post infections (d.p.i.) into naïve female NMRI mice. Blood of these passaged mice was again collected at 30% parasitaemia. After amplification using the subfamily-specific primers for both subfamilies, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RT-PCR RFLP profiles for four mice of subfamily 1 are presented in (A). The restriction digest of subfamily 2 are shown in the upper panel of (B) where only at day 7 p.i. and day 14 p.i. of mouse 1 a few smaller restriction fragments could be detected. Therefore a second digest with Xap I for 3 h at 37°C was performed (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.

    Journal: Malaria Journal

    Article Title: Characterization and tissue-specific expression patterns of the Plasmodium chabaudi cir multigene family

    doi: 10.1186/1475-2875-10-272

    Figure Lengend Snippet: Transcriptional changes of cir gene expression during the course of infection . For RFLP analyses of expression changes of the cir genes during the course of infection, blood of female NMRI mice infected with 100 pRBCs were passaged on days 7, 14 and 21 days post infections (d.p.i.) into naïve female NMRI mice. Blood of these passaged mice was again collected at 30% parasitaemia. After amplification using the subfamily-specific primers for both subfamilies, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RT-PCR RFLP profiles for four mice of subfamily 1 are presented in (A). The restriction digest of subfamily 2 are shown in the upper panel of (B) where only at day 7 p.i. and day 14 p.i. of mouse 1 a few smaller restriction fragments could be detected. Therefore a second digest with Xap I for 3 h at 37°C was performed (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.

    Article Snippet: After amplification using the subfamily 1 and subfamily 2 specific primers, PCR products were digested with the restriction enzyme Alu I and analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer for accurate and reproducible separation and size determination (Figure ).

    Techniques: Expressing, Infection, Mouse Assay, Amplification, Purification, Reverse Transcription Polymerase Chain Reaction, Marker

    Expression profile analyses of cir genes in different tissues of infected mice by RT-PCR RFLP . For RFLP analyses, organs and blood were collected at a parasitaemia of 30% from female NMRI mice infected with 100 pRBCs. After RT-PCR amplification for the six host tissues with the subfamily-specific primers, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I. The DNA fragments (30 ng) were analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer for accurate sizing. Compared are RT-PCR RFLP profiles of blood, liver, spleen, kidney, lung and brain for four mice for cir subfamily 1 (A) and cir subfamily 2 (B). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.

    Journal: Malaria Journal

    Article Title: Characterization and tissue-specific expression patterns of the Plasmodium chabaudi cir multigene family

    doi: 10.1186/1475-2875-10-272

    Figure Lengend Snippet: Expression profile analyses of cir genes in different tissues of infected mice by RT-PCR RFLP . For RFLP analyses, organs and blood were collected at a parasitaemia of 30% from female NMRI mice infected with 100 pRBCs. After RT-PCR amplification for the six host tissues with the subfamily-specific primers, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I. The DNA fragments (30 ng) were analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer for accurate sizing. Compared are RT-PCR RFLP profiles of blood, liver, spleen, kidney, lung and brain for four mice for cir subfamily 1 (A) and cir subfamily 2 (B). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.

    Article Snippet: After amplification using the subfamily 1 and subfamily 2 specific primers, PCR products were digested with the restriction enzyme Alu I and analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer for accurate and reproducible separation and size determination (Figure ).

    Techniques: Expressing, Infection, Mouse Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Purification, Marker

    Transcriptional changes of cir genes during intraerythrocytic development . For expression profiling of the cir genes at three different time points in the life cycle, 30 μl tail vein blood of female NMRI mice infected with 100 pRBCs were collected 3 h (early trophozoites), 10 h (late trophozoites) and 17 h (mature trophozoites and early schizonts) after beginning of the light cycle on day 13 p.i. (parasitaemia about 30%). Amplification was performed using the subfamily-specific primers for both subfamilies and 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RFLP profiles of subfamily 1 are shown for four mice in (A). The restriction digests of subfamily 2 are shown in the upper panel of (B). Only a few restriction fragments were detected in all samples, therefore RT-PCR products were also restricted with Xap I (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker were indicated.

    Journal: Malaria Journal

    Article Title: Characterization and tissue-specific expression patterns of the Plasmodium chabaudi cir multigene family

    doi: 10.1186/1475-2875-10-272

    Figure Lengend Snippet: Transcriptional changes of cir genes during intraerythrocytic development . For expression profiling of the cir genes at three different time points in the life cycle, 30 μl tail vein blood of female NMRI mice infected with 100 pRBCs were collected 3 h (early trophozoites), 10 h (late trophozoites) and 17 h (mature trophozoites and early schizonts) after beginning of the light cycle on day 13 p.i. (parasitaemia about 30%). Amplification was performed using the subfamily-specific primers for both subfamilies and 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RFLP profiles of subfamily 1 are shown for four mice in (A). The restriction digests of subfamily 2 are shown in the upper panel of (B). Only a few restriction fragments were detected in all samples, therefore RT-PCR products were also restricted with Xap I (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker were indicated.

    Article Snippet: After amplification using the subfamily 1 and subfamily 2 specific primers, PCR products were digested with the restriction enzyme Alu I and analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer for accurate and reproducible separation and size determination (Figure ).

    Techniques: Expressing, Mouse Assay, Infection, Amplification, Purification, Reverse Transcription Polymerase Chain Reaction, Marker

    Size distribution of mRNA, cRNA and dsDNA on Agilent 2100 Bioanalyzer 6000 Nanochips. ( a ) Universal Human Reference (UHR) RNA and sense-RNA template library after IVT-amplification. Lane L displays the ladder (25, 200, 500, 1000, 2000 and 4000 nt). Lane 1 contains fresh UHR RNA. Lanes 2, 3 and 4 display three individual IVT-amplifications of sense-RNA using total RNA displayed in lane 1. ( b ) Size distribution of fresh, frozen, FFPE-RNA and amplified cRNA. Lane L displays the same ladder as observed in (a). Lane 1 contains fresh human breast RNA. Lane 2 contains total RNA from the 10-year-old frozen human breast cancer tissue. Lane 3 contains total RNA from the matched 10-year-old FFPE human breast cancer tissue. Lane 4 contains cRNA obtained by IVT-amplifications of 10-year-old frozen RNA (lane 2). Lanes 5 contains cRNA obtained by direct IVT-amplification of the 10-year-old FFPE-RNA (lane 3). Lanes 6 contains amplified cRNA obtained by CT-RT and IVT-amplification of the same 10-year-old FFPE-RNA. ( c ) Size distribution of double-stranded DNA on a Bioanalyzer 2100 Agilent nanochip. Lane L displays the ladder. Lane 1 displays dsDNA obtained from 10-year-old frozen RNA. Lane 2 displays dsDNA obtained from 10-year-old FFPE-RNA. Lane 3 shows dsDNA obtained after CT-RT and double-strand DNA synthesis of the same 10-year-old FFPE-RNA. (See Supplementary Data for fragmented RNA profiles)

    Journal: Nucleic Acids Research

    Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

    doi: 10.1093/nar/gkm510

    Figure Lengend Snippet: Size distribution of mRNA, cRNA and dsDNA on Agilent 2100 Bioanalyzer 6000 Nanochips. ( a ) Universal Human Reference (UHR) RNA and sense-RNA template library after IVT-amplification. Lane L displays the ladder (25, 200, 500, 1000, 2000 and 4000 nt). Lane 1 contains fresh UHR RNA. Lanes 2, 3 and 4 display three individual IVT-amplifications of sense-RNA using total RNA displayed in lane 1. ( b ) Size distribution of fresh, frozen, FFPE-RNA and amplified cRNA. Lane L displays the same ladder as observed in (a). Lane 1 contains fresh human breast RNA. Lane 2 contains total RNA from the 10-year-old frozen human breast cancer tissue. Lane 3 contains total RNA from the matched 10-year-old FFPE human breast cancer tissue. Lane 4 contains cRNA obtained by IVT-amplifications of 10-year-old frozen RNA (lane 2). Lanes 5 contains cRNA obtained by direct IVT-amplification of the 10-year-old FFPE-RNA (lane 3). Lanes 6 contains amplified cRNA obtained by CT-RT and IVT-amplification of the same 10-year-old FFPE-RNA. ( c ) Size distribution of double-stranded DNA on a Bioanalyzer 2100 Agilent nanochip. Lane L displays the ladder. Lane 1 displays dsDNA obtained from 10-year-old frozen RNA. Lane 2 displays dsDNA obtained from 10-year-old FFPE-RNA. Lane 3 shows dsDNA obtained after CT-RT and double-strand DNA synthesis of the same 10-year-old FFPE-RNA. (See Supplementary Data for fragmented RNA profiles)

    Article Snippet: For these experiments, total RNA isolated from the 3-year-old cervical frozen and formalin-fixed tissues, as well as the cRNA obtained by IVT-amplification of frozen RNA or by CT-RT and IVT-ampliication of FFPE-RNA were analyzed on the Agilent 2100 bioanalyzer (Supplementary Data).

    Techniques: Amplification, Formalin-fixed Paraffin-Embedded, DNA Synthesis

    Electropherogram of total RNA recovered from FFPE samples utilized in CT-RT experiments. Total RNA extracted from 10-year-old breast cancer and 3-year-old cervical FFPE tissues were loaded on a Agilent 2100 Bioanalyzer 6000 Nanochip. Electropherograms were obtained with the 2100 expert software from Agilent, version B.02.03.SI307. 18S and 28S ribosomal RNA peaks are not detected in either FFPE sample, indicative of severe degradation.

    Journal: Nucleic Acids Research

    Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

    doi: 10.1093/nar/gkm510

    Figure Lengend Snippet: Electropherogram of total RNA recovered from FFPE samples utilized in CT-RT experiments. Total RNA extracted from 10-year-old breast cancer and 3-year-old cervical FFPE tissues were loaded on a Agilent 2100 Bioanalyzer 6000 Nanochip. Electropherograms were obtained with the 2100 expert software from Agilent, version B.02.03.SI307. 18S and 28S ribosomal RNA peaks are not detected in either FFPE sample, indicative of severe degradation.

    Article Snippet: For these experiments, total RNA isolated from the 3-year-old cervical frozen and formalin-fixed tissues, as well as the cRNA obtained by IVT-amplification of frozen RNA or by CT-RT and IVT-ampliication of FFPE-RNA were analyzed on the Agilent 2100 bioanalyzer (Supplementary Data).

    Techniques: Formalin-fixed Paraffin-Embedded, Software

    Standards for MspI digestion and progressive PCR. A) MspI digestion of human genomic DNA isolated from human post-mortem brain tissues. DNA (200 ng) was digested by MspI and run on a 4–20% precast polyacrylamide gel and stained with EtBr. Arrows show three satellite DNA bands characteristic of this enzymatic digestion. B) Agilent 2100 Bioanalyzer chromatogram of MspI digested genomic DNA. C) Bioanalyzer 2100 image of a single library from an MspI digested DNA sample. Notice that the satellite bands (indicated by arrows) are still visible on the Bioanalyzer image. D) Progressive PCR amplification combined with limited PCR extension time allows for size selection and amplification of six bisulfite converted libraries (Lanes 1–5 are distinct RRBS libraries; lane 6 (‘C’) is a negative control). After different progressive PCR cycles (18X, 22X, 24X, or 26X – the same libraries are shown for each cycle number) band intensity increases as cycle number increases. Arrows indicate the three satellite DNA bands that are still visible in these libraries.

    Journal: BMC Genomics

    Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing

    doi: 10.1186/1471-2164-15-290

    Figure Lengend Snippet: Standards for MspI digestion and progressive PCR. A) MspI digestion of human genomic DNA isolated from human post-mortem brain tissues. DNA (200 ng) was digested by MspI and run on a 4–20% precast polyacrylamide gel and stained with EtBr. Arrows show three satellite DNA bands characteristic of this enzymatic digestion. B) Agilent 2100 Bioanalyzer chromatogram of MspI digested genomic DNA. C) Bioanalyzer 2100 image of a single library from an MspI digested DNA sample. Notice that the satellite bands (indicated by arrows) are still visible on the Bioanalyzer image. D) Progressive PCR amplification combined with limited PCR extension time allows for size selection and amplification of six bisulfite converted libraries (Lanes 1–5 are distinct RRBS libraries; lane 6 (‘C’) is a negative control). After different progressive PCR cycles (18X, 22X, 24X, or 26X – the same libraries are shown for each cycle number) band intensity increases as cycle number increases. Arrows indicate the three satellite DNA bands that are still visible in these libraries.

    Article Snippet: AMPure SPRI bead-purified library was eluted in 60 μL of dH2 O. Purified libraries can be screened on an Agilent 2100 BioAnalyzer (Figure A and B).

    Techniques: Polymerase Chain Reaction, Isolation, Staining, Amplification, Selection, Negative Control

    Agilent 2100 Bioanalyzer images from final reduced representation bisulfite libraries. A) High Sensitivity DNA Chip from 10 RRBS libraries. Notice that the satellite bands are still visible on the Bioanalyzer gel image B) Chromatogram representation of panel A showing high quality RRBS libraries.

    Journal: BMC Genomics

    Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing

    doi: 10.1186/1471-2164-15-290

    Figure Lengend Snippet: Agilent 2100 Bioanalyzer images from final reduced representation bisulfite libraries. A) High Sensitivity DNA Chip from 10 RRBS libraries. Notice that the satellite bands are still visible on the Bioanalyzer gel image B) Chromatogram representation of panel A showing high quality RRBS libraries.

    Article Snippet: AMPure SPRI bead-purified library was eluted in 60 μL of dH2 O. Purified libraries can be screened on an Agilent 2100 BioAnalyzer (Figure A and B).

    Techniques: Chromatin Immunoprecipitation

    Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum

    Article Snippet: Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474).

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Generated

    Bioanalyzer traces of libraries prepared from various sample types and species. a Libraries prepared from samples with a varied degree of formalin fixation; a higher ΔCq indicates more FFPE-induced DNA degradation compared with a positive control. b Increasing FFPE-induced DNA degradation has a small effect on average fragment size but a marked effect on the total library yield. Increasing the DNA input from 100 ng to 150 ng did not increase library yield, indicating bead saturation at a DNA input of around 100 ng regardless of the degree of DNA degradation. c Libraries prepared from gDNA from a range of animal (human, Angus, and mouse), plant (Arabidopsis and alfalfa), and bacterial ( E. coli and B. cereus ) species

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Bioanalyzer traces of libraries prepared from various sample types and species. a Libraries prepared from samples with a varied degree of formalin fixation; a higher ΔCq indicates more FFPE-induced DNA degradation compared with a positive control. b Increasing FFPE-induced DNA degradation has a small effect on average fragment size but a marked effect on the total library yield. Increasing the DNA input from 100 ng to 150 ng did not increase library yield, indicating bead saturation at a DNA input of around 100 ng regardless of the degree of DNA degradation. c Libraries prepared from gDNA from a range of animal (human, Angus, and mouse), plant (Arabidopsis and alfalfa), and bacterial ( E. coli and B. cereus ) species

    Article Snippet: Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474).

    Techniques: Formalin-fixed Paraffin-Embedded, Positive Control

    Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region

    Article Snippet: Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474).

    Techniques: Agarose Gel Electrophoresis, Amplification, Sequencing, Polymerase Chain Reaction

    Specificity of the locked nucleic acid (LNA) probes for the detection of miR and pre-miR using in situ hybridization. Using 2.5 pmol of locked nucleic acid (LNA) probes prelabelled with digoxigenin, we determined in situ hybridization patterns of scramble miR (A; negative control), U6 small nuclear RNA (B; positive control), let-7b (C), mir-365 (D), pre-let-7b (E) and pre-mir-302a (F) probes (lane 1). In the second lane, Digoxigenin-labeled probes were competed with excessive amount (25 pmol ie 10× more) of unlabeled probes. Most of the signal observed in the panels of the first lane are absent from the panels in the second lane. Scale bars = 10 µm. Images are not scaled to the same intensity range. Positive in situ hybridization signals showed were normalized by scramble mirna signal intensity (negative control).

    Journal: PLoS ONE

    Article Title: Pre-microRNA and Mature microRNA in Human Mitochondria

    doi: 10.1371/journal.pone.0020220

    Figure Lengend Snippet: Specificity of the locked nucleic acid (LNA) probes for the detection of miR and pre-miR using in situ hybridization. Using 2.5 pmol of locked nucleic acid (LNA) probes prelabelled with digoxigenin, we determined in situ hybridization patterns of scramble miR (A; negative control), U6 small nuclear RNA (B; positive control), let-7b (C), mir-365 (D), pre-let-7b (E) and pre-mir-302a (F) probes (lane 1). In the second lane, Digoxigenin-labeled probes were competed with excessive amount (25 pmol ie 10× more) of unlabeled probes. Most of the signal observed in the panels of the first lane are absent from the panels in the second lane. Scale bars = 10 µm. Images are not scaled to the same intensity range. Positive in situ hybridization signals showed were normalized by scramble mirna signal intensity (negative control).

    Article Snippet: It was a microfluidic lab-on-a-chip technology using electrophoresis and dye to separate and detect RNA of 0 to 150 nt and the percentage of miRNA which was shorter than 40 nt (Small RNA kit, 2100 Bioanalyzer®, Agilent Technologies) .

    Techniques: In Situ Hybridization, Negative Control, Positive Control, Labeling

    In situ hybridization pattern of digoxigenin-labeled Locked Nucleic Acid (LNA) for specific miR and pre-miR in human skeletal muscle myoblasts cells observed in classic optic microscopy. Using locked nucleic acid (LNA) probes digoxigenin labelled, we determined the in situ hybridization pattern of mir and pre-mir. Hoechst 33342 staining of nuclei (lane 1), specific signal of scramble miRNA (A; negative control), U6 small nuclear RNA (B; positive control), let-7b (C), mir-365 (D), pre-let-7b (E) and pre-mir-302a (F) probes (lane 2) and MitoTracker® Red CM-H 2 XRos staining of respiring mitochondria (lane 3) are represented in gray scale. All these images were acquired using an Olympus BX61 straight microscope controlled with Metamorph software (Molecular Devices, Downington, PA19335) using a 100× oil-immersion objective. In the overlays (lane 4) provided by Image J software, positive in situ hybridization signals are visualized in green, respiring mitochondria signal in red and nuclei staining in blue. Yellow staining suggests co-localization of LNA probes (green fluorescence) and MitoTracker® Red CM-H 2 Ros (red fluorescence). Scale bars = 10 µm. Images are not scaled to the same intensity range. Positive in situ hybridization signals were normalized by scramble miR signal intensity (negative control).

    Journal: PLoS ONE

    Article Title: Pre-microRNA and Mature microRNA in Human Mitochondria

    doi: 10.1371/journal.pone.0020220

    Figure Lengend Snippet: In situ hybridization pattern of digoxigenin-labeled Locked Nucleic Acid (LNA) for specific miR and pre-miR in human skeletal muscle myoblasts cells observed in classic optic microscopy. Using locked nucleic acid (LNA) probes digoxigenin labelled, we determined the in situ hybridization pattern of mir and pre-mir. Hoechst 33342 staining of nuclei (lane 1), specific signal of scramble miRNA (A; negative control), U6 small nuclear RNA (B; positive control), let-7b (C), mir-365 (D), pre-let-7b (E) and pre-mir-302a (F) probes (lane 2) and MitoTracker® Red CM-H 2 XRos staining of respiring mitochondria (lane 3) are represented in gray scale. All these images were acquired using an Olympus BX61 straight microscope controlled with Metamorph software (Molecular Devices, Downington, PA19335) using a 100× oil-immersion objective. In the overlays (lane 4) provided by Image J software, positive in situ hybridization signals are visualized in green, respiring mitochondria signal in red and nuclei staining in blue. Yellow staining suggests co-localization of LNA probes (green fluorescence) and MitoTracker® Red CM-H 2 Ros (red fluorescence). Scale bars = 10 µm. Images are not scaled to the same intensity range. Positive in situ hybridization signals were normalized by scramble miR signal intensity (negative control).

    Article Snippet: It was a microfluidic lab-on-a-chip technology using electrophoresis and dye to separate and detect RNA of 0 to 150 nt and the percentage of miRNA which was shorter than 40 nt (Small RNA kit, 2100 Bioanalyzer®, Agilent Technologies) .

    Techniques: In Situ Hybridization, Labeling, Microscopy, Staining, Negative Control, Positive Control, Software, Fluorescence

    In situ signal of mir-365, pre-mir-let7b and pre-mir-302a co-localized with functioning mitochondria in human myoblasts observed in confocal microscopy. Using locked nucleic acid (LNA) probes, we performed in situ hybridization to localized mir-365, mir-let-7b, pre-let-7b and pre-mir-302a within the cell. Hoechst 33342 staining of nuclei (lane 1), specific signal of scramble miR (A; negative control), U6 small nuclear RNA (B; positive control), let-7b (C), mir-365 (D), pre-let-7b (E) and pre-mir-302a (F) provided by locked nucleic acid (LNA) probes (lane 2) and MitoTracker® Red CM-H 2 XRos staining of functioning mitochondria (lane 3) are represented in gray scale. All these images were acquired with a Leica TSC-P2 confocal microscope using a 63× oil-immersion objective. A sequential mode for three colour of acquisition (FITC for LNA probes signals, Dapi for Hoechst staining and Cy3 for MitoTracker® Red CM-H 2 XRos) has been used. In the overlays (lane 4) provided by Image J software, positive in situ hybridization signal are visualized in green and respiring mitochondria signal in red. Yellow corresponded to red and green overlay. The pixels with co-localized signals (lane 5) from functioning mitochondria and specific LNA probe for mir or pre-mir are determined using the Image J MBF plugging “co-localization highlighter”. Scale bars = 10 µm. The raw images are showed in the figure. The percentage of pixels with co-localized miRNA and mitochondrial signals were determined using Isodata plugging threshold (Image J software) and indicated on the figure (% in lane 5).

    Journal: PLoS ONE

    Article Title: Pre-microRNA and Mature microRNA in Human Mitochondria

    doi: 10.1371/journal.pone.0020220

    Figure Lengend Snippet: In situ signal of mir-365, pre-mir-let7b and pre-mir-302a co-localized with functioning mitochondria in human myoblasts observed in confocal microscopy. Using locked nucleic acid (LNA) probes, we performed in situ hybridization to localized mir-365, mir-let-7b, pre-let-7b and pre-mir-302a within the cell. Hoechst 33342 staining of nuclei (lane 1), specific signal of scramble miR (A; negative control), U6 small nuclear RNA (B; positive control), let-7b (C), mir-365 (D), pre-let-7b (E) and pre-mir-302a (F) provided by locked nucleic acid (LNA) probes (lane 2) and MitoTracker® Red CM-H 2 XRos staining of functioning mitochondria (lane 3) are represented in gray scale. All these images were acquired with a Leica TSC-P2 confocal microscope using a 63× oil-immersion objective. A sequential mode for three colour of acquisition (FITC for LNA probes signals, Dapi for Hoechst staining and Cy3 for MitoTracker® Red CM-H 2 XRos) has been used. In the overlays (lane 4) provided by Image J software, positive in situ hybridization signal are visualized in green and respiring mitochondria signal in red. Yellow corresponded to red and green overlay. The pixels with co-localized signals (lane 5) from functioning mitochondria and specific LNA probe for mir or pre-mir are determined using the Image J MBF plugging “co-localization highlighter”. Scale bars = 10 µm. The raw images are showed in the figure. The percentage of pixels with co-localized miRNA and mitochondrial signals were determined using Isodata plugging threshold (Image J software) and indicated on the figure (% in lane 5).

    Article Snippet: It was a microfluidic lab-on-a-chip technology using electrophoresis and dye to separate and detect RNA of 0 to 150 nt and the percentage of miRNA which was shorter than 40 nt (Small RNA kit, 2100 Bioanalyzer®, Agilent Technologies) .

    Techniques: In Situ, Confocal Microscopy, In Situ Hybridization, Staining, Negative Control, Positive Control, Microscopy, Software

    Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Extraction, Chromatin Immunoprecipitation, Electrophoresis, Polymerase Chain Reaction

    Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Purification, Chromatin Immunoprecipitation, Electrophoresis

    Cerebrospinal fluid (CSF) study design. Pools of CSF were generated for six diagnostic groups (five to 12 subjects/group): neurologically normal subjects (Control) from University of California, San Diego (UCSD); neurodegenerative disease [Alzheimer’s disease (AD) and Parkinson’s disease (PD)] from Oregon Health Science University (OHSU); central nervous system tumour [low-grade glioma (LGG) and glioblastoma multiforme (GBM)] from UCSD; and subarachnoid haemorrhage (SAH) from the Translational Genomics Research Institute (TGen). Aliquots from each pool of CSF were first used to assess the extracellular vesicles (EVs) in pooled CSF samples for each diagnostic group. The remaining aliquots were distributed across three institutes, where RNA isolation was performed in parallel using commercial RNA isolation kits: two designed to isolate total RNA and two designed to isolate EV RNA. The yield and quality of each RNA sample were assessed using RiboGreen and small RNA Bioanalyzer assays performed at each institute, and the outcomes from the studies were compared. QC, quality control.

    Journal: Journal of Extracellular Vesicles

    Article Title: Analysis of extracellular RNA in cerebrospinal fluid

    doi: 10.1080/20013078.2017.1317577

    Figure Lengend Snippet: Cerebrospinal fluid (CSF) study design. Pools of CSF were generated for six diagnostic groups (five to 12 subjects/group): neurologically normal subjects (Control) from University of California, San Diego (UCSD); neurodegenerative disease [Alzheimer’s disease (AD) and Parkinson’s disease (PD)] from Oregon Health Science University (OHSU); central nervous system tumour [low-grade glioma (LGG) and glioblastoma multiforme (GBM)] from UCSD; and subarachnoid haemorrhage (SAH) from the Translational Genomics Research Institute (TGen). Aliquots from each pool of CSF were first used to assess the extracellular vesicles (EVs) in pooled CSF samples for each diagnostic group. The remaining aliquots were distributed across three institutes, where RNA isolation was performed in parallel using commercial RNA isolation kits: two designed to isolate total RNA and two designed to isolate EV RNA. The yield and quality of each RNA sample were assessed using RiboGreen and small RNA Bioanalyzer assays performed at each institute, and the outcomes from the studies were compared. QC, quality control.

    Article Snippet: We used the Agilent Small RNA Assay (Agilent Technologies 2100 Bioanalyzer with 2100 Expert Software) to determine the yield and purity of RNA.

    Techniques: Generated, Diagnostic Assay, Isolation

    Replication of RNA size and purity across sites. RNA from each isolation kit was profiled by small RNA Bioanalyzer assays. Profiles show the intralaboratory ( n = 2 samples) and interlaboratory ( n = 3 sites) of RNA purity for each diagnostic group. y -axis = fluorescent units; x -axis = time (s) (circle = ~ 4 nt, triangle = ~ 150 nt). AD, Alzheimer’s disease; PD, Parkinson’s disease; LGG, low-grade glioma; GBM, glioblastoma multiforme; SAH, subarachnoid haemorrhage; ExRNA, extracellular RNA.

    Journal: Journal of Extracellular Vesicles

    Article Title: Analysis of extracellular RNA in cerebrospinal fluid

    doi: 10.1080/20013078.2017.1317577

    Figure Lengend Snippet: Replication of RNA size and purity across sites. RNA from each isolation kit was profiled by small RNA Bioanalyzer assays. Profiles show the intralaboratory ( n = 2 samples) and interlaboratory ( n = 3 sites) of RNA purity for each diagnostic group. y -axis = fluorescent units; x -axis = time (s) (circle = ~ 4 nt, triangle = ~ 150 nt). AD, Alzheimer’s disease; PD, Parkinson’s disease; LGG, low-grade glioma; GBM, glioblastoma multiforme; SAH, subarachnoid haemorrhage; ExRNA, extracellular RNA.

    Article Snippet: We used the Agilent Small RNA Assay (Agilent Technologies 2100 Bioanalyzer with 2100 Expert Software) to determine the yield and purity of RNA.

    Techniques: Isolation, Diagnostic Assay