Structured Review

Agilent technologies 2100 bioanalyzer system
Appearance of DNA libraries from Agilent <t>2100</t> <t>Bioanalyzer</t> analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
2100 Bioanalyzer System, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 315 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

Journal: Standards in Genomic Sciences

doi: 10.1186/s40793-017-0239-1

Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

Techniques Used: Generated, Marker

2) Product Images from "A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins"

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

Journal: Molecular Vision

doi:

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.
Figure Legend 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.

Techniques Used: 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.
Figure Legend 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.

Techniques Used:

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.
Figure Legend 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.

Techniques Used: 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.
Figure Legend 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.

Techniques Used:

3) Product Images from "A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins"

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

Journal: Molecular Vision

doi:

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.
Figure Legend 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.

Techniques Used: 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.
Figure Legend 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.

Techniques Used:

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.
Figure Legend 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.

Techniques Used: 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.
Figure Legend 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.

Techniques Used:

4) Product Images from "Targeted next generation sequencing for molecular diagnosis of Usher syndrome"

Article Title: Targeted next generation sequencing for molecular diagnosis of Usher syndrome

Journal: Orphanet Journal of Rare Diseases

doi: 10.1186/s13023-014-0168-7

Images obtained in the validation and quantification of the enriched target DNA with the 2100 Bioanalyzer system. A) Typical image obtained in most patients. B) Atypical image obtained in the patient RP-531, in whom CNV analysis could not be performed.
Figure Legend Snippet: Images obtained in the validation and quantification of the enriched target DNA with the 2100 Bioanalyzer system. A) Typical image obtained in most patients. B) Atypical image obtained in the patient RP-531, in whom CNV analysis could not be performed.

Techniques Used:

5) Product Images from "Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases, Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases"

Article Title: Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases, Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases

Journal: Advanced Science

doi: 10.1002/advs.201903354

Confirmation of the fetal origin of ER high trophoblastic cells. a) Representative immunostaining results of candidate cells isolated from sample P26. Twelve single trophoblastic cells are isolated, six cells are stained with β‐HCG and six stained with HLA‐G. NC, negative control, cells are not stained with antibodies. Scale bar, 15 µm. b) ER high trophoblastic cells isolated from seven pregnancies with a male fetus processed with FISH analysis. Representative results of single cells from P31, P35, and P37 are shown. Y chromosome signal is observed in these cells. Green fluorescence and red fluorescence, respectively, represent chromosome X and chromosome Y. c) The fragment size of the WGA product of P24 assessed by Agilent 2100 bioanalyzer. d) The STR profiles of maternal genomic DNA and fetal DNA amplified from rare fetal cells. 28 WGA samples with concentrations greater than 300 ng µL −1 are used for STR analysis. The red squares represent the informative loci between fetal and maternal cells. e) SRY‐PCR for detecting chromosome Y. SRY amplicons are detected in pregnancies with a male fetus. The actin beta (ACTB) gene is used as the internal reference.
Figure Legend Snippet: Confirmation of the fetal origin of ER high trophoblastic cells. a) Representative immunostaining results of candidate cells isolated from sample P26. Twelve single trophoblastic cells are isolated, six cells are stained with β‐HCG and six stained with HLA‐G. NC, negative control, cells are not stained with antibodies. Scale bar, 15 µm. b) ER high trophoblastic cells isolated from seven pregnancies with a male fetus processed with FISH analysis. Representative results of single cells from P31, P35, and P37 are shown. Y chromosome signal is observed in these cells. Green fluorescence and red fluorescence, respectively, represent chromosome X and chromosome Y. c) The fragment size of the WGA product of P24 assessed by Agilent 2100 bioanalyzer. d) The STR profiles of maternal genomic DNA and fetal DNA amplified from rare fetal cells. 28 WGA samples with concentrations greater than 300 ng µL −1 are used for STR analysis. The red squares represent the informative loci between fetal and maternal cells. e) SRY‐PCR for detecting chromosome Y. SRY amplicons are detected in pregnancies with a male fetus. The actin beta (ACTB) gene is used as the internal reference.

Techniques Used: Immunostaining, Isolation, Staining, Negative Control, Fluorescence In Situ Hybridization, Fluorescence, Whole Genome Amplification, Amplification, Polymerase Chain Reaction

6) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

Journal: Standards in Genomic Sciences

doi: 10.1186/s40793-017-0239-1

Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

Techniques Used: Generated, Marker

7) Product Images from "Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus"

Article Title: Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus

Journal: PLoS ONE

doi: 10.1371/journal.pone.0084962

Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.
Figure Legend Snippet: Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.

Techniques Used: Laser Capture Microdissection, Staining, Isolation

8) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

Journal: Standards in Genomic Sciences

doi: 10.1186/s40793-017-0239-1

Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

Techniques Used: Generated, Marker

9) Product Images from "Diagnostic performance of a tear protein panel in early dry eye"

Article Title: Diagnostic performance of a tear protein panel in early dry eye

Journal: Molecular Vision

doi:

Data from 2100 Bioanalyzer analysis.Upper left: Electropherograms from a representative normal subject (blue line) and a dry eye (DE) patient (red line) are here aligned and overlapped. Recognized peaks of interest are numbered 1 through 11. Upper right: The virtual gel images related to both samples are here compared showing different intensity of corresponding bands between normal subject and DE patient. Bands are here also numbered 1 through 11. Table at the bottom summarizes for each peak the following parameters: recognized molecular weight in kDa, name of the protein assigned on the basis of the validation process [ 13 ], concentration of each protein expressed in ng/microliter, percentage of each protein versus total protein content for both (N) normal subject and (DE) patient. The last line of this table reports total protein concentration expressed in ng/microliter
Figure Legend Snippet: Data from 2100 Bioanalyzer analysis.Upper left: Electropherograms from a representative normal subject (blue line) and a dry eye (DE) patient (red line) are here aligned and overlapped. Recognized peaks of interest are numbered 1 through 11. Upper right: The virtual gel images related to both samples are here compared showing different intensity of corresponding bands between normal subject and DE patient. Bands are here also numbered 1 through 11. Table at the bottom summarizes for each peak the following parameters: recognized molecular weight in kDa, name of the protein assigned on the basis of the validation process [ 13 ], concentration of each protein expressed in ng/microliter, percentage of each protein versus total protein content for both (N) normal subject and (DE) patient. The last line of this table reports total protein concentration expressed in ng/microliter

Techniques Used: Molecular Weight, Concentration Assay, Protein Concentration

10) Product Images from "Exonuclease resistant 18S and 25S ribosomal RNA components in yeast are possibly newly transcribed by RNA polymerase II"

Article Title: Exonuclease resistant 18S and 25S ribosomal RNA components in yeast are possibly newly transcribed by RNA polymerase II

Journal: BMC Molecular and Cell Biology

doi: 10.1186/s12860-020-00303-z

Percentage of Terminator resistant ribosomal RNA 18S and 25S molecules, as measured by Agilent Bioanalyzer 2100. a Resistance to Terminator digestion in total RNA isolated from of C. albicans, either from mid-log (ML) and stationary growth phases and mid-log cells treated with BMH21. b Terminator resistance percentage measured in RNA isolated from nuclei under same pre-isolation conditions as in ( a ). c Comparison of Terminator resistance percentages in nuclear versus total RNA from cells in stationary growth phase and ( d ) BMH21 treated cells. For each condition three different experiments were performed. Statistical analysis was done using Agilent Bioanalyzer 2100 Expert Software. P values generated by Student’s test, * p
Figure Legend Snippet: Percentage of Terminator resistant ribosomal RNA 18S and 25S molecules, as measured by Agilent Bioanalyzer 2100. a Resistance to Terminator digestion in total RNA isolated from of C. albicans, either from mid-log (ML) and stationary growth phases and mid-log cells treated with BMH21. b Terminator resistance percentage measured in RNA isolated from nuclei under same pre-isolation conditions as in ( a ). c Comparison of Terminator resistance percentages in nuclear versus total RNA from cells in stationary growth phase and ( d ) BMH21 treated cells. For each condition three different experiments were performed. Statistical analysis was done using Agilent Bioanalyzer 2100 Expert Software. P values generated by Student’s test, * p

Techniques Used: Isolation, Software, Generated

11) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

Journal: Standards in Genomic Sciences

doi: 10.1186/s40793-017-0239-1

Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

Techniques Used: Generated, Marker

12) Product Images from "Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus"

Article Title: Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus

Journal: PLoS ONE

doi: 10.1371/journal.pone.0084962

Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.
Figure Legend Snippet: Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.

Techniques Used: Laser Capture Microdissection, Staining, Isolation

13) Product Images from "Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus"

Article Title: Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus

Journal: PLoS ONE

doi: 10.1371/journal.pone.0084962

Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.
Figure Legend Snippet: Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.

Techniques Used: Laser Capture Microdissection, Staining, Isolation

14) Product Images from "Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B"

Article Title: Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B

Journal: Molecular Medicine Reports

doi: 10.3892/mmr.2016.5329

Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.
Figure Legend Snippet: Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.

Techniques Used: Polymerase Chain Reaction

Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.
Figure Legend Snippet: Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.

Techniques Used: Polymerase Chain Reaction

15) Product Images from "Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read ( > 11 kb), single molecule, real-time sequencing"

Article Title: Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read ( > 11 kb), single molecule, real-time sequencing

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dsw022

Comparison of SMRTbell library preparation efficiency from P. falciparum genomic DNA purified using three different methods. (A) High molecular weight P. falciparum genomic DNA prepared from an asynchronous culture using the Genomic tip kit was purified by three different methods: (i) AMPure PB magnetic bead-based clean up (Lanes 1 2), (ii) electrophoretic DNA extraction using the Aurora System (Lanes 3 4) or (iii) phenol-chloroform extraction (Lanes 5 6), and sheared as described in Materials and Methods. Quality and size distribution of the sheared DNA (140 ng) was assessed using field-inversion gel electrophoresis (Pippin Pulse System, Sage Science). Size markers included CHEF 8-48 kb DNA Size Standard (Bio-Rad) and 2.5 kb Molecular Ruler (Bio-Rad). (B) SMRTbell libraries prepared using the indicated amount of purified genomic DNA was subjected to size selection on the BluePippin System using a 15 kb cut-off. The DNA yield and % recovery of various steps, library preparation efficiency and size-selection distribution (based on Fig. 2C) of the three DNA purification methods were compared. (C) Size, quantity and quality of SMRTbell libraries before and after size-selection were assessed using the Agilent DNA 12000 kit on the Agilent 2100 Bioanalyzer System.
Figure Legend Snippet: Comparison of SMRTbell library preparation efficiency from P. falciparum genomic DNA purified using three different methods. (A) High molecular weight P. falciparum genomic DNA prepared from an asynchronous culture using the Genomic tip kit was purified by three different methods: (i) AMPure PB magnetic bead-based clean up (Lanes 1 2), (ii) electrophoretic DNA extraction using the Aurora System (Lanes 3 4) or (iii) phenol-chloroform extraction (Lanes 5 6), and sheared as described in Materials and Methods. Quality and size distribution of the sheared DNA (140 ng) was assessed using field-inversion gel electrophoresis (Pippin Pulse System, Sage Science). Size markers included CHEF 8-48 kb DNA Size Standard (Bio-Rad) and 2.5 kb Molecular Ruler (Bio-Rad). (B) SMRTbell libraries prepared using the indicated amount of purified genomic DNA was subjected to size selection on the BluePippin System using a 15 kb cut-off. The DNA yield and % recovery of various steps, library preparation efficiency and size-selection distribution (based on Fig. 2C) of the three DNA purification methods were compared. (C) Size, quantity and quality of SMRTbell libraries before and after size-selection were assessed using the Agilent DNA 12000 kit on the Agilent 2100 Bioanalyzer System.

Techniques Used: Purification, Molecular Weight, DNA Extraction, Nucleic Acid Electrophoresis, Selection, DNA Purification

16) Product Images from "Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus"

Article Title: Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus

Journal: Frontiers in Molecular Neuroscience

doi: 10.3389/fnmol.2016.00134

Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.
Figure Legend Snippet: Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.

Techniques Used: Expressing, Laser Capture Microdissection, Staining, Isolation, Software, Real-time Polymerase Chain Reaction, Mouse Assay

17) Product Images from "Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus"

Article Title: Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus

Journal: Frontiers in Molecular Neuroscience

doi: 10.3389/fnmol.2016.00134

Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.
Figure Legend Snippet: Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.

Techniques Used: Expressing, Laser Capture Microdissection, Staining, Isolation, Software, Real-time Polymerase Chain Reaction, Mouse Assay

18) Product Images from "Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B"

Article Title: Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B

Journal: Molecular Medicine Reports

doi: 10.3892/mmr.2016.5329

Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.
Figure Legend Snippet: Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.

Techniques Used: Polymerase Chain Reaction

Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.
Figure Legend Snippet: Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.

Techniques Used: Polymerase Chain Reaction

19) Product Images from "Frequencies of genetic polymorphisms related to triptans metabolism in chronic migraine"

Article Title: Frequencies of genetic polymorphisms related to triptans metabolism in chronic migraine

Journal: The Journal of Headache and Pain

doi: 10.1007/s10194-010-0202-7

Comparison between classic agarose gel electrophoresis and chip technology for resolution and accuracy. The same samples were analyzed by electrophoresis onto 3% agarose gel ( a ) and Bioanalyzer 2100 ( b ). The molecular weight of the upper band in the S1 line of the agarose gel is not unambiguously assignable. b Gel-like image and electropherograms of samples S1 and S2 obtained by Bioanalyzer 2100 analysis. The exact length of the longer fragment is easily determined ( Mk molecular weight marker)
Figure Legend Snippet: Comparison between classic agarose gel electrophoresis and chip technology for resolution and accuracy. The same samples were analyzed by electrophoresis onto 3% agarose gel ( a ) and Bioanalyzer 2100 ( b ). The molecular weight of the upper band in the S1 line of the agarose gel is not unambiguously assignable. b Gel-like image and electropherograms of samples S1 and S2 obtained by Bioanalyzer 2100 analysis. The exact length of the longer fragment is easily determined ( Mk molecular weight marker)

Techniques Used: Agarose Gel Electrophoresis, Chromatin Immunoprecipitation, Electrophoresis, Molecular Weight, Marker

20) Product Images from "A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra"

Article Title: A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra

Journal: Scientific Data

doi: 10.1038/sdata.2018.197

The zebra bullhead shark and sample preparation. ( a ) Juvnile zebra bullhead sharks. ( b ) A schematic diagram of a zebra bullhead shark embryo. Dashed lines, dissected positions; pctr, pectoral fins; plv, pelvic fins. ( c-e ) RNA length distribution analysis of head ( c ), trunk ( d ), and tail ( e ) samples on the 2100 Bioanalyzer, respectively. ( f ) DNA length distribution analysis of prepared libraries on the 2100 Bioanalyzer.
Figure Legend Snippet: The zebra bullhead shark and sample preparation. ( a ) Juvnile zebra bullhead sharks. ( b ) A schematic diagram of a zebra bullhead shark embryo. Dashed lines, dissected positions; pctr, pectoral fins; plv, pelvic fins. ( c-e ) RNA length distribution analysis of head ( c ), trunk ( d ), and tail ( e ) samples on the 2100 Bioanalyzer, respectively. ( f ) DNA length distribution analysis of prepared libraries on the 2100 Bioanalyzer.

Techniques Used: Sample Prep

Related Articles

Amplification:

Article Title: Targeted next generation sequencing for molecular diagnosis of Usher syndrome
Article Snippet: .. A PCR amplification of the captured target libraries was performed following the manufacturer’s instructions and, after its purification with the “AMPure XP beads” (BECKMAN CULTER Inc) , the validation and quantification of the enriched target DNA in each library was performed using the 2100 Bioanalyzer system with the High Sensitivity DNA Kit and the 2100 Expert Software (Agilent Technologies Inc, CA, USA ). .. The last step of the protocol was to pool samples for multiplexed sequencing in the Illumina sequencing platform MiSeq System (Illumina,Inc ).

Whole Genome Amplification:

Article Title: Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases, Nondestructive Identification of Rare Trophoblastic Cells by Endoplasmic Reticulum Staining for Noninvasive Prenatal Testing of Monogenic Diseases
Article Snippet: .. Quality Assessment of WGA Products First, the size distribution of the WGA products was evaluated using the Agilent 2100 bioanalyzer system (Agilent Technologies, Waldbronn, Germany). .. The WGA products were loaded on DNA 1000 Lab Chips according to the manufacturer's instructions.

Next-Generation Sequencing:

Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing
Article Snippet: .. Libraries are made following the PacBio SMRTbell 10kb Library Preparation on the Agilent NGS Workstation and traditionally confirmed with the Agilent 2100 Bioanalyzer System with the DNA 12000 kit, shown in Fig. . .. Thus, with SMRTbell templates around 10 kb in size, it’s difficult to determine the correct sizing for those libraries as these constructs also run with the upper marker shown in red on the virtual gel images.

Purification:

Article Title: Targeted next generation sequencing for molecular diagnosis of Usher syndrome
Article Snippet: .. A PCR amplification of the captured target libraries was performed following the manufacturer’s instructions and, after its purification with the “AMPure XP beads” (BECKMAN CULTER Inc) , the validation and quantification of the enriched target DNA in each library was performed using the 2100 Bioanalyzer system with the High Sensitivity DNA Kit and the 2100 Expert Software (Agilent Technologies Inc, CA, USA ). .. The last step of the protocol was to pool samples for multiplexed sequencing in the Illumina sequencing platform MiSeq System (Illumina,Inc ).

Electrophoresis:

Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing
Article Snippet: .. We will discuss the automation of preparation of libraries with the SMRTbell Template Preparation kit as well as analysis of gDNA, fragmented DNA and the final libraries ready for sequencing with both the Agilent electrophoresis platform: Agilent 2100 Bioanalyzer System using the DNA 12000 assay and the Agilent TapeStation System using the genomic DNA ScreenTape and matching reagents. ..

Polymerase Chain Reaction:

Article Title: Targeted next generation sequencing for molecular diagnosis of Usher syndrome
Article Snippet: .. A PCR amplification of the captured target libraries was performed following the manufacturer’s instructions and, after its purification with the “AMPure XP beads” (BECKMAN CULTER Inc) , the validation and quantification of the enriched target DNA in each library was performed using the 2100 Bioanalyzer system with the High Sensitivity DNA Kit and the 2100 Expert Software (Agilent Technologies Inc, CA, USA ). .. The last step of the protocol was to pool samples for multiplexed sequencing in the Illumina sequencing platform MiSeq System (Illumina,Inc ).

Sequencing:

Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing
Article Snippet: .. We will discuss the automation of preparation of libraries with the SMRTbell Template Preparation kit as well as analysis of gDNA, fragmented DNA and the final libraries ready for sequencing with both the Agilent electrophoresis platform: Agilent 2100 Bioanalyzer System using the DNA 12000 assay and the Agilent TapeStation System using the genomic DNA ScreenTape and matching reagents. ..

Chromatin Immunoprecipitation:

Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins
Article Snippet: .. Agilent 2100 Bioanalyzer system Chip-based analysis was performed with the Agilent 2100 Bioanalyzer system (Agilent, Waldbronn, Germany). ..

Software:

Article Title: Targeted next generation sequencing for molecular diagnosis of Usher syndrome
Article Snippet: .. A PCR amplification of the captured target libraries was performed following the manufacturer’s instructions and, after its purification with the “AMPure XP beads” (BECKMAN CULTER Inc) , the validation and quantification of the enriched target DNA in each library was performed using the 2100 Bioanalyzer system with the High Sensitivity DNA Kit and the 2100 Expert Software (Agilent Technologies Inc, CA, USA ). .. The last step of the protocol was to pool samples for multiplexed sequencing in the Illumina sequencing platform MiSeq System (Illumina,Inc ).

Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins
Article Snippet: .. The Agilent 2100 Bioanalyzer system included protein assay analysis software and software for managing patient data. .. Commercially purified albumin, lysozyme, lactoferrin (all from Sigma), and recombinant lipophilin A and C (courtesy gift from Dr. Joerg Klug, Institut fuer Anatomie und Zellbiologie, JLU Giessen, Germany) and lipocalin (courtesy gift from Prof. Bernhard Redl, Division of Molecular Biology Biocenter-Innsbruck Medical University, Austria) were run as standards to observe and evaluate their separation and migration patterns.

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    Agilent technologies dna chips
    Amplification results using the proposed <t>DNA</t> extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( <t>CSRM60</t> ), 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 ).
    Dna Chips, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna chips/product/Agilent technologies
    Average 91 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    dna chips - by Bioz Stars, 2020-09
    91/100 stars
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    99
    Agilent technologies agilent 2100 bioanalyzer
    Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using <t>Agilent</t> 2100 <t>Bioanalyzer</t> with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.
    Agilent 2100 Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 6798 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agilent 2100 bioanalyzer/product/Agilent technologies
    Average 99 stars, based on 6798 article reviews
    Price from $9.99 to $1999.99
    agilent 2100 bioanalyzer - by Bioz Stars, 2020-09
    99/100 stars
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    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

    Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.

    Journal: BMC Research Notes

    Article Title: Ensuring good quality rna for quantitative real-time pcr isolated from renal proximal tubular cells using laser capture microdissection

    doi: 10.1186/1756-0500-7-62

    Figure Lengend Snippet: Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.

    Article Snippet: RNA integrity number (RIN) RIN was measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit.

    Techniques: Concentration Assay, Produced

    Analyses of the various antibody formats ( A ) To assess the purity and confirm the size of each reagent, the various antibody formats were analyzed by Agilent 2100 bioanalyzer. Proteins were assessed under non-reduced (NR) and reduced conditions (R). 1, IgG; 2, heavy chain; 3, light chain; 4, F(ab)’ 2 ; 5, VH-CH1-hinge; 6, monovalent antibody; 7, hinge-Fc; 8, Fab; 9, light chain and VH-CH1. ( B ) The binding of Hu 15C1 (black circles), monovalent Hu 15C1 (gray triangles), F(ab)’ 2 Hu 15C1 (open circles) and Fab Hu 15C1 (open diamonds) to TLR4 was analyzed by competitive ELISA. To compare the different antibody formats, the same number of binding site was used, i.e., the molar concentration of monovalent and Fab is twice the molar concentration of IgG and F(ab)’ 2 . Results are normalized and expressed as mean ± SD of duplicates. An F test was used to compare the fitted curves of different groups. ns: not significant.

    Journal: mAbs

    Article Title: Maximizing the potency of an anti-TLR4 monoclonal antibody by exploiting proximity to Fcγ receptors

    doi: 10.4161/19420862.2014.975098

    Figure Lengend Snippet: Analyses of the various antibody formats ( A ) To assess the purity and confirm the size of each reagent, the various antibody formats were analyzed by Agilent 2100 bioanalyzer. Proteins were assessed under non-reduced (NR) and reduced conditions (R). 1, IgG; 2, heavy chain; 3, light chain; 4, F(ab)’ 2 ; 5, VH-CH1-hinge; 6, monovalent antibody; 7, hinge-Fc; 8, Fab; 9, light chain and VH-CH1. ( B ) The binding of Hu 15C1 (black circles), monovalent Hu 15C1 (gray triangles), F(ab)’ 2 Hu 15C1 (open circles) and Fab Hu 15C1 (open diamonds) to TLR4 was analyzed by competitive ELISA. To compare the different antibody formats, the same number of binding site was used, i.e., the molar concentration of monovalent and Fab is twice the molar concentration of IgG and F(ab)’ 2 . Results are normalized and expressed as mean ± SD of duplicates. An F test was used to compare the fitted curves of different groups. ns: not significant.

    Article Snippet: The purity and chain composition of each reagent was assessed using an Agilent 2100 bioanalyzer ( ).

    Techniques: Binding Assay, Competitive ELISA, Concentration Assay

    Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.

    Journal: BMC Research Notes

    Article Title: Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank – evaluation of RNA quality and stability

    doi: 10.1186/1756-0500-7-633

    Figure Lengend Snippet: Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.

    Article Snippet: The RNA integrity was assessed by an Agilent 2100 Bioanalyzer using the Eukaryote total RNA 6000 Nano LabChip kit and Eukaryote total RNA Nano assay according to the manufacturer’s instructions (Agilent Technologies, Palo Alto, CA).

    Techniques: Isolation