Structured Review

Agilent technologies 2100 bioanalyzer
Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and <t>2100</t> <t>Bioanalyzer</t> electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.
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Images

1) Product Images from "MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits"

Article Title: MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits

Journal: BMC Research Notes

doi: 10.1186/1756-0500-4-217

Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.
Figure Legend Snippet: Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.

Techniques Used: Software, Electrophoresis, Standard Deviation

2) Product Images from "RNase L Interacts with Filamin A To Regulate Actin Dynamics and Barrier Function for Viral Entry"

Article Title: RNase L Interacts with Filamin A To Regulate Actin Dynamics and Barrier Function for Viral Entry

Journal: mBio

doi: 10.1128/mBio.02012-14

Effect of Filamin A and actin cytoskeleton on RNase L activity. M2 stable cell lines expressing Myc-Filamin A and/or Flag-RNase L WT or Flag-RNase L R667A were analyzed for expression of RNase L and Filamin A on immunoblots (A) and transfected with 10 µM 2-5A (B), and RNase L-mediated cleavage of rRNA (arrows) was analyzed on RNA chips using an Agilent 2100 Bioanalyzer. (C) HT1080 cells were pretreated with Cytochalasin D (Cyto D; 5 µM), Latrunculin A (Lat A; 0.5 µM), or vehicle (DMSO) for 1 h followed by transfection with 10 µM 2-5A or 2 µg/ml of poly(I·C). Characteristic RNase L-generated rRNA cleavage products (arrows) were detected as described for panel B. Representative images from three independent experiments are shown.
Figure Legend Snippet: Effect of Filamin A and actin cytoskeleton on RNase L activity. M2 stable cell lines expressing Myc-Filamin A and/or Flag-RNase L WT or Flag-RNase L R667A were analyzed for expression of RNase L and Filamin A on immunoblots (A) and transfected with 10 µM 2-5A (B), and RNase L-mediated cleavage of rRNA (arrows) was analyzed on RNA chips using an Agilent 2100 Bioanalyzer. (C) HT1080 cells were pretreated with Cytochalasin D (Cyto D; 5 µM), Latrunculin A (Lat A; 0.5 µM), or vehicle (DMSO) for 1 h followed by transfection with 10 µM 2-5A or 2 µg/ml of poly(I·C). Characteristic RNase L-generated rRNA cleavage products (arrows) were detected as described for panel B. Representative images from three independent experiments are shown.

Techniques Used: Activity Assay, Stable Transfection, Expressing, Western Blot, Transfection, Generated

3) Product Images from "The Effect of Formaldehyde Fixation on RNA"

Article Title: The Effect of Formaldehyde Fixation on RNA

Journal: The Journal of Molecular Diagnostics : JMD

doi: 10.1016/j.jmoldx.2011.01.010

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
Figure Legend 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

Techniques Used:

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
Figure Legend 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

Techniques Used:

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
Figure Legend 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

Techniques Used:

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
Figure Legend 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

Techniques Used:

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
Figure Legend 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

Techniques Used: Fluorescence

4) Product Images from "High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases"

Article Title: High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases

Journal: RNA

doi: 10.1261/rna.054809.115

Bioanalyzer traces showing size profiles of plasma RNAs before and after various treatments. Total plasma RNA was prepared by the Direct-zol method, and a 1-µL portion was analyzed with an RNA 6000 Pico Kit (mRNA assay) on a 2100 Bioanalyzer (Agilent)
Figure Legend Snippet: Bioanalyzer traces showing size profiles of plasma RNAs before and after various treatments. Total plasma RNA was prepared by the Direct-zol method, and a 1-µL portion was analyzed with an RNA 6000 Pico Kit (mRNA assay) on a 2100 Bioanalyzer (Agilent)

Techniques Used:

5) Product Images from "Effect of lesion proximity on the regenerative response of long descending propriospinal neurons after spinal transection injury"

Article Title: Effect of lesion proximity on the regenerative response of long descending propriospinal neurons after spinal transection injury

Journal: BMC Neuroscience

doi: 10.1186/s12868-019-0491-y

RNA Quality Pseudogel and R.I.N. Fluorogold retrograde labelled neurons were collected by laser capture microdissection, and processed to collect the RNA that was used to measure the changes in genetic expression. The quality of the RNA was assessed using the Qiagen 2100 bioanalyzer (Agilent Technologies; Santa Clara, CA) which provided both an RNA Integrity Number (RIN), and corresponding pseudo gel. L = Ladder, C = Control Animal, and I = Animal receiving spinal transection injury
Figure Legend Snippet: RNA Quality Pseudogel and R.I.N. Fluorogold retrograde labelled neurons were collected by laser capture microdissection, and processed to collect the RNA that was used to measure the changes in genetic expression. The quality of the RNA was assessed using the Qiagen 2100 bioanalyzer (Agilent Technologies; Santa Clara, CA) which provided both an RNA Integrity Number (RIN), and corresponding pseudo gel. L = Ladder, C = Control Animal, and I = Animal receiving spinal transection injury

Techniques Used: Laser Capture Microdissection, Expressing

6) Product Images from "A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA"

Article Title: A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA

Journal: BMC Medical Genomics

doi: 10.1186/s12920-017-0290-1

Bioanalyser images demonstrating quality of two FFPE RRBS libraries. Each of the RRBS libraries (FFPE1 and FFPE2) was run on an Agilent 2100 Bioanalyzer using the high sensitivity DNA kit. The electropherogram displays a plot of fragment size (bp) versus fluorescence intensity. Peaks at 35 bp and 10,380 bp represent lower and upper markers. The 160–340 bp peaks represent the RRBS library
Figure Legend Snippet: Bioanalyser images demonstrating quality of two FFPE RRBS libraries. Each of the RRBS libraries (FFPE1 and FFPE2) was run on an Agilent 2100 Bioanalyzer using the high sensitivity DNA kit. The electropherogram displays a plot of fragment size (bp) versus fluorescence intensity. Peaks at 35 bp and 10,380 bp represent lower and upper markers. The 160–340 bp peaks represent the RRBS library

Techniques Used: Formalin-fixed Paraffin-Embedded, Fluorescence

7) Product Images from "Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates"

Article Title: Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates

Journal: Journal of Molecular Biology

doi: 10.1016/j.jmb.2008.03.077

Redox states of BsTrxA monomers and dimers. (a) Purified His6-tagged BsTrxA proteins were separated by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies). WT, BsTrxA with wild-type active site; C29S, C29S single-mutant BsTrxA; C32S, C32S single-mutant BsTrxA; C29S–C32S, C29S–C32S double-mutant BsTrxA. To monitor the presence of free thiols in the purified BsTrxA proteins, samples were incubated in the presence or in the absence of 0.3 mM AMS (lanes marked + AMS or − AMS). To test whether the C29S and C32S dimers are formed by disulfide bonding, these proteins were incubated with 10 mM DTT (lanes marked + DTT). DTT was absent from all other samples. The image of the Bioanalyzer chromatogram was generated using the 2100 Expert Software package (Agilent Technologies). (b) C32S BsTrxA protein (∼ 2.5 μg) was reduced with increasing concentrations of DTT (shown on top of the panel) and separated by capillary electrophoresis as described for (a). The dimer-to-monomer ratios (Dimer [%]) are shown at the bottom of the panel.
Figure Legend Snippet: Redox states of BsTrxA monomers and dimers. (a) Purified His6-tagged BsTrxA proteins were separated by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies). WT, BsTrxA with wild-type active site; C29S, C29S single-mutant BsTrxA; C32S, C32S single-mutant BsTrxA; C29S–C32S, C29S–C32S double-mutant BsTrxA. To monitor the presence of free thiols in the purified BsTrxA proteins, samples were incubated in the presence or in the absence of 0.3 mM AMS (lanes marked + AMS or − AMS). To test whether the C29S and C32S dimers are formed by disulfide bonding, these proteins were incubated with 10 mM DTT (lanes marked + DTT). DTT was absent from all other samples. The image of the Bioanalyzer chromatogram was generated using the 2100 Expert Software package (Agilent Technologies). (b) C32S BsTrxA protein (∼ 2.5 μg) was reduced with increasing concentrations of DTT (shown on top of the panel) and separated by capillary electrophoresis as described for (a). The dimer-to-monomer ratios (Dimer [%]) are shown at the bottom of the panel.

Techniques Used: Purification, Electrophoresis, Mutagenesis, Incubation, Affinity Magnetic Separation, Generated, Software

8) Product Images from "Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner"

Article Title: Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner

Journal: Cytoskeleton (Hoboken, N.J.)

doi: 10.1002/cm.21489

Analysis of lev-11 mRNAs by RT-PCR. (Lanes 1–6) Total RNAs from synchronized wild-type L1 larvae were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with an on-chip capillary electrophoresis system, 2100 BioAnalyzer (Agilent). Results are shown in gel-like presentations. (Lanes 7–9) Total RNAs from mixed-stage wild-type worms were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with conventional agarose gel electrophoresis. Major cDNA species were cloned and sequenced, and identified isoforms are indicated. DNA size markers are shown on the left of lanes 1 and 7. The presented data are representative results from at least three separate experiments.
Figure Legend Snippet: Analysis of lev-11 mRNAs by RT-PCR. (Lanes 1–6) Total RNAs from synchronized wild-type L1 larvae were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with an on-chip capillary electrophoresis system, 2100 BioAnalyzer (Agilent). Results are shown in gel-like presentations. (Lanes 7–9) Total RNAs from mixed-stage wild-type worms were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with conventional agarose gel electrophoresis. Major cDNA species were cloned and sequenced, and identified isoforms are indicated. DNA size markers are shown on the left of lanes 1 and 7. The presented data are representative results from at least three separate experiments.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Chromatin Immunoprecipitation, Electrophoresis, Agarose Gel Electrophoresis, Clone Assay

9) Product Images from "Tropomyosin isoforms differentially affect muscle contractility in the head and body regions of the nematode Caenorhabditis elegans"

Article Title: Tropomyosin isoforms differentially affect muscle contractility in the head and body regions of the nematode Caenorhabditis elegans

Journal: Molecular Biology of the Cell

doi: 10.1091/mbc.E17-03-0152

Characterization of mutually exclusive seventh exons of the C. elegans lev-11 tropomyosin gene. (A) Structure of the lev-11 gene is shown schematically (top) with numbered boxes indicating exons. Recently characterized alternative exons 7a and 7b are shown in green. Below the gene structure are splicing patterns of LEV-11A/CeTMI, a newly identified isoform, LEV-11O, and three previously characterized isoforms, LEV-11D/CeTMII, LEV-11E/CeTMIII, and LEV-11C/CeTMIV. Coding and noncoding regions are shown in orange and light yellow, respectively. Note that exon 9c is used in all known isoforms either as a coding region (LEV-11A and LEV-11O) or as a noncoding region when 9a or 9b is used as a coding region (LEV-11C, LEV-11D, and LEV-11E). (B) Analysis of lev-11 mRNAs by RT-PCR. Total RNAs from synchronized wild-type L1 larvae were subjected to RT-PCR with indicated primer pairs and cycle numbers, and the PCR products were analyzed with a 2100 BioAnalyzer (Agilent). DNA size markers are shown on the left. Results are shown in gel-like presentations. Exon combinations of representative bands a–d are shown below. Multiple bands in E7b/E9c (lane 6) were cloned and sequenced, and the exon combinations are indicated on the right. Asterisks indicate artificial PCR products due to excessive cycles. (C) Alignment of amino acid sequences encoded by exons 7a and 7b. Identical residues are indicated with black backgrounds. Point mutations in lev-11(gk334531) and lev-11(x12) are shown at the top and bottom of the sequences, respectively. (D) Probability of coiled-coil formation (0–1) was calculated from the full-length sequences of LEV-11A and LEV-11O by COILS ( Lupas et al. , 1991 ), and plots of exon 7-coded regions are shown.
Figure Legend Snippet: Characterization of mutually exclusive seventh exons of the C. elegans lev-11 tropomyosin gene. (A) Structure of the lev-11 gene is shown schematically (top) with numbered boxes indicating exons. Recently characterized alternative exons 7a and 7b are shown in green. Below the gene structure are splicing patterns of LEV-11A/CeTMI, a newly identified isoform, LEV-11O, and three previously characterized isoforms, LEV-11D/CeTMII, LEV-11E/CeTMIII, and LEV-11C/CeTMIV. Coding and noncoding regions are shown in orange and light yellow, respectively. Note that exon 9c is used in all known isoforms either as a coding region (LEV-11A and LEV-11O) or as a noncoding region when 9a or 9b is used as a coding region (LEV-11C, LEV-11D, and LEV-11E). (B) Analysis of lev-11 mRNAs by RT-PCR. Total RNAs from synchronized wild-type L1 larvae were subjected to RT-PCR with indicated primer pairs and cycle numbers, and the PCR products were analyzed with a 2100 BioAnalyzer (Agilent). DNA size markers are shown on the left. Results are shown in gel-like presentations. Exon combinations of representative bands a–d are shown below. Multiple bands in E7b/E9c (lane 6) were cloned and sequenced, and the exon combinations are indicated on the right. Asterisks indicate artificial PCR products due to excessive cycles. (C) Alignment of amino acid sequences encoded by exons 7a and 7b. Identical residues are indicated with black backgrounds. Point mutations in lev-11(gk334531) and lev-11(x12) are shown at the top and bottom of the sequences, respectively. (D) Probability of coiled-coil formation (0–1) was calculated from the full-length sequences of LEV-11A and LEV-11O by COILS ( Lupas et al. , 1991 ), and plots of exon 7-coded regions are shown.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Clone Assay

10) Product Images from "Defining nonsense-mediated mRNA decay intermediates in human cells"

Article Title: Defining nonsense-mediated mRNA decay intermediates in human cells

Journal: Methods (San Diego, Calif.)

doi: 10.1016/j.ymeth.2018.12.005

Quality check of IP specificity and first and second PCR-sample sizes and amounts used for NMD-DegSeq. (A) Western blot of lysates of HEK293T cells using the specified antibodies prior to (Input) or after IP using anti(α)-p-UFP1 S1116 antibody (i.e. (α)-p-UFPl) or, as a negative control, rabbit (r)IgG. The left-most five lanes are 3-fold dilutions of Input sample (i.e. before IP). (B) SYBR Gold staining after the second PCR-amplification for the purpose of quality control. Analyses are of RNA samples prior to (Input); after (+) IP using anti(α)-p-UFP1 S1116 antibody or, as a negative control, rabbit (r)IgG; or no RNA (None). These RNAs were subjected to the first PCR and, subsequently, as second PCR, after which PCR products were (+) or were not (−) size-selected (the latter has Adapter self-ligation products that should be eliminated prior to library construction). (C) Agilent Bioanalyzer 2100 analyses using capillary electrophoresis (upper) and tracing (lower) of fluorescent samples after the first PCR. Results confirm adequate quality and quantity of samples before (Input) and after IP so that index PCR can be performed to generate samples for Illumina sequencing. FU, fluorescence units; bp, base pairs.
Figure Legend Snippet: Quality check of IP specificity and first and second PCR-sample sizes and amounts used for NMD-DegSeq. (A) Western blot of lysates of HEK293T cells using the specified antibodies prior to (Input) or after IP using anti(α)-p-UFP1 S1116 antibody (i.e. (α)-p-UFPl) or, as a negative control, rabbit (r)IgG. The left-most five lanes are 3-fold dilutions of Input sample (i.e. before IP). (B) SYBR Gold staining after the second PCR-amplification for the purpose of quality control. Analyses are of RNA samples prior to (Input); after (+) IP using anti(α)-p-UFP1 S1116 antibody or, as a negative control, rabbit (r)IgG; or no RNA (None). These RNAs were subjected to the first PCR and, subsequently, as second PCR, after which PCR products were (+) or were not (−) size-selected (the latter has Adapter self-ligation products that should be eliminated prior to library construction). (C) Agilent Bioanalyzer 2100 analyses using capillary electrophoresis (upper) and tracing (lower) of fluorescent samples after the first PCR. Results confirm adequate quality and quantity of samples before (Input) and after IP so that index PCR can be performed to generate samples for Illumina sequencing. FU, fluorescence units; bp, base pairs.

Techniques Used: Polymerase Chain Reaction, Western Blot, Negative Control, Staining, Amplification, Ligation, Electrophoresis, Sequencing, Fluorescence

11) Product Images from "Identification of deleterious rare variants in MTTP, PNPLA3, and TM6SF2 in Japanese males and association studies with NAFLD"

Article Title: Identification of deleterious rare variants in MTTP, PNPLA3, and TM6SF2 in Japanese males and association studies with NAFLD

Journal: Lipids in Health and Disease

doi: 10.1186/s12944-017-0570-y

Functional assessment of variants at intron-exon junctions. a Intron 6 to intron 8 of TM6SF2 was inserted into intron 1 of ACKR1 under control of the CMV promoter. b Intron 4 to 5 of PNPLA3 was inserted into intron 1 of TRIB2 . The constructs were transfected into Huh-7 cells. Twenty-four hours after transfection, total RNA was extracted from the transfected cells, and the corresponding cDNA was used as a template for RT-PCR. The amplicon sizes of each RT-PCR product were measured with a 2100 BioAnalyzer. Estimated splicing variants from amplicon sizes are shown on the left side
Figure Legend Snippet: Functional assessment of variants at intron-exon junctions. a Intron 6 to intron 8 of TM6SF2 was inserted into intron 1 of ACKR1 under control of the CMV promoter. b Intron 4 to 5 of PNPLA3 was inserted into intron 1 of TRIB2 . The constructs were transfected into Huh-7 cells. Twenty-four hours after transfection, total RNA was extracted from the transfected cells, and the corresponding cDNA was used as a template for RT-PCR. The amplicon sizes of each RT-PCR product were measured with a 2100 BioAnalyzer. Estimated splicing variants from amplicon sizes are shown on the left side

Techniques Used: Functional Assay, Construct, Transfection, Reverse Transcription Polymerase Chain Reaction, Amplification

12) Product Images from "MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits"

Article Title: MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits

Journal: BMC Research Notes

doi: 10.1186/1756-0500-4-217

Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.
Figure Legend Snippet: Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.

Techniques Used: Software, Electrophoresis, Standard Deviation

13) Product Images from "Generating Exome Enriched Sequencing Libraries from Formalin-Fixed, Paraffin-Embedded Tissue DNA for Next Generation Sequencing"

Article Title: Generating Exome Enriched Sequencing Libraries from Formalin-Fixed, Paraffin-Embedded Tissue DNA for Next Generation Sequencing

Journal: Current protocols in human genetics

doi: 10.1002/cphg.27

DNA fragmentation quality check. 50ng of FFPE derived DNA was sheared using the Covaris E220 instrument. Following clean up each sample was diluted 1:5 and run on a 2100 BioAnalyzer High Sensitivity DNA chip to check the DNA fragment size distribution and sample concentration. A broad distribution of sizes should be expected between 100-2000bp is typical, with the majority of the fragments in the 200-800bp range.
Figure Legend Snippet: DNA fragmentation quality check. 50ng of FFPE derived DNA was sheared using the Covaris E220 instrument. Following clean up each sample was diluted 1:5 and run on a 2100 BioAnalyzer High Sensitivity DNA chip to check the DNA fragment size distribution and sample concentration. A broad distribution of sizes should be expected between 100-2000bp is typical, with the majority of the fragments in the 200-800bp range.

Techniques Used: Formalin-fixed Paraffin-Embedded, Derivative Assay, Chromatin Immunoprecipitation, Concentration Assay

Pre-Capture amplification quality check. Adapter ligated libraries were amplified prior to hybridization capture. Following clean up each sample was diluted 1:100 and run on a 2100 BioAnalyzer High Sensitivity DNA chip to confirm library fragment size and concentration. A focused size distribution between 200-800bp is typical. Quality of FFPE samples may affect how this distribution appears (average size between 250-550bp). Fragment size includes the added length of bases (123bp) from the ligated adapters.
Figure Legend Snippet: Pre-Capture amplification quality check. Adapter ligated libraries were amplified prior to hybridization capture. Following clean up each sample was diluted 1:100 and run on a 2100 BioAnalyzer High Sensitivity DNA chip to confirm library fragment size and concentration. A focused size distribution between 200-800bp is typical. Quality of FFPE samples may affect how this distribution appears (average size between 250-550bp). Fragment size includes the added length of bases (123bp) from the ligated adapters.

Techniques Used: Amplification, Hybridization, Chromatin Immunoprecipitation, Concentration Assay, Formalin-fixed Paraffin-Embedded

14) Product Images from "Defining nonsense-mediated mRNA decay intermediates in human cells"

Article Title: Defining nonsense-mediated mRNA decay intermediates in human cells

Journal: Methods (San Diego, Calif.)

doi: 10.1016/j.ymeth.2018.12.005

Quality check of IP specificity and first and second PCR-sample sizes and amounts used for NMD-DegSeq. (A) Western blot of lysates of HEK293T cells using the specified antibodies prior to (Input) or after IP using anti(α)-p-UFP1 S1116 antibody (i.e. (α)-p-UFPl) or, as a negative control, rabbit (r)IgG. The left-most five lanes are 3-fold dilutions of Input sample (i.e. before IP). (B) SYBR Gold staining after the second PCR-amplification for the purpose of quality control. Analyses are of RNA samples prior to (Input); after (+) IP using anti(α)-p-UFP1 S1116 antibody or, as a negative control, rabbit (r)IgG; or no RNA (None). These RNAs were subjected to the first PCR and, subsequently, as second PCR, after which PCR products were (+) or were not (−) size-selected (the latter has Adapter self-ligation products that should be eliminated prior to library construction). (C) Agilent Bioanalyzer 2100 analyses using capillary electrophoresis (upper) and tracing (lower) of fluorescent samples after the first PCR. Results confirm adequate quality and quantity of samples before (Input) and after IP so that index PCR can be performed to generate samples for Illumina sequencing. FU, fluorescence units; bp, base pairs.
Figure Legend Snippet: Quality check of IP specificity and first and second PCR-sample sizes and amounts used for NMD-DegSeq. (A) Western blot of lysates of HEK293T cells using the specified antibodies prior to (Input) or after IP using anti(α)-p-UFP1 S1116 antibody (i.e. (α)-p-UFPl) or, as a negative control, rabbit (r)IgG. The left-most five lanes are 3-fold dilutions of Input sample (i.e. before IP). (B) SYBR Gold staining after the second PCR-amplification for the purpose of quality control. Analyses are of RNA samples prior to (Input); after (+) IP using anti(α)-p-UFP1 S1116 antibody or, as a negative control, rabbit (r)IgG; or no RNA (None). These RNAs were subjected to the first PCR and, subsequently, as second PCR, after which PCR products were (+) or were not (−) size-selected (the latter has Adapter self-ligation products that should be eliminated prior to library construction). (C) Agilent Bioanalyzer 2100 analyses using capillary electrophoresis (upper) and tracing (lower) of fluorescent samples after the first PCR. Results confirm adequate quality and quantity of samples before (Input) and after IP so that index PCR can be performed to generate samples for Illumina sequencing. FU, fluorescence units; bp, base pairs.

Techniques Used: Polymerase Chain Reaction, Western Blot, Negative Control, Staining, Amplification, Ligation, Electrophoresis, Sequencing, Fluorescence

15) Product Images from "Genotyping of KRAS Mutational Status by the In-Check Lab-on-Chip Platform"

Article Title: Genotyping of KRAS Mutational Status by the In-Check Lab-on-Chip Platform

Journal: Sensors (Basel, Switzerland)

doi: 10.3390/s18010131

Analysis performed by 2100-Bioanalyzer system of amplicons generated after PCR amplification onto Lab-on chip. The products obtained show an appropriate size difference to allow the discrimination and a good differentiation between the exons 2, 3, and 4.
Figure Legend Snippet: Analysis performed by 2100-Bioanalyzer system of amplicons generated after PCR amplification onto Lab-on chip. The products obtained show an appropriate size difference to allow the discrimination and a good differentiation between the exons 2, 3, and 4.

Techniques Used: Generated, Polymerase Chain Reaction, Amplification, Lab-on-a-Chip

16) Product Images from "Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner"

Article Title: Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner

Journal: Cytoskeleton (Hoboken, N.J.)

doi: 10.1002/cm.21489

Analysis of lev-11 mRNAs by RT-PCR. (Lanes 1–6) Total RNAs from synchronized wild-type L1 larvae were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with an on-chip capillary electrophoresis system, 2100 BioAnalyzer (Agilent). Results are shown in gel-like presentations. (Lanes 7–9) Total RNAs from mixed-stage wild-type worms were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with conventional agarose gel electrophoresis. Major cDNA species were cloned and sequenced, and identified isoforms are indicated. DNA size markers are shown on the left of lanes 1 and 7. The presented data are representative results from at least three separate experiments.
Figure Legend Snippet: Analysis of lev-11 mRNAs by RT-PCR. (Lanes 1–6) Total RNAs from synchronized wild-type L1 larvae were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with an on-chip capillary electrophoresis system, 2100 BioAnalyzer (Agilent). Results are shown in gel-like presentations. (Lanes 7–9) Total RNAs from mixed-stage wild-type worms were subjected to RT-PCR with indicated primer pairs (shown on top) and cycle numbers (shown on bottom), and the PCR products were analyzed with conventional agarose gel electrophoresis. Major cDNA species were cloned and sequenced, and identified isoforms are indicated. DNA size markers are shown on the left of lanes 1 and 7. The presented data are representative results from at least three separate experiments.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Chromatin Immunoprecipitation, Electrophoresis, Agarose Gel Electrophoresis, Clone Assay

17) Product Images from "Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates"

Article Title: Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates

Journal: Journal of Molecular Biology

doi: 10.1016/j.jmb.2008.03.077

Redox states of BsTrxA monomers and dimers. (a) Purified His6-tagged BsTrxA proteins were separated by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies). WT, BsTrxA with wild-type active site; C29S, C29S single-mutant BsTrxA; C32S, C32S single-mutant BsTrxA; C29S–C32S, C29S–C32S double-mutant BsTrxA. To monitor the presence of free thiols in the purified BsTrxA proteins, samples were incubated in the presence or in the absence of 0.3 mM AMS (lanes marked + AMS or − AMS). To test whether the C29S and C32S dimers are formed by disulfide bonding, these proteins were incubated with 10 mM DTT (lanes marked + DTT). DTT was absent from all other samples. The image of the Bioanalyzer chromatogram was generated using the 2100 Expert Software package (Agilent Technologies). (b) C32S BsTrxA protein (∼ 2.5 μg) was reduced with increasing concentrations of DTT (shown on top of the panel) and separated by capillary electrophoresis as described for (a). The dimer-to-monomer ratios (Dimer [%]) are shown at the bottom of the panel.
Figure Legend Snippet: Redox states of BsTrxA monomers and dimers. (a) Purified His6-tagged BsTrxA proteins were separated by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies). WT, BsTrxA with wild-type active site; C29S, C29S single-mutant BsTrxA; C32S, C32S single-mutant BsTrxA; C29S–C32S, C29S–C32S double-mutant BsTrxA. To monitor the presence of free thiols in the purified BsTrxA proteins, samples were incubated in the presence or in the absence of 0.3 mM AMS (lanes marked + AMS or − AMS). To test whether the C29S and C32S dimers are formed by disulfide bonding, these proteins were incubated with 10 mM DTT (lanes marked + DTT). DTT was absent from all other samples. The image of the Bioanalyzer chromatogram was generated using the 2100 Expert Software package (Agilent Technologies). (b) C32S BsTrxA protein (∼ 2.5 μg) was reduced with increasing concentrations of DTT (shown on top of the panel) and separated by capillary electrophoresis as described for (a). The dimer-to-monomer ratios (Dimer [%]) are shown at the bottom of the panel.

Techniques Used: Purification, Electrophoresis, Mutagenesis, Incubation, Affinity Magnetic Separation, Generated, Software

18) Product Images from "Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates"

Article Title: Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates

Journal: Journal of Molecular Biology

doi: 10.1016/j.jmb.2008.03.077

Redox states of BsTrxA monomers and dimers. (a) Purified His6-tagged BsTrxA proteins were separated by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies). WT, BsTrxA with wild-type active site; C29S, C29S single-mutant BsTrxA; C32S, C32S single-mutant BsTrxA; C29S–C32S, C29S–C32S double-mutant BsTrxA. To monitor the presence of free thiols in the purified BsTrxA proteins, samples were incubated in the presence or in the absence of 0.3 mM AMS (lanes marked + AMS or − AMS). To test whether the C29S and C32S dimers are formed by disulfide bonding, these proteins were incubated with 10 mM DTT (lanes marked + DTT). DTT was absent from all other samples. The image of the Bioanalyzer chromatogram was generated using the 2100 Expert Software package (Agilent Technologies). (b) C32S BsTrxA protein (∼ 2.5 μg) was reduced with increasing concentrations of DTT (shown on top of the panel) and separated by capillary electrophoresis as described for (a). The dimer-to-monomer ratios (Dimer [%]) are shown at the bottom of the panel.
Figure Legend Snippet: Redox states of BsTrxA monomers and dimers. (a) Purified His6-tagged BsTrxA proteins were separated by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies). WT, BsTrxA with wild-type active site; C29S, C29S single-mutant BsTrxA; C32S, C32S single-mutant BsTrxA; C29S–C32S, C29S–C32S double-mutant BsTrxA. To monitor the presence of free thiols in the purified BsTrxA proteins, samples were incubated in the presence or in the absence of 0.3 mM AMS (lanes marked + AMS or − AMS). To test whether the C29S and C32S dimers are formed by disulfide bonding, these proteins were incubated with 10 mM DTT (lanes marked + DTT). DTT was absent from all other samples. The image of the Bioanalyzer chromatogram was generated using the 2100 Expert Software package (Agilent Technologies). (b) C32S BsTrxA protein (∼ 2.5 μg) was reduced with increasing concentrations of DTT (shown on top of the panel) and separated by capillary electrophoresis as described for (a). The dimer-to-monomer ratios (Dimer [%]) are shown at the bottom of the panel.

Techniques Used: Purification, Electrophoresis, Mutagenesis, Incubation, Affinity Magnetic Separation, Generated, Software

19) Product Images from "Effects of Acute Aerobic Exercise on Rats Serum Extracellular Vesicles Diameter, Concentration and Small RNAs Content"

Article Title: Effects of Acute Aerobic Exercise on Rats Serum Extracellular Vesicles Diameter, Concentration and Small RNAs Content

Journal: Frontiers in Physiology

doi: 10.3389/fphys.2018.00532

Acute aerobic exercise decreases rat serum EVs modal diameter and increases serum EVs concentration. (A) Workflow representing the acute exercise protocol used to provide aerobic exercise for Wistar rats running on a treadmill. (B) Immunoelectron micrograph of rat serum EVs purified by Exoquick. Black dots are 10 nm gold particle linked to the exosome marker CD63. (C) Tunable resistive pulse sensing (TRPS) analysis showed a slightly reduction in EVs modal diameter in high intensity exercised group compared to non-exercised ( p = 0.057) and moderate intensity exercised groups ( p = 0.028). The median groups for EVs modal diameter range from 88 nm in non-exercised, through 87 nm in low intensity, 91.5 nm in moderate intensity and 85 nm in high intensity exercised group (D) . The concentration of EVs purified from rat’s serum after exercise measured by TRPS. There is a statistical increase in median EVs concentration after exercise, which range from 1.1 × 10 9 in non-exercised group to 3 × 10 9 in low intensity exercised group ( p = 0.014), 2.5 × 10 9 in moderate intensity exercised group ( p = 0.021) and 3 × 10 9 in high intensity exercised group ( p = 0.02). (E) The median concentration of rat serum EVs proteins. Proteins were purified from EVs and quantified. There is a statistical significance increase in EVs protein concentration median after exercise ranging from 0.935 mg.mL -1 in non-exercised group to 4.33 mg.mL -1 in low intensity exercised group ( p = 0.014), 4.31 mg.mL -1 in moderate intensity exercised group ( p = 0.014) and 4.31 mg.mL -1 in high intensity exercised group ( p = 0.014). (F) Total rat serum protein profile after Exoquick purification analyzed by SDS-PAGE 12%. Exoquick fraction contains EVs proteins while supernatant fraction contains free proteins that were not precipitated by Exoquick. (G) Western blotting of EVs proteins shows an increase in the exosome marker CD63 while increasing the intensity of exercise. ApoA-IV protein levels remained stable regardless of exercise intensity. Calnexin was used to show the absence of endoplasmic reticulum proteins in purified EVs. (H) The concentration of EVs small RNAs from rat’s serum. Small RNAs were purified, quantified and characterized by 2100 Bioanalyzer (Agilent) using a small RNA chip. There is no statistical difference between group medians.
Figure Legend Snippet: Acute aerobic exercise decreases rat serum EVs modal diameter and increases serum EVs concentration. (A) Workflow representing the acute exercise protocol used to provide aerobic exercise for Wistar rats running on a treadmill. (B) Immunoelectron micrograph of rat serum EVs purified by Exoquick. Black dots are 10 nm gold particle linked to the exosome marker CD63. (C) Tunable resistive pulse sensing (TRPS) analysis showed a slightly reduction in EVs modal diameter in high intensity exercised group compared to non-exercised ( p = 0.057) and moderate intensity exercised groups ( p = 0.028). The median groups for EVs modal diameter range from 88 nm in non-exercised, through 87 nm in low intensity, 91.5 nm in moderate intensity and 85 nm in high intensity exercised group (D) . The concentration of EVs purified from rat’s serum after exercise measured by TRPS. There is a statistical increase in median EVs concentration after exercise, which range from 1.1 × 10 9 in non-exercised group to 3 × 10 9 in low intensity exercised group ( p = 0.014), 2.5 × 10 9 in moderate intensity exercised group ( p = 0.021) and 3 × 10 9 in high intensity exercised group ( p = 0.02). (E) The median concentration of rat serum EVs proteins. Proteins were purified from EVs and quantified. There is a statistical significance increase in EVs protein concentration median after exercise ranging from 0.935 mg.mL -1 in non-exercised group to 4.33 mg.mL -1 in low intensity exercised group ( p = 0.014), 4.31 mg.mL -1 in moderate intensity exercised group ( p = 0.014) and 4.31 mg.mL -1 in high intensity exercised group ( p = 0.014). (F) Total rat serum protein profile after Exoquick purification analyzed by SDS-PAGE 12%. Exoquick fraction contains EVs proteins while supernatant fraction contains free proteins that were not precipitated by Exoquick. (G) Western blotting of EVs proteins shows an increase in the exosome marker CD63 while increasing the intensity of exercise. ApoA-IV protein levels remained stable regardless of exercise intensity. Calnexin was used to show the absence of endoplasmic reticulum proteins in purified EVs. (H) The concentration of EVs small RNAs from rat’s serum. Small RNAs were purified, quantified and characterized by 2100 Bioanalyzer (Agilent) using a small RNA chip. There is no statistical difference between group medians.

Techniques Used: Concentration Assay, Purification, Marker, Tunable Resistive Pulse Sensing, Protein Concentration, SDS Page, Western Blot, Chromatin Immunoprecipitation

20) Product Images from "Retinoid Expression in Onchocercal Skin Disease: Pilot Study"

Article Title: Retinoid Expression in Onchocercal Skin Disease: Pilot Study

Journal: Infectious Diseases

doi: 10.1177/1178633617731741

RNA quality results from the 2100 Bioanalyzer.
Figure Legend Snippet: RNA quality results from the 2100 Bioanalyzer.

Techniques Used:

21) Product Images from "Stranded Whole Transcriptome RNA-Seq for All RNA Types"

Article Title: Stranded Whole Transcriptome RNA-Seq for All RNA Types

Journal: Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.]

doi: 10.1002/0471142905.hg1114s84

RNA profiles. RNA fractions were run on the 2100 Agilent Bioanalyzer RNA pico chip to demonstrate successful size fractionation and fragmentation profiles. Abbreviations; small RNA (smRNA), large RNA (LgRNA), fragmented large RNA (FLgRNA).
Figure Legend Snippet: RNA profiles. RNA fractions were run on the 2100 Agilent Bioanalyzer RNA pico chip to demonstrate successful size fractionation and fragmentation profiles. Abbreviations; small RNA (smRNA), large RNA (LgRNA), fragmented large RNA (FLgRNA).

Techniques Used: Chromatin Immunoprecipitation, Fractionation

22) Product Images from "High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis"

Article Title: High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis

Journal: Arthritis Research & Therapy

doi:

Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .
Figure Legend Snippet: Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Derivative Assay

23) Product Images from "Genotyping of KRAS Mutational Status by the In-Check Lab-on-Chip Platform"

Article Title: Genotyping of KRAS Mutational Status by the In-Check Lab-on-Chip Platform

Journal: Sensors (Basel, Switzerland)

doi: 10.3390/s18010131

Analysis performed by 2100-Bioanalyzer system of amplicons generated after PCR amplification onto Lab-on chip. The products obtained show an appropriate size difference to allow the discrimination and a good differentiation between the exons 2, 3, and 4.
Figure Legend Snippet: Analysis performed by 2100-Bioanalyzer system of amplicons generated after PCR amplification onto Lab-on chip. The products obtained show an appropriate size difference to allow the discrimination and a good differentiation between the exons 2, 3, and 4.

Techniques Used: Generated, Polymerase Chain Reaction, Amplification, Lab-on-a-Chip

24) Product Images from "The stage-specific testicular germ cell apoptotic response to low dose X-irradiation and 2,5-hexanedione combined exposure. I. Validation of the laser capture microdissection method for qRT-PCR array application"

Article Title: The stage-specific testicular germ cell apoptotic response to low dose X-irradiation and 2,5-hexanedione combined exposure. I. Validation of the laser capture microdissection method for qRT-PCR array application

Journal: Toxicologic pathology

doi: 10.1177/0192623314526319

LCM-derived seminiferous tubule RNA quality assessment. Digital gel (A) and electropherogram results (B–C) obtained with the Agilent 2100 Bioanalyzer. Electropherogram results are shown for before (B) and after (C) DNase treatment and RNA concentration,
Figure Legend Snippet: LCM-derived seminiferous tubule RNA quality assessment. Digital gel (A) and electropherogram results (B–C) obtained with the Agilent 2100 Bioanalyzer. Electropherogram results are shown for before (B) and after (C) DNase treatment and RNA concentration,

Techniques Used: Laser Capture Microdissection, Derivative Assay, Concentration Assay

25) Product Images from "Transcriptomic analyses of Hand2 transgenic embryos"

Article Title: Transcriptomic analyses of Hand2 transgenic embryos

Journal: Genomics Data

doi: 10.1016/j.gdata.2016.06.015

RNA quality control. A. RNA quality was measured using the Agilent 2100 Bioanalyzer for wild-type (a, c) and Hand2 NC mutant (b, d) samples at E11.5 (a, b) and E12.5 (c, d). The RNA Integrity Number (RIN; value assigned from 0 to 10) and histograms are shown. B. Scatter plots showing the correlation of signal values between two samples from E11.5 (a) and E12.5 (b) embryos. Data assigned to absent calls were omitted. C. qPCR analysis of the Hand2 transcript levels from wild-type (WT) and Hand2 NC (Tg) embryos at E11.5 (a) and E12.5 (b). Hand2 expression was upregulated in the Hand2 NC embryos. The experimental data were analyzed using two-tailed Student's t -tests and were expressed as the mean ± standard error of the mean (SEM). P -values less than 0.05 were considered as significant.
Figure Legend Snippet: RNA quality control. A. RNA quality was measured using the Agilent 2100 Bioanalyzer for wild-type (a, c) and Hand2 NC mutant (b, d) samples at E11.5 (a, b) and E12.5 (c, d). The RNA Integrity Number (RIN; value assigned from 0 to 10) and histograms are shown. B. Scatter plots showing the correlation of signal values between two samples from E11.5 (a) and E12.5 (b) embryos. Data assigned to absent calls were omitted. C. qPCR analysis of the Hand2 transcript levels from wild-type (WT) and Hand2 NC (Tg) embryos at E11.5 (a) and E12.5 (b). Hand2 expression was upregulated in the Hand2 NC embryos. The experimental data were analyzed using two-tailed Student's t -tests and were expressed as the mean ± standard error of the mean (SEM). P -values less than 0.05 were considered as significant.

Techniques Used: Mutagenesis, Real-time Polymerase Chain Reaction, Expressing, Two Tailed Test

26) Product Images from "Dynamic Reorganization of Nucleosome Positioning in Somatic Cells after Transfer into Porcine Enucleated Oocytes"

Article Title: Dynamic Reorganization of Nucleosome Positioning in Somatic Cells after Transfer into Porcine Enucleated Oocytes

Journal: Stem Cell Reports

doi: 10.1016/j.stemcr.2017.06.004

Establishment of MNase-Seq Using 1,000 Cells (A) Isolation of mononucleosomes by MNase digestion of 10 6 PEF. M, 100-bp ladder; 1–2, 10 6 PEF; 1N, isolation of mononucleosomes; 2N, isolation of dinucleosomes. (B) Detection of the adaptor-ligated mononucleosome library derived from 1,000 PEF with the Agilent 2100 Bioanalyzer. (C) Heatmap of the Pearson correlations among PEF-1, PEF-2, and PEF-3.
Figure Legend Snippet: Establishment of MNase-Seq Using 1,000 Cells (A) Isolation of mononucleosomes by MNase digestion of 10 6 PEF. M, 100-bp ladder; 1–2, 10 6 PEF; 1N, isolation of mononucleosomes; 2N, isolation of dinucleosomes. (B) Detection of the adaptor-ligated mononucleosome library derived from 1,000 PEF with the Agilent 2100 Bioanalyzer. (C) Heatmap of the Pearson correlations among PEF-1, PEF-2, and PEF-3.

Techniques Used: Isolation, Derivative Assay

27) Product Images from "Stranded Whole Transcriptome RNA-Seq for All RNA Types"

Article Title: Stranded Whole Transcriptome RNA-Seq for All RNA Types

Journal: Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.]

doi: 10.1002/0471142905.hg1114s84

RNA profiles. RNA fractions were run on the 2100 Agilent Bioanalyzer RNA pico chip to demonstrate successful size fractionation and fragmentation profiles. Abbreviations; small RNA (smRNA), large RNA (LgRNA), fragmented large RNA (FLgRNA).
Figure Legend Snippet: RNA profiles. RNA fractions were run on the 2100 Agilent Bioanalyzer RNA pico chip to demonstrate successful size fractionation and fragmentation profiles. Abbreviations; small RNA (smRNA), large RNA (LgRNA), fragmented large RNA (FLgRNA).

Techniques Used: Chromatin Immunoprecipitation, Fractionation

28) Product Images from "Generation of Genetically Modified Mice using the CRISPR-Cas9 Genome-Editing System"

Article Title: Generation of Genetically Modified Mice using the CRISPR-Cas9 Genome-Editing System

Journal: Cold Spring Harbor protocols

doi: 10.1101/pdb.prot090704

Quality control of Cas9 mRNA in a 2100 Bioanalyzer and ssDNA donor oligo design A . Electrophoresis of in vitro transcribed Cas9 mRNA prior poly-polyadenylation and post poly-adenylation. B . Electropherogram of in vitro transcribed Cas9 mRNA prior poly-polyadenylation and post poly-adenylation. C . Representation of a sequence that can be targeted with a specific sgRNA. Insertion of EcoRI (as an example) adjacent to the PAM sequence will preclude the Cas9 nuclease from cutting again after the genome has been repaired by HDR.
Figure Legend Snippet: Quality control of Cas9 mRNA in a 2100 Bioanalyzer and ssDNA donor oligo design A . Electrophoresis of in vitro transcribed Cas9 mRNA prior poly-polyadenylation and post poly-adenylation. B . Electropherogram of in vitro transcribed Cas9 mRNA prior poly-polyadenylation and post poly-adenylation. C . Representation of a sequence that can be targeted with a specific sgRNA. Insertion of EcoRI (as an example) adjacent to the PAM sequence will preclude the Cas9 nuclease from cutting again after the genome has been repaired by HDR.

Techniques Used: Electrophoresis, In Vitro, Sequencing

29) Product Images from "Stranded Whole Transcriptome RNA-Seq for All RNA Types"

Article Title: Stranded Whole Transcriptome RNA-Seq for All RNA Types

Journal: Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.]

doi: 10.1002/0471142905.hg1114s84

RNA profiles. RNA fractions were run on the 2100 Agilent Bioanalyzer RNA pico chip to demonstrate successful size fractionation and fragmentation profiles. Abbreviations; small RNA (smRNA), large RNA (LgRNA), fragmented large RNA (FLgRNA).
Figure Legend Snippet: RNA profiles. RNA fractions were run on the 2100 Agilent Bioanalyzer RNA pico chip to demonstrate successful size fractionation and fragmentation profiles. Abbreviations; small RNA (smRNA), large RNA (LgRNA), fragmented large RNA (FLgRNA).

Techniques Used: Chromatin Immunoprecipitation, Fractionation

30) Product Images from "Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)"

Article Title: Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)

Journal: BMC Genomics

doi: 10.1186/s12864-015-1572-7

Bisulfite conversion and long-range amplification. (A) Six commercially available bisulfite conversion kits were tested and treated DNAs were examined using an Agilent 2100 Bioanalyzer to assess size distributions. (B) Two bisulfite-converted DNAs from each of the six kits were subjected to PCR with two amplicons (655 and 1109 bp) and three different extension temperatures (65°C, 68°C and 72°C) to assess capacity for long amplicon amplification. Bisulfite-converted DNA from two kits (Epigentek Methylamp and Qiagen EpiTect) with a PCR extension temperature of 65°C had the most robust amplification of the longer 1109 bp amplicon. (C) Eight amplicons ranging in size from 655–4027 bp (overlapping the MEST CpG island) were designed to determine the upper amplicon size limit of bisulfite PCR. (D) Agarose gel image of bisulfite PCR with the eight primer sets using DNA converted by the Epigentek Methylamp and Qiagen EpiTect kits revealing stable amplification of the 1631 bp amplicon with the Epigentek Methylamp converted DNA and the reported PCR conditions.
Figure Legend Snippet: Bisulfite conversion and long-range amplification. (A) Six commercially available bisulfite conversion kits were tested and treated DNAs were examined using an Agilent 2100 Bioanalyzer to assess size distributions. (B) Two bisulfite-converted DNAs from each of the six kits were subjected to PCR with two amplicons (655 and 1109 bp) and three different extension temperatures (65°C, 68°C and 72°C) to assess capacity for long amplicon amplification. Bisulfite-converted DNA from two kits (Epigentek Methylamp and Qiagen EpiTect) with a PCR extension temperature of 65°C had the most robust amplification of the longer 1109 bp amplicon. (C) Eight amplicons ranging in size from 655–4027 bp (overlapping the MEST CpG island) were designed to determine the upper amplicon size limit of bisulfite PCR. (D) Agarose gel image of bisulfite PCR with the eight primer sets using DNA converted by the Epigentek Methylamp and Qiagen EpiTect kits revealing stable amplification of the 1631 bp amplicon with the Epigentek Methylamp converted DNA and the reported PCR conditions.

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

31) Product Images from "Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks"

Article Title: Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks

Journal: Bioinformatics and Biology Insights

doi: 10.4137/BBI.S40628

Overview and effect of the reshearing method. ( A ) The relevant steps of ChIP-seq sample preparation, using the traditional method. After the fragmentation of the protein, we have a mixture of fragments of different sizes. The ones that carry our protein of interest can be bound by immunoprecipitation. After the decrosslinking and purification step, we get the DNA fragments, where the ones over the optimal size range are shown in red, and the ones under the size range are in green for better visual interpretation. During the size selection before library preparation and sequencing, these fragments are discarded; thus, a significant amount of the sample is lost. ( B ) The reshearing method preserves the fragments that are out of the ideal size range. By doing additional rounds of sonication on the eluted DNA, the long fragments break up into shorter ones (see the fragments in red), which enables them to proceed to library preparation and sonication. Sample loss is reduced significantly. ( C – E ) Demonstrating the effect of the reshearing on the actual H3K27me3 sample. The fragment range distribution is measured by a 2100 Bioanalyzer, images were generated by its software provided by Agilent; the control marks are at 35 bp and 10380 bp. ( C ) The original fragment distribution, before the reshearing step. ( D ) The size distribution after two rounds of five cycles of reshearing. A reduction of the large peak in the large size range and a slight shift toward the smaller sizes is already visible. ( E ) The distribution after the third round of reshearing. Here the shift is already complete: the large fragments have disappeared and the middle short section of the size range is enlarged, showing that we have reached the desired size distribution.
Figure Legend Snippet: Overview and effect of the reshearing method. ( A ) The relevant steps of ChIP-seq sample preparation, using the traditional method. After the fragmentation of the protein, we have a mixture of fragments of different sizes. The ones that carry our protein of interest can be bound by immunoprecipitation. After the decrosslinking and purification step, we get the DNA fragments, where the ones over the optimal size range are shown in red, and the ones under the size range are in green for better visual interpretation. During the size selection before library preparation and sequencing, these fragments are discarded; thus, a significant amount of the sample is lost. ( B ) The reshearing method preserves the fragments that are out of the ideal size range. By doing additional rounds of sonication on the eluted DNA, the long fragments break up into shorter ones (see the fragments in red), which enables them to proceed to library preparation and sonication. Sample loss is reduced significantly. ( C – E ) Demonstrating the effect of the reshearing on the actual H3K27me3 sample. The fragment range distribution is measured by a 2100 Bioanalyzer, images were generated by its software provided by Agilent; the control marks are at 35 bp and 10380 bp. ( C ) The original fragment distribution, before the reshearing step. ( D ) The size distribution after two rounds of five cycles of reshearing. A reduction of the large peak in the large size range and a slight shift toward the smaller sizes is already visible. ( E ) The distribution after the third round of reshearing. Here the shift is already complete: the large fragments have disappeared and the middle short section of the size range is enlarged, showing that we have reached the desired size distribution.

Techniques Used: Chromatin Immunoprecipitation, Sample Prep, Immunoprecipitation, Purification, Selection, Sequencing, Sonication, Generated, Software

32) Product Images from "VR09 Cell Line: An EBV-Positive Lymphoblastoid Cell Line with In Vivo Characteristics of Diffuse Large B Cell Lymphoma of Activated B-Cell Type"

Article Title: VR09 Cell Line: An EBV-Positive Lymphoblastoid Cell Line with In Vivo Characteristics of Diffuse Large B Cell Lymphoma of Activated B-Cell Type

Journal: PLoS ONE

doi: 10.1371/journal.pone.0052811

EBV positivity in the original tumor and in the VR09 cell line. PCR products analysis by Agilent 2100 Bioanalyzer showed the presence of the same 151 bp specific amplicon for EBV RPMS1 gene, thus demonstrating that EBV infection was present in the original cells from patient. A normal DNA from pancreas was used as negative control.
Figure Legend Snippet: EBV positivity in the original tumor and in the VR09 cell line. PCR products analysis by Agilent 2100 Bioanalyzer showed the presence of the same 151 bp specific amplicon for EBV RPMS1 gene, thus demonstrating that EBV infection was present in the original cells from patient. A normal DNA from pancreas was used as negative control.

Techniques Used: Polymerase Chain Reaction, Amplification, Infection, Negative Control

33) Product Images from "MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits"

Article Title: MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits

Journal: BMC Research Notes

doi: 10.1186/1756-0500-4-217

Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.
Figure Legend Snippet: Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.

Techniques Used: Software, Electrophoresis, Standard Deviation

34) Product Images from "Gene expression profiling of the olfactory tissues of sex-separated and sex-combined female and male mice"

Article Title: Gene expression profiling of the olfactory tissues of sex-separated and sex-combined female and male mice

Journal: Scientific Data

doi: 10.1038/sdata.2018.260

RNA integrity analysis. The integrity of ( a ) MOE, ( b ) VNO, and ( c ) OB samples was analyzed using an Agilent Bioanalyzer 2100 instrument. RNA integrity number (RIN) values for all samples are listed in Table 1 .
Figure Legend Snippet: RNA integrity analysis. The integrity of ( a ) MOE, ( b ) VNO, and ( c ) OB samples was analyzed using an Agilent Bioanalyzer 2100 instrument. RNA integrity number (RIN) values for all samples are listed in Table 1 .

Techniques Used:

35) Product Images from "Retinoid Expression in Onchocercal Skin Disease: Pilot Study"

Article Title: Retinoid Expression in Onchocercal Skin Disease: Pilot Study

Journal: Infectious Diseases

doi: 10.1177/1178633617731741

RNA quality results from the 2100 Bioanalyzer.
Figure Legend Snippet: RNA quality results from the 2100 Bioanalyzer.

Techniques Used:

36) Product Images from "A highly effective and versatile technology for the isolation of RNAs from grapevines and other woody perennials for use in virus diagnostics"

Article Title: A highly effective and versatile technology for the isolation of RNAs from grapevines and other woody perennials for use in virus diagnostics

Journal: Virology Journal

doi: 10.1186/s12985-015-0376-3

Profile of total RNA isolated by using five commercial kits. a Denaturing gel electrophoresis of total RNA isolated from peach. b Denaturing gel electrophoresis of total RNA from grapevine leaves. 50 mg of young peach and grapevine leaves (indicated as Y), and mature (M) grapevine leaves was used in RNA isolation with Spectrum™ Plant Total RNA kit (Sigma), RNeasy Plant mini kit (Qiagen), Plant/fungi total RNA kit (Norgen), AccuPrep viral RNA extraction kit (Bioneer) and TRIzol Reagent (Life Technologies). The total RNA yield (μg), A260/A280 and A260/A230 ratios averaged from two replicates are given below each gel panel. 28S rRNA, 18S rRNA and small RNAs are indicated with arrows. c Capillary electrophoresis of total RNA with Agilent Bioanalyzer. One ml of each of the total RNA preparations isolated using these five systems was used for the analysis with an Agilent Bioanalyzer 2100 equipped with an RNA Nano chip
Figure Legend Snippet: Profile of total RNA isolated by using five commercial kits. a Denaturing gel electrophoresis of total RNA isolated from peach. b Denaturing gel electrophoresis of total RNA from grapevine leaves. 50 mg of young peach and grapevine leaves (indicated as Y), and mature (M) grapevine leaves was used in RNA isolation with Spectrum™ Plant Total RNA kit (Sigma), RNeasy Plant mini kit (Qiagen), Plant/fungi total RNA kit (Norgen), AccuPrep viral RNA extraction kit (Bioneer) and TRIzol Reagent (Life Technologies). The total RNA yield (μg), A260/A280 and A260/A230 ratios averaged from two replicates are given below each gel panel. 28S rRNA, 18S rRNA and small RNAs are indicated with arrows. c Capillary electrophoresis of total RNA with Agilent Bioanalyzer. One ml of each of the total RNA preparations isolated using these five systems was used for the analysis with an Agilent Bioanalyzer 2100 equipped with an RNA Nano chip

Techniques Used: Isolation, Nucleic Acid Electrophoresis, RNA Extraction, Electrophoresis, Chromatin Immunoprecipitation

37) Product Images from "Sequence-Specific Cleavage of Small-Subunit (SSU) rRNA with Oligonucleotides and RNase H: a Rapid and Simple Approach to SSU rRNA-Based Quantitative Detection of Microorganisms"

Article Title: Sequence-Specific Cleavage of Small-Subunit (SSU) rRNA with Oligonucleotides and RNase H: a Rapid and Simple Approach to SSU rRNA-Based Quantitative Detection of Microorganisms

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.70.6.3650-3663.2004

Application of the sequence-specific rRNA cleavage method to quantify microbes in actual community samples. (A) Gel-like images of total RNA extracted from various community samples showing virtually intact rRNA peaks, as resolved by an Agilent 2100 bioanalyzer. (B to E) Electropherograms of community RNAs digested with group-specific scissor probes and RNase H. Digestion of total RNA from cow feces (I) with the UNI530 probe specific for virtually all prokaryotes (B), from digested sewage sludge with the ARC915m probe specific for Archaea (C), from digested sewage sludge with the MX825m probe specific for the genus Methanosaeta (D), and from activated sludge (I) with the G123T probe specific for the genus Thiothrix (E) are shown. Numbers with arrows indicate approximate estimates of the molecular size (in nucleotides) of each peak.
Figure Legend Snippet: Application of the sequence-specific rRNA cleavage method to quantify microbes in actual community samples. (A) Gel-like images of total RNA extracted from various community samples showing virtually intact rRNA peaks, as resolved by an Agilent 2100 bioanalyzer. (B to E) Electropherograms of community RNAs digested with group-specific scissor probes and RNase H. Digestion of total RNA from cow feces (I) with the UNI530 probe specific for virtually all prokaryotes (B), from digested sewage sludge with the ARC915m probe specific for Archaea (C), from digested sewage sludge with the MX825m probe specific for the genus Methanosaeta (D), and from activated sludge (I) with the G123T probe specific for the genus Thiothrix (E) are shown. Numbers with arrows indicate approximate estimates of the molecular size (in nucleotides) of each peak.

Techniques Used: Sequencing

Effect of oligonucleotide type (G+C% and nucleotide length) on the 16S rRNA cleavage reaction. (A) Electropherogram of E. coli RNA digested with the 907-16 probe at 41°C, as resolved by an Agilent 2100 bioanalyzer with an RNA 6000 nano kit. Numbers with arrows indicate approximate estimates of the molecular weight of each peak (unit, nt). A gel-like image of the electropherogram is also shown in the graph; lane 1, RNA 6000 ladder marker (TaKaRa); lane 2, digested E. coli RNA fragments. (B) Temperature dependence of the rRNA cleavage reaction with the 907 probes. Percentages of cleaved 16S rRNA in the total 16S rRNA were directly estimated based on the peak areas of intact and cleaved 16S rRNA fragments in the electro- pherograms, and the percentages were plotted with the hybridization and digestion temperatures at which the respective reactions were performed. Error bars indicate the standard deviation of duplicate determinations. (C) Temperature dependence of the rRNA cleavage reaction with the 530 probes. Percentages of cleaved 16S rRNA in the total 16S rRNA were calculated in the same manner used for the graph in panel B and were plotted along with the hybridization and digestion temperatures used. Error bars indicate the standard deviation of duplicate determinations.
Figure Legend Snippet: Effect of oligonucleotide type (G+C% and nucleotide length) on the 16S rRNA cleavage reaction. (A) Electropherogram of E. coli RNA digested with the 907-16 probe at 41°C, as resolved by an Agilent 2100 bioanalyzer with an RNA 6000 nano kit. Numbers with arrows indicate approximate estimates of the molecular weight of each peak (unit, nt). A gel-like image of the electropherogram is also shown in the graph; lane 1, RNA 6000 ladder marker (TaKaRa); lane 2, digested E. coli RNA fragments. (B) Temperature dependence of the rRNA cleavage reaction with the 907 probes. Percentages of cleaved 16S rRNA in the total 16S rRNA were directly estimated based on the peak areas of intact and cleaved 16S rRNA fragments in the electro- pherograms, and the percentages were plotted with the hybridization and digestion temperatures at which the respective reactions were performed. Error bars indicate the standard deviation of duplicate determinations. (C) Temperature dependence of the rRNA cleavage reaction with the 530 probes. Percentages of cleaved 16S rRNA in the total 16S rRNA were calculated in the same manner used for the graph in panel B and were plotted along with the hybridization and digestion temperatures used. Error bars indicate the standard deviation of duplicate determinations.

Techniques Used: Molecular Weight, Marker, Hybridization, Standard Deviation

38) Product Images from "Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA"

Article Title: Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0008147

Profiles of cfDNA extracted from intact hydatid cysts. (A) Size of cfDNA from HCF samples analyzed on a 2100 bioanalyzer. Molecular weight (bp) is indicated (left lane). Green lines:15bp. Purple lines: 1500bp. (B) Profile of the cfDNA sequencing reads mapped to the E . granulosus genome (ASM52419v1) and human genome (hg38).
Figure Legend Snippet: Profiles of cfDNA extracted from intact hydatid cysts. (A) Size of cfDNA from HCF samples analyzed on a 2100 bioanalyzer. Molecular weight (bp) is indicated (left lane). Green lines:15bp. Purple lines: 1500bp. (B) Profile of the cfDNA sequencing reads mapped to the E . granulosus genome (ASM52419v1) and human genome (hg38).

Techniques Used: Molecular Weight, Sequencing

39) Product Images from "Arabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation"

Article Title: Arabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation

Journal: The Plant Cell

doi: 10.1105/tpc.18.00245

45S rDNA VAR Expression in smo4-3 and rrp7-1 . (A) and (B) Schematic representation of the 45S pre-rRNA (A) and its 3′-ETS polymorphic region (B) ). (C) to (E) PCR analysis of the relative abundance of 45S rDNA variants ( VAR1-VAR4 ) in reverse-transcribed RNA (C) , and genomic DNA (D) and (E) , from Col-0, smo4-3 , and rrp7-1 plants as indicated. Relative amounts of each 45S rDNA variant (E) were determined using the Agilent DNA 1000 kit on an Agilent 2100 Bioanalyzer. VAR4 was not detected. The ORNITHINE TRANSCARBAMYLASE ( OTC ) was used as an internal control in (C) .
Figure Legend Snippet: 45S rDNA VAR Expression in smo4-3 and rrp7-1 . (A) and (B) Schematic representation of the 45S pre-rRNA (A) and its 3′-ETS polymorphic region (B) ). (C) to (E) PCR analysis of the relative abundance of 45S rDNA variants ( VAR1-VAR4 ) in reverse-transcribed RNA (C) , and genomic DNA (D) and (E) , from Col-0, smo4-3 , and rrp7-1 plants as indicated. Relative amounts of each 45S rDNA variant (E) were determined using the Agilent DNA 1000 kit on an Agilent 2100 Bioanalyzer. VAR4 was not detected. The ORNITHINE TRANSCARBAMYLASE ( OTC ) was used as an internal control in (C) .

Techniques Used: Expressing, Polymerase Chain Reaction, Variant Assay

40) Product Images from "Arabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation"

Article Title: Arabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation

Journal: The Plant Cell

doi: 10.1105/tpc.18.00245

45S rDNA VAR Expression in smo4-3 and rrp7-1 . (A) and (B) Schematic representation of the 45S pre-rRNA (A) and its 3′-ETS polymorphic region (B) ). (C) to (E) PCR analysis of the relative abundance of 45S rDNA variants ( VAR1-VAR4 ) in reverse-transcribed RNA (C) , and genomic DNA (D) and (E) , from Col-0, smo4-3 , and rrp7-1 plants as indicated. Relative amounts of each 45S rDNA variant (E) were determined using the Agilent DNA 1000 kit on an Agilent 2100 Bioanalyzer. VAR4 was not detected. The ORNITHINE TRANSCARBAMYLASE ( OTC ) was used as an internal control in (C) .
Figure Legend Snippet: 45S rDNA VAR Expression in smo4-3 and rrp7-1 . (A) and (B) Schematic representation of the 45S pre-rRNA (A) and its 3′-ETS polymorphic region (B) ). (C) to (E) PCR analysis of the relative abundance of 45S rDNA variants ( VAR1-VAR4 ) in reverse-transcribed RNA (C) , and genomic DNA (D) and (E) , from Col-0, smo4-3 , and rrp7-1 plants as indicated. Relative amounts of each 45S rDNA variant (E) were determined using the Agilent DNA 1000 kit on an Agilent 2100 Bioanalyzer. VAR4 was not detected. The ORNITHINE TRANSCARBAMYLASE ( OTC ) was used as an internal control in (C) .

Techniques Used: Expressing, Polymerase Chain Reaction, Variant Assay

Related Articles

Methylation Sequencing:

Article Title: A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA
Article Snippet: .. Preparation of libraries for reduced representation bisulfite sequencing (RRBS) or other genome-wide methylation applications (from FFPE samples) The quality of the RRBS libraries prepared from melanoma FFPE slices was assessed on a 2100 Bioanalyzer (Agilent Technologies) using the high sensitivity DNA chip. .. Bioanalyzer analysis of two representative FFPE derived RRBS libraries are shown in Fig. .

RNA Extraction:

Article Title: Effect of lesion proximity on the regenerative response of long descending propriospinal neurons after spinal transection injury
Article Snippet: .. Quality of the RNA extraction was determined utilizing a 2100 bioanalyzer (Agilent Technologies; Santa Clara, CA) which provided an RNA Integrity Number (RIN), and corresponding pseudo gel (Fig. ). ..

Agarose Gel Electrophoresis:

Article Title: Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner
Article Snippet: .. RT-PCR products were analyzed by using 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA) or conventional agarose-gel electrophoresis and ethidium bromide staining. ..

Methylation:

Article Title: A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA
Article Snippet: .. Preparation of libraries for reduced representation bisulfite sequencing (RRBS) or other genome-wide methylation applications (from FFPE samples) The quality of the RRBS libraries prepared from melanoma FFPE slices was assessed on a 2100 Bioanalyzer (Agilent Technologies) using the high sensitivity DNA chip. .. Bioanalyzer analysis of two representative FFPE derived RRBS libraries are shown in Fig. .

Purification:

Article Title: Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates
Article Snippet: .. Redox state of BsTrxA To study the properties of the C29S and C32S single-mutant BsTrxA protein variants, the purified His-tagged proteins were analyzed both by standard SDS-PAGE and by capillary electrophoresis with a 2100 Bioanalyzer (Agilent Technologies) under reducing and nonreducing conditions. ..

Electrophoresis:

Article Title: Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner
Article Snippet: .. RT-PCR products were analyzed by using 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA) or conventional agarose-gel electrophoresis and ethidium bromide staining. ..

Article Title: Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates
Article Snippet: .. Redox state of BsTrxA To study the properties of the C29S and C32S single-mutant BsTrxA protein variants, the purified His-tagged proteins were analyzed both by standard SDS-PAGE and by capillary electrophoresis with a 2100 Bioanalyzer (Agilent Technologies) under reducing and nonreducing conditions. ..

Article Title: The Effect of Formaldehyde Fixation on RNA
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). .. Each RNA solution, 1 μL (0.5 to 1 μg per well), was loaded into a nano total RNA chip (Agilent 6000) and run according to the manufacturer's instructions.

Generated:

Article Title: RNase L Interacts with Filamin A To Regulate Actin Dynamics and Barrier Function for Viral Entry
Article Snippet: .. RNAs (2 µg) were separated on RNA chips and analyzed with a 2100 Bioanalyzer (Agilent Technologies) to monitor characteristic rRNA cleavage products generated by RNase L activity as described previously ( ). ..

Formalin-fixed Paraffin-Embedded:

Article Title: A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA
Article Snippet: .. Preparation of libraries for reduced representation bisulfite sequencing (RRBS) or other genome-wide methylation applications (from FFPE samples) The quality of the RRBS libraries prepared from melanoma FFPE slices was assessed on a 2100 Bioanalyzer (Agilent Technologies) using the high sensitivity DNA chip. .. Bioanalyzer analysis of two representative FFPE derived RRBS libraries are shown in Fig. .

Activity Assay:

Article Title: RNase L Interacts with Filamin A To Regulate Actin Dynamics and Barrier Function for Viral Entry
Article Snippet: .. RNAs (2 µg) were separated on RNA chips and analyzed with a 2100 Bioanalyzer (Agilent Technologies) to monitor characteristic rRNA cleavage products generated by RNase L activity as described previously ( ). ..

Genome Wide:

Article Title: A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA
Article Snippet: .. Preparation of libraries for reduced representation bisulfite sequencing (RRBS) or other genome-wide methylation applications (from FFPE samples) The quality of the RRBS libraries prepared from melanoma FFPE slices was assessed on a 2100 Bioanalyzer (Agilent Technologies) using the high sensitivity DNA chip. .. Bioanalyzer analysis of two representative FFPE derived RRBS libraries are shown in Fig. .

Reverse Transcription Polymerase Chain Reaction:

Article Title: Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner
Article Snippet: .. RT-PCR products were analyzed by using 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA) or conventional agarose-gel electrophoresis and ethidium bromide staining. ..

Staining:

Article Title: Alternative splicing of the Caenorhabditis elegans lev-11 tropomyosin gene is regulated in a tissue-specific manner
Article Snippet: .. RT-PCR products were analyzed by using 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA) or conventional agarose-gel electrophoresis and ethidium bromide staining. ..

Chromatin Immunoprecipitation:

Article Title: A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA
Article Snippet: .. Preparation of libraries for reduced representation bisulfite sequencing (RRBS) or other genome-wide methylation applications (from FFPE samples) The quality of the RRBS libraries prepared from melanoma FFPE slices was assessed on a 2100 Bioanalyzer (Agilent Technologies) using the high sensitivity DNA chip. .. Bioanalyzer analysis of two representative FFPE derived RRBS libraries are shown in Fig. .

SDS Page:

Article Title: Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme-Substrate Reaction Intermediates
Article Snippet: .. Redox state of BsTrxA To study the properties of the C29S and C32S single-mutant BsTrxA protein variants, the purified His-tagged proteins were analyzed both by standard SDS-PAGE and by capillary electrophoresis with a 2100 Bioanalyzer (Agilent Technologies) under reducing and nonreducing conditions. ..

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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
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    dna chips - by Bioz Stars, 2020-08
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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
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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