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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.
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1) Product Images from "Ensuring good quality rna for quantitative real-time pcr isolated from renal proximal tubular cells using laser capture microdissection"

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

Journal: BMC Research Notes

doi: 10.1186/1756-0500-7-62

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.
Figure Legend 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.

Techniques Used: Concentration Assay, Produced

2) Product Images from "Maximizing the potency of an anti-TLR4 monoclonal antibody by exploiting proximity to Fcγ receptors"

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

Journal: mAbs

doi: 10.4161/19420862.2014.975098

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.
Figure Legend 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.

Techniques Used: Binding Assay, Competitive ELISA, Concentration Assay

3) Product Images from "Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank – evaluation of RNA quality and stability"

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

Journal: BMC Research Notes

doi: 10.1186/1756-0500-7-633

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.
Figure Legend 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.

Techniques Used: Isolation

4) Product Images from "Plant-Made Trastuzumab (Herceptin) Inhibits HER2/Neu+ Cell Proliferation and Retards Tumor Growth"

Article Title: Plant-Made Trastuzumab (Herceptin) Inhibits HER2/Neu+ Cell Proliferation and Retards Tumor Growth

Journal: PLoS ONE

doi: 10.1371/journal.pone.0017541

Accumulation and purification of assembled PMT in N. benthamiana leaves co-injected with light-chain-encoding PVX-based and heavy-chain-encoding TMV-based vectors. A – Schematic representation of PVX- and crTMV-based vectors. LB and RB, binary vector left and right borders, respectively; 35S, 35S promoter; Act 2, Arabidopsis actin 2 promoter; T, nos terminator; RdRp, RNA-dependent RNA polymerase; Bars 1–8, introns; MP, TMV movement protein; 25K, 12K, 8K, PVX movement protein genes. B–E - Western blot analysis of purified PMT. Purification of mAbs on protein A sepharose. Proteins were separated in a 10% polyacrylamide gel under non-reducing conditions ( B , C ) and in a 12% gel under reducing conditions ( D , E ) and transferred to a PVDF membrane. Western blots: B and D were probed with gamma-chain-specific antibodies; membranes C and E were incubated with kappa-chain-specific antibodies. 1–2, fractions from the protein A sepharose column; M, protein molecular weight markers; S, standard - 20 ng hIgG. F - Capillary electrophoresis analysis of PMT in reducing conditions on Agilent 2100 Bioanalyzer. Peak 12 corresponds to HC; peak 8 corresponds to LC. G , H – Comparison of PMT and trastuzumab. Proteins were separated in a 7.5% polyacrylamide gel under non-reducing conditions ( G ) and in a 12% gel under reducing conditions ( H ) and stained with Coomassie blue. I - RP-HPLC trace analysis of PMT and trastuzumab. The linear gradient was 0–60% acetonitrile for 20 min and then 60–100% acetonitrile for 5 min; the flow rate was 80 µL·min −1 . The buffer blank was 10 mM Na-phosphate (pH 7.0). Absorbance at 214 nm and 280 nm is shown.
Figure Legend Snippet: Accumulation and purification of assembled PMT in N. benthamiana leaves co-injected with light-chain-encoding PVX-based and heavy-chain-encoding TMV-based vectors. A – Schematic representation of PVX- and crTMV-based vectors. LB and RB, binary vector left and right borders, respectively; 35S, 35S promoter; Act 2, Arabidopsis actin 2 promoter; T, nos terminator; RdRp, RNA-dependent RNA polymerase; Bars 1–8, introns; MP, TMV movement protein; 25K, 12K, 8K, PVX movement protein genes. B–E - Western blot analysis of purified PMT. Purification of mAbs on protein A sepharose. Proteins were separated in a 10% polyacrylamide gel under non-reducing conditions ( B , C ) and in a 12% gel under reducing conditions ( D , E ) and transferred to a PVDF membrane. Western blots: B and D were probed with gamma-chain-specific antibodies; membranes C and E were incubated with kappa-chain-specific antibodies. 1–2, fractions from the protein A sepharose column; M, protein molecular weight markers; S, standard - 20 ng hIgG. F - Capillary electrophoresis analysis of PMT in reducing conditions on Agilent 2100 Bioanalyzer. Peak 12 corresponds to HC; peak 8 corresponds to LC. G , H – Comparison of PMT and trastuzumab. Proteins were separated in a 7.5% polyacrylamide gel under non-reducing conditions ( G ) and in a 12% gel under reducing conditions ( H ) and stained with Coomassie blue. I - RP-HPLC trace analysis of PMT and trastuzumab. The linear gradient was 0–60% acetonitrile for 20 min and then 60–100% acetonitrile for 5 min; the flow rate was 80 µL·min −1 . The buffer blank was 10 mM Na-phosphate (pH 7.0). Absorbance at 214 nm and 280 nm is shown.

Techniques Used: Purification, Injection, Plasmid Preparation, Activated Clotting Time Assay, Western Blot, Incubation, Molecular Weight, Electrophoresis, Staining, High Performance Liquid Chromatography, Flow Cytometry

5) Product Images from "Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens"

Article Title: Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

Journal: BMC Cancer

doi: 10.1186/1471-2407-11-253

Comparison of total RNA and microarray signals between FNAB and FFPE specimens . (A) Comparison of Agilent 2100 Bioanalyzer analysis of total RNA between FNAB and FFPE from a breast cancer sample E(+)H(-)-2. (B) Noise levels of the microarray signals. The average numbers of under-detectable probes from Illumina Human-Ref8 24 K BeadChip are 7906.8 ± 27.9 in 25 FNAB arrays and 9531.4 ± 74.3 in 25 FFPE arrays, respectively. (C) Reproducibility of microarray signal. The averages of Correlation Coefficients are 0.87 ± 0.04 within 25 FNAB arrays, 0.87 ± 0.08 within 25 FFPE arrays, 0.45 ± 0.02 between the 25 FNAB arrays and 25 FFPE arrays, and 0.47 ± 0.02 between the 25 paired FNAB and FFPE arrays, respectively.
Figure Legend Snippet: Comparison of total RNA and microarray signals between FNAB and FFPE specimens . (A) Comparison of Agilent 2100 Bioanalyzer analysis of total RNA between FNAB and FFPE from a breast cancer sample E(+)H(-)-2. (B) Noise levels of the microarray signals. The average numbers of under-detectable probes from Illumina Human-Ref8 24 K BeadChip are 7906.8 ± 27.9 in 25 FNAB arrays and 9531.4 ± 74.3 in 25 FFPE arrays, respectively. (C) Reproducibility of microarray signal. The averages of Correlation Coefficients are 0.87 ± 0.04 within 25 FNAB arrays, 0.87 ± 0.08 within 25 FFPE arrays, 0.45 ± 0.02 between the 25 FNAB arrays and 25 FFPE arrays, and 0.47 ± 0.02 between the 25 paired FNAB and FFPE arrays, respectively.

Techniques Used: Microarray, Formalin-fixed Paraffin-Embedded

6) Product Images from "Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta 1"

Article Title: Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta 1

Journal: Applications in Plant Sciences

doi: 10.3732/apps.1400105

Examples of Agilent 2100 Bioanalyzer spectra of total RNA showing improvement with Options 1 and 2 compared to Option 3. Each graph shows the intensity of the peaks of the ribosomal RNA subunits: nuclear large-28S, small-18S, cytoplasmic, mitochondrial, and chloroplastic (smaller subunits). The electrophoretic gel for each sample is shown to the right indicating the subunit bands or degradation (i.e., smear). nt = number of estimated nucleotides based on ladder; FU = fluorescence unit (i.e., intensity of peak). (A) Degraded ribosomal RNA subunits of Canella winterana (L.) Gaertn. extracted with Option 3 that resulted in an estimation of 27 μg of RNA, but the subunits are degraded. (B) A second example using Option 3, Muntingia calabura L., also shows an inflated quantity reading with degraded subunits. (C) Canella winterana , extracted with Option 1, indicating peaks for intact ribosomal RNA subunits. (D) Muntingia calabura extracted with Option 2.
Figure Legend Snippet: Examples of Agilent 2100 Bioanalyzer spectra of total RNA showing improvement with Options 1 and 2 compared to Option 3. Each graph shows the intensity of the peaks of the ribosomal RNA subunits: nuclear large-28S, small-18S, cytoplasmic, mitochondrial, and chloroplastic (smaller subunits). The electrophoretic gel for each sample is shown to the right indicating the subunit bands or degradation (i.e., smear). nt = number of estimated nucleotides based on ladder; FU = fluorescence unit (i.e., intensity of peak). (A) Degraded ribosomal RNA subunits of Canella winterana (L.) Gaertn. extracted with Option 3 that resulted in an estimation of 27 μg of RNA, but the subunits are degraded. (B) A second example using Option 3, Muntingia calabura L., also shows an inflated quantity reading with degraded subunits. (C) Canella winterana , extracted with Option 1, indicating peaks for intact ribosomal RNA subunits. (D) Muntingia calabura extracted with Option 2.

Techniques Used: Fluorescence

7) Product Images from "Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta 1"

Article Title: Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta 1

Journal: Applications in Plant Sciences

doi: 10.3732/apps.1400105

Examples of Agilent 2100 Bioanalyzer spectra of total RNA showing improvement with Options 1 and 2 compared to Option 3. Each graph shows the intensity of the peaks of the ribosomal RNA subunits: nuclear large-28S, small-18S, cytoplasmic, mitochondrial, and chloroplastic (smaller subunits). The electrophoretic gel for each sample is shown to the right indicating the subunit bands or degradation (i.e., smear). nt = number of estimated nucleotides based on ladder; FU = fluorescence unit (i.e., intensity of peak). (A) Degraded ribosomal RNA subunits of Canella winterana (L.) Gaertn. extracted with Option 3 that resulted in an estimation of 27 μg of RNA, but the subunits are degraded. (B) A second example using Option 3, Muntingia calabura L., also shows an inflated quantity reading with degraded subunits. (C) Canella winterana , extracted with Option 1, indicating peaks for intact ribosomal RNA subunits. (D) Muntingia calabura extracted with Option 2.
Figure Legend Snippet: Examples of Agilent 2100 Bioanalyzer spectra of total RNA showing improvement with Options 1 and 2 compared to Option 3. Each graph shows the intensity of the peaks of the ribosomal RNA subunits: nuclear large-28S, small-18S, cytoplasmic, mitochondrial, and chloroplastic (smaller subunits). The electrophoretic gel for each sample is shown to the right indicating the subunit bands or degradation (i.e., smear). nt = number of estimated nucleotides based on ladder; FU = fluorescence unit (i.e., intensity of peak). (A) Degraded ribosomal RNA subunits of Canella winterana (L.) Gaertn. extracted with Option 3 that resulted in an estimation of 27 μg of RNA, but the subunits are degraded. (B) A second example using Option 3, Muntingia calabura L., also shows an inflated quantity reading with degraded subunits. (C) Canella winterana , extracted with Option 1, indicating peaks for intact ribosomal RNA subunits. (D) Muntingia calabura extracted with Option 2.

Techniques Used: Fluorescence

8) Product Images from "Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure"

Article Title: Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure

Journal: PLoS ONE

doi: 10.1371/journal.pone.0126049

Improvement of 5’ adaptor ligation efficiency with designed adaptors. (A) Scheme depicting a miRNA (blue) attached to a 3’ A1 adaptor (brown) and designed 5’ adaptors that have a region complementary to the miRNA sequence (designed; red) or the 3’ adaptor sequence (C3; violet). (B,C) Comparison of 5’ ligation reaction products for four different miRNAs. Each ligation reaction contained a miRNA-3’ A1 hybrid and either the 5’ A1 adaptor, designed 5’ adaptor (B) or C3 5’ adaptor (C), ATP and T4 RNA ligase 1. The reaction products were resolved using an Agilent Small RNA kit and an Agilent 2100 Bioanalyzer (Agilent Technologies).
Figure Legend Snippet: Improvement of 5’ adaptor ligation efficiency with designed adaptors. (A) Scheme depicting a miRNA (blue) attached to a 3’ A1 adaptor (brown) and designed 5’ adaptors that have a region complementary to the miRNA sequence (designed; red) or the 3’ adaptor sequence (C3; violet). (B,C) Comparison of 5’ ligation reaction products for four different miRNAs. Each ligation reaction contained a miRNA-3’ A1 hybrid and either the 5’ A1 adaptor, designed 5’ adaptor (B) or C3 5’ adaptor (C), ATP and T4 RNA ligase 1. The reaction products were resolved using an Agilent Small RNA kit and an Agilent 2100 Bioanalyzer (Agilent Technologies).

Techniques Used: Ligation, Sequencing

9) Product Images from "ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles"

Article Title: ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles

Journal: Scientific Reports

doi: 10.1038/srep23978

Extracellular vesicles harvested by ExtraPEG contain small RNAs. Exosome and cellular RNA were analyzed using the Agilent 2100 Bioanalyzer. ( a ) Gel-like image displaying RNA separated by size, for cell lysate (CL), differential centrifugation (DC), and the ExtraPEG (PEG) methods samples. ( b ) Electropherograms of RNA profiles from CL, DC, and PEG samples. [nt], nucleotide length. [FU], fluorescent units.
Figure Legend Snippet: Extracellular vesicles harvested by ExtraPEG contain small RNAs. Exosome and cellular RNA were analyzed using the Agilent 2100 Bioanalyzer. ( a ) Gel-like image displaying RNA separated by size, for cell lysate (CL), differential centrifugation (DC), and the ExtraPEG (PEG) methods samples. ( b ) Electropherograms of RNA profiles from CL, DC, and PEG samples. [nt], nucleotide length. [FU], fluorescent units.

Techniques Used: Centrifugation

10) Product Images from "Quantitation of Gene Expression in Formaldehyde-Fixed and Fluorescence-Activated Sorted Cells"

Article Title: Quantitation of Gene Expression in Formaldehyde-Fixed and Fluorescence-Activated Sorted Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0073849

Analysis of RNA integrity in unfixed and fixed cells. RNA integrity analysis of RNA isolated from unfixed and fixed samples was performed using Agilent 2100 Bioanalyzer. Representative electropherograms for unfixed (A, C, E) and fixed (B, D, F) samples of each cell type, K562 (A, B), CEMx174 (C, D), human PBMCs (E, F), are shown. The RNA Integrity Number (RIN) is shown for each sample.
Figure Legend Snippet: Analysis of RNA integrity in unfixed and fixed cells. RNA integrity analysis of RNA isolated from unfixed and fixed samples was performed using Agilent 2100 Bioanalyzer. Representative electropherograms for unfixed (A, C, E) and fixed (B, D, F) samples of each cell type, K562 (A, B), CEMx174 (C, D), human PBMCs (E, F), are shown. The RNA Integrity Number (RIN) is shown for each sample.

Techniques Used: Isolation

11) Product Images from "Measurement of Gene Expression in Archival Paraffin-Embedded Tissues "

Article Title: Measurement of Gene Expression in Archival Paraffin-Embedded Tissues

Journal: The American Journal of Pathology

doi:

Size distribution of FPE tissue RNA from 12 tumor specimens. Total RNA was extracted from breast cancer specimens as described in Materials and Methods. One μl from each RNA extract (1/30 of the sample) was analyzed using an Agilent 2100 Bioanalyzer, RNA 6000 Nanochip. Lanes 1–4 , 5–8 , and 9–12 contain RNA from samples archived 1, 6, and 17 years, respectively. Lanes M1 and M2 contain two different sets of molecular weight marker RNA (sizes denoted in bases).
Figure Legend Snippet: Size distribution of FPE tissue RNA from 12 tumor specimens. Total RNA was extracted from breast cancer specimens as described in Materials and Methods. One μl from each RNA extract (1/30 of the sample) was analyzed using an Agilent 2100 Bioanalyzer, RNA 6000 Nanochip. Lanes 1–4 , 5–8 , and 9–12 contain RNA from samples archived 1, 6, and 17 years, respectively. Lanes M1 and M2 contain two different sets of molecular weight marker RNA (sizes denoted in bases).

Techniques Used: Molecular Weight, Marker

RNA size analysis of paired frozen and FPE tissue RNAs. Total RNA was extracted from frozen and FPE tissue specimens as described in Materials and Methods then analyzed for size profile using an Agilent 2100 Bioanalyzer, RNA 6000 Nanochip. One μl from each RNA preparation (1/30 of the sample) was analyzed. Lanes 2 and 3 contain frozen and FPE RNA, respectively, from the same breast tumor (from a 1995 surgery). Lanes M1 and M2 contain different sets of molecular weight RNAs (band sizes denoted in bases).
Figure Legend Snippet: RNA size analysis of paired frozen and FPE tissue RNAs. Total RNA was extracted from frozen and FPE tissue specimens as described in Materials and Methods then analyzed for size profile using an Agilent 2100 Bioanalyzer, RNA 6000 Nanochip. One μl from each RNA preparation (1/30 of the sample) was analyzed. Lanes 2 and 3 contain frozen and FPE RNA, respectively, from the same breast tumor (from a 1995 surgery). Lanes M1 and M2 contain different sets of molecular weight RNAs (band sizes denoted in bases).

Techniques Used: Molecular Weight

12) Product Images from "Stage-Regulated GFP Expression in Trypanosoma cruzi: Applications from Host-Parasite Interactions to Drug Screening"

Article Title: Stage-Regulated GFP Expression in Trypanosoma cruzi: Applications from Host-Parasite Interactions to Drug Screening

Journal: PLoS ONE

doi: 10.1371/journal.pone.0067441

Integration of the green fluorescent protein (GFP) gene following parasite transfection. (A) Schematic representation of the pBEX/GFP construct. The expression vector has the Trypanosoma cruzi 18S ribosomal sequences flanking the intergenic regions between the alpha and beta tubulin genes that provides the spliced leader and polyadenylation sites for the GFP mRNA and the neomycin resistance gene (NeoR) used as a selectable marker. (B and C) Southern-blot analyses of transfected parasites. High-molecular weight DNA, isolated from wild-type (WT) epimastigotes of T. cruzi Dm28c (B1 and C1) and Dm28c transfected (T) with pBEX/GFP (fluorescent epimastigotes) (B2 and C2) were separated by PFGE and stained with ethidium bromide. The bands were transferred to nylon membranes and hybridized with [ 32 P]-labeled probes corresponding to the 24S alpha rDNA (B3 and B4), 18S rDNA (C3 and C4) and GFP (B5, B6, C5 and C6) sequences. (D) Total RNA was isolated from wild-type epimastigotes and pBEX fluorescent epimastigotes and analyzed with an Agilent 2100 Bioanalyzer; data are displayed as a densitometry plot (gel-like image). In this analysis, the fluorescent parasites display a rRNA band pattern (D3) similar to that of the wild-type parasites (D2), suggesting that the mobility shift of the 1.4 Mbp chromosome did not affect the production of functional rRNA molecules. D1 = molecular weight marker.
Figure Legend Snippet: Integration of the green fluorescent protein (GFP) gene following parasite transfection. (A) Schematic representation of the pBEX/GFP construct. The expression vector has the Trypanosoma cruzi 18S ribosomal sequences flanking the intergenic regions between the alpha and beta tubulin genes that provides the spliced leader and polyadenylation sites for the GFP mRNA and the neomycin resistance gene (NeoR) used as a selectable marker. (B and C) Southern-blot analyses of transfected parasites. High-molecular weight DNA, isolated from wild-type (WT) epimastigotes of T. cruzi Dm28c (B1 and C1) and Dm28c transfected (T) with pBEX/GFP (fluorescent epimastigotes) (B2 and C2) were separated by PFGE and stained with ethidium bromide. The bands were transferred to nylon membranes and hybridized with [ 32 P]-labeled probes corresponding to the 24S alpha rDNA (B3 and B4), 18S rDNA (C3 and C4) and GFP (B5, B6, C5 and C6) sequences. (D) Total RNA was isolated from wild-type epimastigotes and pBEX fluorescent epimastigotes and analyzed with an Agilent 2100 Bioanalyzer; data are displayed as a densitometry plot (gel-like image). In this analysis, the fluorescent parasites display a rRNA band pattern (D3) similar to that of the wild-type parasites (D2), suggesting that the mobility shift of the 1.4 Mbp chromosome did not affect the production of functional rRNA molecules. D1 = molecular weight marker.

Techniques Used: Transfection, Construct, Expressing, Plasmid Preparation, Marker, Southern Blot, Molecular Weight, Isolation, Staining, Labeling, Mobility Shift, Functional Assay

13) Product Images from "An integrated disposable device for DNA extraction and helicase dependent amplification"

Article Title: An integrated disposable device for DNA extraction and helicase dependent amplification

Journal: Biomedical microdevices

doi: 10.1007/s10544-009-9391-8

On-chip detection of whole bacterial cells. ( a ) Fluorescence imaging of a representative integrated μSPE-HDA chip showing positive HDA reactions done in triplicate and a negative control water reaction. Reactions were positive for HDA of E. coli dxs from broth culture containing 10 9 CFU loaded into the integrated chip. DNA was extracted by the μSPE column, mixed with HDA reaction mix in the HDA chamber, and flowed into the separate reaction wells. ( b ) The HDA products from three integrated chips (imaged in a ) were analyzed for yield concentrations and compared to products from reactions done in an RT thermocycler from integrated chip μSPE DNA extractions. ( c ) Dilutions of E. coli were prepared and 10 5 –10 1 CFU were run through the μSPE channels and then HDA was performed on-chip and in an RT thermocycler. The product yields were compared using an Agilent 2100 Bioanalyzer and were shown to be positive for the correct size 70 bp product
Figure Legend Snippet: On-chip detection of whole bacterial cells. ( a ) Fluorescence imaging of a representative integrated μSPE-HDA chip showing positive HDA reactions done in triplicate and a negative control water reaction. Reactions were positive for HDA of E. coli dxs from broth culture containing 10 9 CFU loaded into the integrated chip. DNA was extracted by the μSPE column, mixed with HDA reaction mix in the HDA chamber, and flowed into the separate reaction wells. ( b ) The HDA products from three integrated chips (imaged in a ) were analyzed for yield concentrations and compared to products from reactions done in an RT thermocycler from integrated chip μSPE DNA extractions. ( c ) Dilutions of E. coli were prepared and 10 5 –10 1 CFU were run through the μSPE channels and then HDA was performed on-chip and in an RT thermocycler. The product yields were compared using an Agilent 2100 Bioanalyzer and were shown to be positive for the correct size 70 bp product

Techniques Used: Chromatin Immunoprecipitation, Fluorescence, Imaging, Helicase-dependent Amplification, Negative Control

14) Product Images from "Meclofenamic Acid Reduces Reactive Oxygen Species Accumulation and Apoptosis, Inhibits Excessive Autophagy, and Protects Hair Cell-Like HEI-OC1 Cells From Cisplatin-Induced Damage"

Article Title: Meclofenamic Acid Reduces Reactive Oxygen Species Accumulation and Apoptosis, Inhibits Excessive Autophagy, and Protects Hair Cell-Like HEI-OC1 Cells From Cisplatin-Induced Damage

Journal: Frontiers in Cellular Neuroscience

doi: 10.3389/fncel.2018.00139

(A) The quality of mRNA analyzed by an Agilent 2100 Bioanalyzer. (B) The m 6 A/A ratio in the four groups of samples normalized to the DMSO control group. There were no significant differences in the m 6 A/A ratio in any of the groups.
Figure Legend Snippet: (A) The quality of mRNA analyzed by an Agilent 2100 Bioanalyzer. (B) The m 6 A/A ratio in the four groups of samples normalized to the DMSO control group. There were no significant differences in the m 6 A/A ratio in any of the groups.

Techniques Used:

15) Product Images from "Novel Approach to Quantitative Detection of Specific rRNA in a Microbial Community, Using Catalytic DNA"

Article Title: Novel Approach to Quantitative Detection of Specific rRNA in a Microbial Community, Using Catalytic DNA

Journal:

doi: 10.1128/AEM.71.8.4879-4884.2005

Analysis of RNA fragments using the Agilent 2100 bioanalyzer. (A) A gel-like electropherogram image shows the results of the incubation of total RNA extracted from E. coli with three kinds of sequence-specific DNAzymes. (B and C) An electrophoretogram
Figure Legend Snippet: Analysis of RNA fragments using the Agilent 2100 bioanalyzer. (A) A gel-like electropherogram image shows the results of the incubation of total RNA extracted from E. coli with three kinds of sequence-specific DNAzymes. (B and C) An electrophoretogram

Techniques Used: Incubation, Sequencing

16) Product Images from "Extraction of microRNAs from biological matrices with titanium dioxide nanofibers"

Article Title: Extraction of microRNAs from biological matrices with titanium dioxide nanofibers

Journal: Analytical and bioanalytical chemistry

doi: 10.1007/s00216-017-0649-3

Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000
Figure Legend Snippet: Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000

Techniques Used: RNA Extraction, Multiple Displacement Amplification

17) Product Images from "Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs"

Article Title: Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs

Journal: Scientific Data

doi: 10.1038/sdata.2018.287

Polysome profiling followed by RNA-seq during cardiomyogenic differentiation. ( a ) Schematic representation of the sucrose gradient used to segregate ribosome-free and ribosome-bound RNAs and representative polysome profile (hESCs - D0 replicate 2) recorded at 254 nm. Ribosome-free and polysome fractions are indicated. ( b - d ) Representative quality analysis of ribosome-free and polysome-bound samples. ( a ) RNA quality analysis using Agilent 2100 Bioanalyzer. ( b ) cDNA library quality analysis using Agilent 2100 Bioanalyzer. ( c ) RNA-sequencing reads quality analysis using FastQC. All representative images correspond to D0 hESC sample, replicate 2.
Figure Legend Snippet: Polysome profiling followed by RNA-seq during cardiomyogenic differentiation. ( a ) Schematic representation of the sucrose gradient used to segregate ribosome-free and ribosome-bound RNAs and representative polysome profile (hESCs - D0 replicate 2) recorded at 254 nm. Ribosome-free and polysome fractions are indicated. ( b - d ) Representative quality analysis of ribosome-free and polysome-bound samples. ( a ) RNA quality analysis using Agilent 2100 Bioanalyzer. ( b ) cDNA library quality analysis using Agilent 2100 Bioanalyzer. ( c ) RNA-sequencing reads quality analysis using FastQC. All representative images correspond to D0 hESC sample, replicate 2.

Techniques Used: RNA Sequencing Assay, cDNA Library Assay

18) Product Images from "Use of the Agilent 2100 Bioanalyzer for Rapid and Reproducible Molecular Typing of Streptococcus pneumoniae ▿"

Article Title: Use of the Agilent 2100 Bioanalyzer for Rapid and Reproducible Molecular Typing of Streptococcus pneumoniae ▿

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.02169-06

PCR products of three pneumococcal strains were digested with DdeI in three separate experiments performed on different days, and the DNA fragments were analyzed using the Agilent 2100 bioanalyzer. a, b, and c show the simulated gels for experiments 1,
Figure Legend Snippet: PCR products of three pneumococcal strains were digested with DdeI in three separate experiments performed on different days, and the DNA fragments were analyzed using the Agilent 2100 bioanalyzer. a, b, and c show the simulated gels for experiments 1,

Techniques Used: Polymerase Chain Reaction

19) Product Images from "Use of the Agilent 2100 Bioanalyzer for Rapid and Reproducible Molecular Typing of Streptococcus pneumoniae ▿"

Article Title: Use of the Agilent 2100 Bioanalyzer for Rapid and Reproducible Molecular Typing of Streptococcus pneumoniae ▿

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.02169-06

PCR products of three pneumococcal strains were digested with DdeI in three separate experiments performed on different days, and the DNA fragments were analyzed using the Agilent 2100 bioanalyzer. a, b, and c show the simulated gels for experiments 1,
Figure Legend Snippet: PCR products of three pneumococcal strains were digested with DdeI in three separate experiments performed on different days, and the DNA fragments were analyzed using the Agilent 2100 bioanalyzer. a, b, and c show the simulated gels for experiments 1,

Techniques Used: Polymerase Chain Reaction

20) Product Images from "Characterization of monoclonal antibody size variants containing extra light chains"

Article Title: Characterization of monoclonal antibody size variants containing extra light chains

Journal: mAbs

doi: 10.4161/mabs.22965

Figure 5. Electropherograms of non-reduced (A) and reduced (B) MAb-A reference material (Ref) and SEC Peak 1 fraction obtained using Agilent 2100 Bioanalyzer with Protein 250 Kit. NG: non-glycosylated heavy chain.
Figure Legend Snippet: Figure 5. Electropherograms of non-reduced (A) and reduced (B) MAb-A reference material (Ref) and SEC Peak 1 fraction obtained using Agilent 2100 Bioanalyzer with Protein 250 Kit. NG: non-glycosylated heavy chain.

Techniques Used: Size-exclusion Chromatography

21) Product Images from "Characterization of monoclonal antibody size variants containing extra light chains"

Article Title: Characterization of monoclonal antibody size variants containing extra light chains

Journal: mAbs

doi: 10.4161/mabs.22965

Figure 5. Electropherograms of non-reduced (A) and reduced (B) MAb-A reference material (Ref) and SEC Peak 1 fraction obtained using Agilent 2100 Bioanalyzer with Protein 250 Kit. NG: non-glycosylated heavy chain.
Figure Legend Snippet: Figure 5. Electropherograms of non-reduced (A) and reduced (B) MAb-A reference material (Ref) and SEC Peak 1 fraction obtained using Agilent 2100 Bioanalyzer with Protein 250 Kit. NG: non-glycosylated heavy chain.

Techniques Used: Size-exclusion Chromatography

22) Product Images from "Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs"

Article Title: Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs

Journal: Scientific Data

doi: 10.1038/sdata.2018.287

Polysome profiling followed by RNA-seq during cardiomyogenic differentiation. ( a ) Schematic representation of the sucrose gradient used to segregate ribosome-free and ribosome-bound RNAs and representative polysome profile (hESCs - D0 replicate 2) recorded at 254 nm. Ribosome-free and polysome fractions are indicated. ( b - d ) Representative quality analysis of ribosome-free and polysome-bound samples. ( a ) RNA quality analysis using Agilent 2100 Bioanalyzer. ( b ) cDNA library quality analysis using Agilent 2100 Bioanalyzer. ( c ) RNA-sequencing reads quality analysis using FastQC. All representative images correspond to D0 hESC sample, replicate 2.
Figure Legend Snippet: Polysome profiling followed by RNA-seq during cardiomyogenic differentiation. ( a ) Schematic representation of the sucrose gradient used to segregate ribosome-free and ribosome-bound RNAs and representative polysome profile (hESCs - D0 replicate 2) recorded at 254 nm. Ribosome-free and polysome fractions are indicated. ( b - d ) Representative quality analysis of ribosome-free and polysome-bound samples. ( a ) RNA quality analysis using Agilent 2100 Bioanalyzer. ( b ) cDNA library quality analysis using Agilent 2100 Bioanalyzer. ( c ) RNA-sequencing reads quality analysis using FastQC. All representative images correspond to D0 hESC sample, replicate 2.

Techniques Used: RNA Sequencing Assay, cDNA Library Assay

23) Product Images from "Genome-Wide Analysis of Periodontal and Peri-Implant Cells and Tissues"

Article Title: Genome-Wide Analysis of Periodontal and Peri-Implant Cells and Tissues

Journal: Methods in molecular biology (Clifton, N.J.)

doi: 10.1007/978-1-4939-6685-1_18

Example for RNA-quantitation by agilent 2100 bioanalyzer ( a ) Two sharp peaks for the 18S and 28S subunit are visible. The RNA integrity number (RIN) of 10 indicates a clean and undegraded sample of high quality, which is useful for further processing.
Figure Legend Snippet: Example for RNA-quantitation by agilent 2100 bioanalyzer ( a ) Two sharp peaks for the 18S and 28S subunit are visible. The RNA integrity number (RIN) of 10 indicates a clean and undegraded sample of high quality, which is useful for further processing.

Techniques Used: Quantitation Assay

24) Product Images from "Identification of tick-borne pathogen diversity by metagenomic analysis in Haemaphysalis longicornis from Xinyang, China"

Article Title: Identification of tick-borne pathogen diversity by metagenomic analysis in Haemaphysalis longicornis from Xinyang, China

Journal: Infectious Diseases of Poverty

doi: 10.1186/s40249-018-0417-4

The fragments’ distribution of sequencing library. Quality of the libraries were analysed using the Agilent 2100 Bioanalyzer. The fragments length of the constructed library mainly ranged between 300 and 400 bp
Figure Legend Snippet: The fragments’ distribution of sequencing library. Quality of the libraries were analysed using the Agilent 2100 Bioanalyzer. The fragments length of the constructed library mainly ranged between 300 and 400 bp

Techniques Used: Sequencing, Construct

25) Product Images from "Sumo-dependent substrate targeting of the SUMO protease Ulp1"

Article Title: Sumo-dependent substrate targeting of the SUMO protease Ulp1

Journal: BMC Biology

doi: 10.1186/1741-7007-9-74

The Ulp1(3) (C580S) truncation binds SUMO and SUMO-modified proteins . (A) and (B) Immobilized Ulp1(3) (C580S) was analyzed for its ability to affinity-purify Smt3 from yeast whole-cell extracts (WCEs). WCEs containing FLAG-tagged Smt3 (YOK 428) (left) or GFP-Smt3 (YOK 1857) (right) (input) were prepared under nondenaturing conditions and incubated with immobilized maltose-binding protein (MBP)-Ulp1(3) (C580S) (3 (C580S) ), MBP-Ulp1(3) (C580S) lacking the small ubiquitin-like modifier (SUMO)-binding surface (3 (C580S) ΔSBS) or unbound resin (amylose). After washing and elution, bound Smt3 and Smt3 conjugates were detected using either anti-Flag or anti-GFP antibody. (C) Immobilized Ulp1(3) (C580S) was analyzed for its ability to affinity-purify Cdc11 from yeast WCEs. WCE containing GFP-Smt3 (YOK 1857) was prepared under nondenaturing conditions and incubated with immobilized MBP-Ulp1(3) (C580S) , MBP-Ulp1(3) (C580S) lacking the SUMO-binding surface (3 (C580S) ΔSBS) or unbound resin (amylose). After washing and dilution, bound Cdc11 was detected using an anti-Cdc11 antibody (Santa Cruz Biotechnology). (D) WCEs from logarithmically growing yeast cells expressing GFP-tagged Ulp1(3), Ulp1(3) (C580S) and Ulp1(3) (C580S) ΔSBS (YOK 1839, YOK 1907, YOK 1903) (input) were prepared under nondenaturing conditions. Extracts were then incubated with SUMO2 immobilized on agarose beads (Boston Biochem). After washing and elution with sample buffer, bound proteins were detected using an anti-GFP antibody. (E) SUMO2 chains (Boston Biochem) were incubated with resin-bound MBP-Ulp1(3) (C580S) or unbound resin (amylose). After washing and elution with sample buffer, bound proteins were detected using an anti-SUMO2 antibody. SUMO2 chains loading control (input). Concentrations of immobilized MBP-Ulp1(3) (C580S) and MBP-Ulp1(3) (C580S) lacking the SUMO-binding surface (3 (C580S) ΔSBS) were confirmed by Coomassie staining of eluted proteins and quantitation on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Figure Legend Snippet: The Ulp1(3) (C580S) truncation binds SUMO and SUMO-modified proteins . (A) and (B) Immobilized Ulp1(3) (C580S) was analyzed for its ability to affinity-purify Smt3 from yeast whole-cell extracts (WCEs). WCEs containing FLAG-tagged Smt3 (YOK 428) (left) or GFP-Smt3 (YOK 1857) (right) (input) were prepared under nondenaturing conditions and incubated with immobilized maltose-binding protein (MBP)-Ulp1(3) (C580S) (3 (C580S) ), MBP-Ulp1(3) (C580S) lacking the small ubiquitin-like modifier (SUMO)-binding surface (3 (C580S) ΔSBS) or unbound resin (amylose). After washing and elution, bound Smt3 and Smt3 conjugates were detected using either anti-Flag or anti-GFP antibody. (C) Immobilized Ulp1(3) (C580S) was analyzed for its ability to affinity-purify Cdc11 from yeast WCEs. WCE containing GFP-Smt3 (YOK 1857) was prepared under nondenaturing conditions and incubated with immobilized MBP-Ulp1(3) (C580S) , MBP-Ulp1(3) (C580S) lacking the SUMO-binding surface (3 (C580S) ΔSBS) or unbound resin (amylose). After washing and dilution, bound Cdc11 was detected using an anti-Cdc11 antibody (Santa Cruz Biotechnology). (D) WCEs from logarithmically growing yeast cells expressing GFP-tagged Ulp1(3), Ulp1(3) (C580S) and Ulp1(3) (C580S) ΔSBS (YOK 1839, YOK 1907, YOK 1903) (input) were prepared under nondenaturing conditions. Extracts were then incubated with SUMO2 immobilized on agarose beads (Boston Biochem). After washing and elution with sample buffer, bound proteins were detected using an anti-GFP antibody. (E) SUMO2 chains (Boston Biochem) were incubated with resin-bound MBP-Ulp1(3) (C580S) or unbound resin (amylose). After washing and elution with sample buffer, bound proteins were detected using an anti-SUMO2 antibody. SUMO2 chains loading control (input). Concentrations of immobilized MBP-Ulp1(3) (C580S) and MBP-Ulp1(3) (C580S) lacking the SUMO-binding surface (3 (C580S) ΔSBS) were confirmed by Coomassie staining of eluted proteins and quantitation on an Agilent 2100 Bioanalyzer (Agilent Technologies).

Techniques Used: Modification, Incubation, Binding Assay, Expressing, Staining, Quantitation Assay

26) Product Images from "The postpartum effect of maternal diabetes on the circulating levels of sirtuins and superoxide dismutase"

Article Title: The postpartum effect of maternal diabetes on the circulating levels of sirtuins and superoxide dismutase

Journal: FEBS Open Bio

doi: 10.1002/2211-5463.12370

A representative image of the total RNA isolated from whole blood collected in PAX tube and evaluated using the Agilent 2100 Bioanalyzer. The gel electrophoresis showed the ratio of the ribosomal RNA bands of 2 : 1 for 28S and 18S, respectively. L, ladder.
Figure Legend Snippet: A representative image of the total RNA isolated from whole blood collected in PAX tube and evaluated using the Agilent 2100 Bioanalyzer. The gel electrophoresis showed the ratio of the ribosomal RNA bands of 2 : 1 for 28S and 18S, respectively. L, ladder.

Techniques Used: Isolation, Nucleic Acid Electrophoresis

27) Product Images from "Screening and analysis of differentially expressed genes of human melanocytes in skin cells mixed culture"

Article Title: Screening and analysis of differentially expressed genes of human melanocytes in skin cells mixed culture

Journal: American Journal of Translational Research

doi:

Total RNA electrophoresis and tests of different generations (P0, P1, P2, and P3) through Agilent 2100 Bioanalyzer. All the RIN values were greater than 8.
Figure Legend Snippet: Total RNA electrophoresis and tests of different generations (P0, P1, P2, and P3) through Agilent 2100 Bioanalyzer. All the RIN values were greater than 8.

Techniques Used: Electrophoresis

28) Product Images from "A reverse transcriptase-mediated ribosomal RNA depletion (RTR2D) strategy for the cost-effective construction of RNA sequencing libraries"

Article Title: A reverse transcriptase-mediated ribosomal RNA depletion (RTR2D) strategy for the cost-effective construction of RNA sequencing libraries

Journal: Journal of Advanced Research

doi: 10.1016/j.jare.2019.12.005

Specificity and efficiency of the designed rRNA-specific probes. ( A ) Removal efficiency and specificity of 28S and 18S rRNA-specific probes. Human total RNA (1.0 µg) was subjected to the RTR2D procedure and analyzed with an Agilent 2100 Bioanalyzer. The representative gel image ( a ) and electropherograms ( b ) are shown. “Input” and “No probes (NP)” groups were used as controls. ( B ) Quantitative analysis of rRNA expression profiles after 28S rRNA ( a ) or 18S rRNA ( b ) specific probe mediated removal. Mitochondrial rRNAs 12S and 16S were also included in the studies. “**” p
Figure Legend Snippet: Specificity and efficiency of the designed rRNA-specific probes. ( A ) Removal efficiency and specificity of 28S and 18S rRNA-specific probes. Human total RNA (1.0 µg) was subjected to the RTR2D procedure and analyzed with an Agilent 2100 Bioanalyzer. The representative gel image ( a ) and electropherograms ( b ) are shown. “Input” and “No probes (NP)” groups were used as controls. ( B ) Quantitative analysis of rRNA expression profiles after 28S rRNA ( a ) or 18S rRNA ( b ) specific probe mediated removal. Mitochondrial rRNAs 12S and 16S were also included in the studies. “**” p

Techniques Used: Expressing

29) Product Images from "Cells release subpopulations of exosomes with distinct molecular and biological properties"

Article Title: Cells release subpopulations of exosomes with distinct molecular and biological properties

Journal: Scientific Reports

doi: 10.1038/srep22519

EV subpopulations have different RNA profiles. RNA from MV, LD-Exo and HD-Exo was extracted using Trizol and analyzed using capillary electrophoresis with the Agilent RNA 6000 Pico chip (left panel) and Agilent small RNA chip (right panel) on an Agilent 2100 Bioanalyzer®. The y-axis of the electropherograms represents fluorescence units (FU) and the x-axis represents the nucleotide length of the RNA (nt). Peaks at 25 nt (left panels) or at 4 nt (right panels) represent internal standards. Data shown are representative of two independent experiments.
Figure Legend Snippet: EV subpopulations have different RNA profiles. RNA from MV, LD-Exo and HD-Exo was extracted using Trizol and analyzed using capillary electrophoresis with the Agilent RNA 6000 Pico chip (left panel) and Agilent small RNA chip (right panel) on an Agilent 2100 Bioanalyzer®. The y-axis of the electropherograms represents fluorescence units (FU) and the x-axis represents the nucleotide length of the RNA (nt). Peaks at 25 nt (left panels) or at 4 nt (right panels) represent internal standards. Data shown are representative of two independent experiments.

Techniques Used: Electrophoresis, Chromatin Immunoprecipitation, Fluorescence

30) Product Images from "An improved method for isolation of RNA from bone"

Article Title: An improved method for isolation of RNA from bone

Journal: BMC Biotechnology

doi: 10.1186/1472-6750-12-5

Extracting High Quality RNA from Bone in a Single Step . (A) Isolated liver RNA was incubated with RNase free beads (lane 1) or untreated beads (lane 2) provided by the manufacturer (Next Advance) for four hours before analyzing the 18S and 28S rRNA bands using agarose gel chromatography. Subsequent experiments with the Bullet Blender were carried out using untreated beads. (B) Bone RNA was homogenized in near freezing conditions using the Bullet Blender centrifuge (lanes 2-4) or a Polytron (lanes 5-6). The results are compared to bone RNA isolated using standard homogenization conditions (lane 1) and intact liver RNA that was previously isolated (control). (C) The RNA Integrity Number (RIN) for RNA homogenized in near freezing conditions was determined using the Agilent RNA 6000 Nano LabChip Kit and the Agilent 2100 Bioanalyzer. RNA with a RIN = 7 or greater is suitable for microarray analysis of gene expression. (D) The maximum RIN for the two-step approach (lane 2) is compared to the maximum RIN obtained in the one-step approach (lane 3) and each RIN is compared to the RIN of the degraded RNA sample (lane 1) shown in the agarose gel in lane 1, Figure 2B. (E) The electropherograms associated with the samples shown in (D).
Figure Legend Snippet: Extracting High Quality RNA from Bone in a Single Step . (A) Isolated liver RNA was incubated with RNase free beads (lane 1) or untreated beads (lane 2) provided by the manufacturer (Next Advance) for four hours before analyzing the 18S and 28S rRNA bands using agarose gel chromatography. Subsequent experiments with the Bullet Blender were carried out using untreated beads. (B) Bone RNA was homogenized in near freezing conditions using the Bullet Blender centrifuge (lanes 2-4) or a Polytron (lanes 5-6). The results are compared to bone RNA isolated using standard homogenization conditions (lane 1) and intact liver RNA that was previously isolated (control). (C) The RNA Integrity Number (RIN) for RNA homogenized in near freezing conditions was determined using the Agilent RNA 6000 Nano LabChip Kit and the Agilent 2100 Bioanalyzer. RNA with a RIN = 7 or greater is suitable for microarray analysis of gene expression. (D) The maximum RIN for the two-step approach (lane 2) is compared to the maximum RIN obtained in the one-step approach (lane 3) and each RIN is compared to the RIN of the degraded RNA sample (lane 1) shown in the agarose gel in lane 1, Figure 2B. (E) The electropherograms associated with the samples shown in (D).

Techniques Used: Isolation, Incubation, Agarose Gel Electrophoresis, Chromatography, Homogenization, Microarray, Expressing

31) Product Images from "Extracellular Vesicles in Luminal Fluid of the Ovine Uterus"

Article Title: Extracellular Vesicles in Luminal Fluid of the Ovine Uterus

Journal: PLoS ONE

doi: 10.1371/journal.pone.0090913

RNA content of extracellular vesicles. (A) The RNA profiles of extracellular vesicles, endometrium and conceptus samples using an Agilent 2100 Bioanalyzer. Note the cluster of RNA species at or below 200 base pairs in the extracellular vesicle samples both cyclic and pregnant; in contrast to endometrium and conceptus samples which display profiles characteristic of eukaryotic tissue with clearly defined 18S and 28S rRNA peaks and comparatively low percentages of transcripts below 200 base pairs. (B) Endogenous Jaagsiekte retrovirus (enJRSVs) env and gag RNA is present in extracellular vesicles from ULF of cyclic and pregnant ewes by RT-PCR. Day 14 conceptus and endometrium were used as positive controls for env . RT-PCR for gag utilized RNA from day 14 conceptus and 100 day placentome as positive controls. Negative control (NC) was performed by omitting cDNA in the reaction mix.
Figure Legend Snippet: RNA content of extracellular vesicles. (A) The RNA profiles of extracellular vesicles, endometrium and conceptus samples using an Agilent 2100 Bioanalyzer. Note the cluster of RNA species at or below 200 base pairs in the extracellular vesicle samples both cyclic and pregnant; in contrast to endometrium and conceptus samples which display profiles characteristic of eukaryotic tissue with clearly defined 18S and 28S rRNA peaks and comparatively low percentages of transcripts below 200 base pairs. (B) Endogenous Jaagsiekte retrovirus (enJRSVs) env and gag RNA is present in extracellular vesicles from ULF of cyclic and pregnant ewes by RT-PCR. Day 14 conceptus and endometrium were used as positive controls for env . RT-PCR for gag utilized RNA from day 14 conceptus and 100 day placentome as positive controls. Negative control (NC) was performed by omitting cDNA in the reaction mix.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Negative Control

32) Product Images from "Transcriptomic Biomarkers for Individual Risk Assessment in New-Onset Heart Failure"

Article Title: Transcriptomic Biomarkers for Individual Risk Assessment in New-Onset Heart Failure

Journal: Circulation

doi: 10.1161/CIRCULATIONAHA.107.756544

Analysis of extracted total RNA with Agilent 2100 Bioanalyzer
Figure Legend Snippet: Analysis of extracted total RNA with Agilent 2100 Bioanalyzer

Techniques Used:

33) Product Images from "Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis"

Article Title: Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis

Journal: The Human Virome

doi: 10.1007/978-1-4939-8682-8_10

Analysis of fragment library using Agilent 2100 Bioanalyzer and DNA 7500 kit
Figure Legend Snippet: Analysis of fragment library using Agilent 2100 Bioanalyzer and DNA 7500 kit

Techniques Used:

Analysis of post-enrichment TruSeq RVP RNA Access library using Agilent 2100 Bioanalyzer and DNA 7500 kit
Figure Legend Snippet: Analysis of post-enrichment TruSeq RVP RNA Access library using Agilent 2100 Bioanalyzer and DNA 7500 kit

Techniques Used:

34) Product Images from "All-in-one sequencing: an improved library preparation method for cost-effective and high-throughput next-generation sequencing"

Article Title: All-in-one sequencing: an improved library preparation method for cost-effective and high-throughput next-generation sequencing

Journal: Plant Methods

doi: 10.1186/s13007-020-00615-3

Flowchart for the All-in-One sequencing (AIO-seq) method. a The libraries were prepared using Tn5 transposase. b The process of mechanical fragmentation was used to prepare the libraries. c In the traditional protocol, the size selection, and quantification were processed using a one sample one tube method. d With the AIO-seq method, the library analyzed by the Agilent 2100 Bioanalyzer will give the fragment distribution pattern and the ratio of the target region (between the two blue lines) to the total library. e The concentration of the total library could be obtained by Qubit™ 4.0 Fluorometer. f The target region concentrations (TRC) were calculated within each library by multiplying the proportion of the target region from ( d ) and the total library concentration from ( e ). g Mixing the libraries in one tube according to the calculated TRC and their expected yields of the sequence data. h – i One size selection by Sage HT. j Quantification of the selected fragment by qPCR and sequencing
Figure Legend Snippet: Flowchart for the All-in-One sequencing (AIO-seq) method. a The libraries were prepared using Tn5 transposase. b The process of mechanical fragmentation was used to prepare the libraries. c In the traditional protocol, the size selection, and quantification were processed using a one sample one tube method. d With the AIO-seq method, the library analyzed by the Agilent 2100 Bioanalyzer will give the fragment distribution pattern and the ratio of the target region (between the two blue lines) to the total library. e The concentration of the total library could be obtained by Qubit™ 4.0 Fluorometer. f The target region concentrations (TRC) were calculated within each library by multiplying the proportion of the target region from ( d ) and the total library concentration from ( e ). g Mixing the libraries in one tube according to the calculated TRC and their expected yields of the sequence data. h – i One size selection by Sage HT. j Quantification of the selected fragment by qPCR and sequencing

Techniques Used: Sequencing, Selection, Concentration Assay, Real-time Polymerase Chain Reaction

35) Product Images from "A Panel of Plasma Exosomal miRNAs as Potential Biomarkers for Differential Diagnosis of Thyroid Nodules"

Article Title: A Panel of Plasma Exosomal miRNAs as Potential Biomarkers for Differential Diagnosis of Thyroid Nodules

Journal: Frontiers in Genetics

doi: 10.3389/fgene.2020.00449

Technical pipeline for identification of plasma exosomal miRNAs by next-generation sequencing. (A) Representative size distribution of exosomes isolated from plasma determined using nano-flow cytometry. (B) Representative particle concentration of exosomes isolated from plasma determined by nano-flow cytometry. (C) Western blot showing the expression level of the typical exosome markers Calnexin (negative in exosomes), TSG-101, CD63, and CD81(positive in exosomes) in the four randomly selected exosomal samples from each group. S1–4, sample 1–4. PC, positive control using whole cell lysate prepared from HEK 293 cells. (D) Transmission electron microscopy picture showing the morphology of the exosomes. Scale bar on the left represents 200 nm, on the right 100 nm. (E) Polyacrylamide gel electrophoresis (PAGE) analysis for the established small RNA libraries. DNA ladders are shown in the 1st, 4th, and 7th lanes of the panel, while the DNA bands of prepared libraries are shown between the marker lanes. The anticipated size of the RNA sequencing constructs is ~150 bp. The DNA bands corresponding to 130 bp are the adaptor dimmers. M, DNA ladder. L1–4, library 1–4. (F) High-sensitivity DNA chip run on Agilent 2100 bioanalyzer demonstrates the quality and quantity of the gel-recovered library. (G) Illustrated RNA species and their abundance in the raw reads of exosomal RNA. Mappable reads are the sequences that are mapped to known human RNAs. lncRNA, long noncoding RNA; miRNA, microRNA; piRNA, piwi-interacting RNA; rRNA, ribosomal RNA; snRNA, small nuclear RNA; snoRNA, small nucleolar RNA; tRNA, transfer RNA. (H) Top 30 known miRNAs with the highest expression levels in exosomal miRNA libraries. (I) Top 10 novel miRNAs predicted by miRDeep2 and miREvo with the highest expression levels in exosomal miRNA libraries.
Figure Legend Snippet: Technical pipeline for identification of plasma exosomal miRNAs by next-generation sequencing. (A) Representative size distribution of exosomes isolated from plasma determined using nano-flow cytometry. (B) Representative particle concentration of exosomes isolated from plasma determined by nano-flow cytometry. (C) Western blot showing the expression level of the typical exosome markers Calnexin (negative in exosomes), TSG-101, CD63, and CD81(positive in exosomes) in the four randomly selected exosomal samples from each group. S1–4, sample 1–4. PC, positive control using whole cell lysate prepared from HEK 293 cells. (D) Transmission electron microscopy picture showing the morphology of the exosomes. Scale bar on the left represents 200 nm, on the right 100 nm. (E) Polyacrylamide gel electrophoresis (PAGE) analysis for the established small RNA libraries. DNA ladders are shown in the 1st, 4th, and 7th lanes of the panel, while the DNA bands of prepared libraries are shown between the marker lanes. The anticipated size of the RNA sequencing constructs is ~150 bp. The DNA bands corresponding to 130 bp are the adaptor dimmers. M, DNA ladder. L1–4, library 1–4. (F) High-sensitivity DNA chip run on Agilent 2100 bioanalyzer demonstrates the quality and quantity of the gel-recovered library. (G) Illustrated RNA species and their abundance in the raw reads of exosomal RNA. Mappable reads are the sequences that are mapped to known human RNAs. lncRNA, long noncoding RNA; miRNA, microRNA; piRNA, piwi-interacting RNA; rRNA, ribosomal RNA; snRNA, small nuclear RNA; snoRNA, small nucleolar RNA; tRNA, transfer RNA. (H) Top 30 known miRNAs with the highest expression levels in exosomal miRNA libraries. (I) Top 10 novel miRNAs predicted by miRDeep2 and miREvo with the highest expression levels in exosomal miRNA libraries.

Techniques Used: Next-Generation Sequencing, Isolation, Flow Cytometry, Concentration Assay, Western Blot, Expressing, Positive Control, Transmission Assay, Electron Microscopy, Polyacrylamide Gel Electrophoresis, Marker, RNA Sequencing Assay, Construct, Chromatin Immunoprecipitation

36) Product Images from "OsCpn60β1 is Essential for Chloroplast Development in Rice (Oryza sativa L.)"

Article Title: OsCpn60β1 is Essential for Chloroplast Development in Rice (Oryza sativa L.)

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms21114023

OsCpn60β1 affects the development of chloroplast ribosome. ( A ) rRNA analysis using an Agilent 2100 bioanalyzer. The rRNAs isolated from 7-day-old WT and OsCpn60β1 mutants seedlings. ( B ) qRT-PCR analysis of rRNA accumulation in WT and OsCpn60β1 mutants seedlings. The data are mean ± SD (n = 3) and ** indicates statistical significance at p
Figure Legend Snippet: OsCpn60β1 affects the development of chloroplast ribosome. ( A ) rRNA analysis using an Agilent 2100 bioanalyzer. The rRNAs isolated from 7-day-old WT and OsCpn60β1 mutants seedlings. ( B ) qRT-PCR analysis of rRNA accumulation in WT and OsCpn60β1 mutants seedlings. The data are mean ± SD (n = 3) and ** indicates statistical significance at p

Techniques Used: Isolation, Quantitative RT-PCR

37) Product Images from "Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis"

Article Title: Rapid separation of developing Arabidopsis seeds from siliques for RNA or metabolite analysis

Journal: Plant Methods

doi: 10.1186/1746-4811-9-9

Comparison of RNA extracted from dissected and popped siliques. The RNA Integrity Number (RIN) is a measure of RNA degradation to estimate RNA quality for gene expression analysis as measured by an Agilent 2100 bioanalyzer. RIN ranges from 10 (totally intact) to 1 (totally degraded) [ 11 ]. A RIN of at least 8 indicates high quality RNA suitable for RNAseq or other analyses. Whisker box plot with four replicates.
Figure Legend Snippet: Comparison of RNA extracted from dissected and popped siliques. The RNA Integrity Number (RIN) is a measure of RNA degradation to estimate RNA quality for gene expression analysis as measured by an Agilent 2100 bioanalyzer. RIN ranges from 10 (totally intact) to 1 (totally degraded) [ 11 ]. A RIN of at least 8 indicates high quality RNA suitable for RNAseq or other analyses. Whisker box plot with four replicates.

Techniques Used: Expressing, Whisker Assay

38) Product Images from "Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq"

Article Title: Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2014.00142

Validation and quantification of representative, final RNA-Seq cDNA libraries prior to GA II, using an Agilent 2100 Bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA) . The RNA-Seq cDNA libraries were prepared from RNA extracted from C. thermocellum cells grown on cellobiose or PYP. (A) Electrophoresis run of the cDNA libraries by the Bioanalyzer; (B) bioanalyzer trace of cDNA libraries.
Figure Legend Snippet: Validation and quantification of representative, final RNA-Seq cDNA libraries prior to GA II, using an Agilent 2100 Bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA) . The RNA-Seq cDNA libraries were prepared from RNA extracted from C. thermocellum cells grown on cellobiose or PYP. (A) Electrophoresis run of the cDNA libraries by the Bioanalyzer; (B) bioanalyzer trace of cDNA libraries.

Techniques Used: RNA Sequencing Assay, Chromatin Immunoprecipitation, Electrophoresis

39) Product Images from "Comparison of target labeling methods for use with Affymetrix GeneChips"

Article Title: Comparison of target labeling methods for use with Affymetrix GeneChips

Journal: BMC Biotechnology

doi: 10.1186/1472-6750-7-24

Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).
Figure Legend Snippet: Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).

Techniques Used: Labeling, Purification, Concentration Assay, Marker

40) Product Images from "Comparison of target labeling methods for use with Affymetrix GeneChips"

Article Title: Comparison of target labeling methods for use with Affymetrix GeneChips

Journal: BMC Biotechnology

doi: 10.1186/1472-6750-7-24

Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).
Figure Legend Snippet: Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).

Techniques Used: Labeling, Purification, Concentration Assay, Marker

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Ligation:

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Article Snippet: .. The ligation reaction was incubated at 25°C for 1 h and then the products of the reaction were analyzed on an Agilent 2100 Bioanalyzer (Agilent Biotechnologies) using an Agilent Small RNA Kit. .. Bias in small RNA library construction measured by high throughput sequencing of a defined pool of 962 miRNAs The use of a defined mixture of small RNAs allowed us to directly compare the results of different library preparation conditions to an expected result.

Purification:

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Article Snippet: .. Further PMT purification on an AKTApurifier (GE Healthcare) was used to obtain assembled PMT that was free of additional complexes between heavy and light chains ( ). shows capillary electrophoresis of PMT performed on an Agilent 2100 Bioanalyzer under reducing conditions, where peak 12 corresponds to HC and peak 8 corresponds to LC. ..

Electrophoresis:

Article Title: Plant-Made Trastuzumab (Herceptin) Inhibits HER2/Neu+ Cell Proliferation and Retards Tumor Growth
Article Snippet: .. Further PMT purification on an AKTApurifier (GE Healthcare) was used to obtain assembled PMT that was free of additional complexes between heavy and light chains ( ). shows capillary electrophoresis of PMT performed on an Agilent 2100 Bioanalyzer under reducing conditions, where peak 12 corresponds to HC and peak 8 corresponds to LC. ..

Concentration Assay:

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Incubation:

Article Title: Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure
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Formalin-fixed Paraffin-Embedded:

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other:

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