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Agilent technologies rna 6000 nano kit
RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the <t>RNA</t> 6000 <t>Nano-Kit</t> (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.
Rna 6000 Nano Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 1508 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research"

Article Title: Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research

Journal: Scientific Reports

doi: 10.1038/s41598-019-56509-5

RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.
Figure Legend Snippet: RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.

Techniques Used:

2) Product Images from "Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei)"

Article Title: Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei)

Journal: PLoS ONE

doi: 10.1371/journal.pone.0044969

Transcription levels of putative genes involved in conidiation and sexual potency. Total RNAs were extracted from 8 different experimental conditions as indicated. The quality of extracted RNA samples was further analyzed with the RNA 6000 Nano kit by Agilent 2100 Bioanalyzer (see Materials and Methods). ( A ) Northern blots analysis of act1 (actin) and env1 transcription. The denaturing RNA agarose gel was stained with ethidium bromide, the 18S rRNA and 28S rRNA bands were clearly visible in the intact RNA samples. ( B–H ) qRT-PCR. Relative transcript abundance of representative genes in sexually potent and impotent conditions. Data were given as relative quantitative (RQ) values to one of the eight conditions as indicated. The transcripts of the ribosome protein gene rpl6e were used for normalization of the qRT-PCR data [43] .
Figure Legend Snippet: Transcription levels of putative genes involved in conidiation and sexual potency. Total RNAs were extracted from 8 different experimental conditions as indicated. The quality of extracted RNA samples was further analyzed with the RNA 6000 Nano kit by Agilent 2100 Bioanalyzer (see Materials and Methods). ( A ) Northern blots analysis of act1 (actin) and env1 transcription. The denaturing RNA agarose gel was stained with ethidium bromide, the 18S rRNA and 28S rRNA bands were clearly visible in the intact RNA samples. ( B–H ) qRT-PCR. Relative transcript abundance of representative genes in sexually potent and impotent conditions. Data were given as relative quantitative (RQ) values to one of the eight conditions as indicated. The transcripts of the ribosome protein gene rpl6e were used for normalization of the qRT-PCR data [43] .

Techniques Used: Northern Blot, Agarose Gel Electrophoresis, Staining, Quantitative RT-PCR

3) Product Images from "Inhibition of stationary phase respiration impairs persister formation in E. coli"

Article Title: Inhibition of stationary phase respiration impairs persister formation in E. coli

Journal: Nature communications

doi: 10.1038/ncomms8983

RNA integrity, protein levels and degradation, and cells size of stationary phase cells ( A–C, E–F ) Cell cultures at early stationary phase (t=6 h) were treated with 1mM KCN or transferred to an anaerobic chamber. At t=24 h, cells were pelleted for RNA, protein, and microscope analyses. For controls, untreated overnight cultures (t=24 h) and early stationary phase cultures (t=6 h) were used. ( A–B ) RNA quality was determined with a bioanalyzer using an RNA 6000 Nano kit. The degradation of rRNA was assessed with RNA integrity values which range from 10 (intact) to 1 (totally degraded). (C) Cells were sonicated and the protein content in the supernatant was determined with Bradford assays. (D) Before KCN treatment at t=6 h, the inducer for gfp expression was removed in the cultures with the cells carrying pQE-80L gfp-ssrA . After the KCN treatment, GFP levels were measured. Background fluorescence was determined using cells with empty vectors. (E–F) Phase contrast images of fixed cells were taken using a microscope, and cell size (fold change relative to 24 h untreated overnight cultures) were determined with ImageJ. (G–H) KCN treatment was performed at t=9 h. At t=24 h, microscope images were taken, and ampicillin and ofloxacin persister levels were determined. * signifies significant differences for comparisons to control groups (p-value
Figure Legend Snippet: RNA integrity, protein levels and degradation, and cells size of stationary phase cells ( A–C, E–F ) Cell cultures at early stationary phase (t=6 h) were treated with 1mM KCN or transferred to an anaerobic chamber. At t=24 h, cells were pelleted for RNA, protein, and microscope analyses. For controls, untreated overnight cultures (t=24 h) and early stationary phase cultures (t=6 h) were used. ( A–B ) RNA quality was determined with a bioanalyzer using an RNA 6000 Nano kit. The degradation of rRNA was assessed with RNA integrity values which range from 10 (intact) to 1 (totally degraded). (C) Cells were sonicated and the protein content in the supernatant was determined with Bradford assays. (D) Before KCN treatment at t=6 h, the inducer for gfp expression was removed in the cultures with the cells carrying pQE-80L gfp-ssrA . After the KCN treatment, GFP levels were measured. Background fluorescence was determined using cells with empty vectors. (E–F) Phase contrast images of fixed cells were taken using a microscope, and cell size (fold change relative to 24 h untreated overnight cultures) were determined with ImageJ. (G–H) KCN treatment was performed at t=9 h. At t=24 h, microscope images were taken, and ampicillin and ofloxacin persister levels were determined. * signifies significant differences for comparisons to control groups (p-value

Techniques Used: Microscopy, Sonication, Expressing, Fluorescence, Significance Assay

4) Product Images from "Identification of an optimal method for extracting RNA from human skin biopsy, using domestic pig as a model system"

Article Title: Identification of an optimal method for extracting RNA from human skin biopsy, using domestic pig as a model system

Journal: Scientific Reports

doi: 10.1038/s41598-019-56579-5

RNA quality values from human skin derived RNA samples. ( A ) RNA Integrity Numbers (RIN) obtained by applying the Agilent 2100 Bioanalyzer and RNA 6000 Nano kit. ( B ) The RNA absorbance spectrum measured with NanoDrop spectrophotometer.
Figure Legend Snippet: RNA quality values from human skin derived RNA samples. ( A ) RNA Integrity Numbers (RIN) obtained by applying the Agilent 2100 Bioanalyzer and RNA 6000 Nano kit. ( B ) The RNA absorbance spectrum measured with NanoDrop spectrophotometer.

Techniques Used: Derivative Assay, Spectrophotometry

5) Product Images from "Microparticle conferred microRNA profiles - implications in the transfer and dominance of cancer traits"

Article Title: Microparticle conferred microRNA profiles - implications in the transfer and dominance of cancer traits

Journal: Molecular Cancer

doi: 10.1186/1476-4598-11-37

RNA integrity of samples. RNA derived from ( A ) the drug sensitive-recipient cell (CEM), ( B ) drug-resistant VLB 100 cells, ( C ) their isolated MPs (VLBMP) and ( D ) the drug sensitive-recipient cells after MP transfer (CEM + VLBMP) was analysed using Agilent RNA 6000 Nano kit by Agilent 2100 Bioanalyzer. The RIN value of the samples ranged between 6.2-9.2. Data is representative of a typical experiment
Figure Legend Snippet: RNA integrity of samples. RNA derived from ( A ) the drug sensitive-recipient cell (CEM), ( B ) drug-resistant VLB 100 cells, ( C ) their isolated MPs (VLBMP) and ( D ) the drug sensitive-recipient cells after MP transfer (CEM + VLBMP) was analysed using Agilent RNA 6000 Nano kit by Agilent 2100 Bioanalyzer. The RIN value of the samples ranged between 6.2-9.2. Data is representative of a typical experiment

Techniques Used: Derivative Assay, Isolation

6) Product Images from "Multiple links between 5-methylcytosine content of mRNA and translation"

Article Title: Multiple links between 5-methylcytosine content of mRNA and translation

Journal: bioRxiv

doi: 10.1101/2020.02.04.933499

Quality controls for polysome profiling and bsRNA-seq sample preparation. Related to Figure 1. A: Distribution of tRNA and rRNA across gradients. Equal proportions of total RNA from each RNA fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; equal proportions of recovered RNA were loaded). Pseudo-gel images for each of the three biological replicates are shown. B: Distribution of additional representative mRNAs across gradients. mRNA levels in each RNA fraction were determined by RT-qPCR. Results for three mRNAs of different coding region length are shown: RPL13a (ribosomal protein L13a), MAP2K2 (mitogen-activated protein kinase kinase 2) and NDUFB7 (NADH:ubiquinone oxidoreductase subunit B7). mRNA levels per fraction were normalised to the level of a spike-in control, rescaled as percentage of total signal across all fractions, and are shown as mean ± standard deviation across the three biological replicates. A representative absorbance trace (254nm) is shown at the top for reference. C: RNA quality of bsRNA-seq fractions prior to bisulfite treatment. RNA from each bsRNA-seq fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; an equal amount of RNA was loaded per well). Pseudo-gel images for each of the three biological replicates are shown. D: Microfluidic electrophograms for biological replicate E tracing the RNA quality at each step from input to the final library (from left to right). Data shown are exemplary for all biological replicates.
Figure Legend Snippet: Quality controls for polysome profiling and bsRNA-seq sample preparation. Related to Figure 1. A: Distribution of tRNA and rRNA across gradients. Equal proportions of total RNA from each RNA fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; equal proportions of recovered RNA were loaded). Pseudo-gel images for each of the three biological replicates are shown. B: Distribution of additional representative mRNAs across gradients. mRNA levels in each RNA fraction were determined by RT-qPCR. Results for three mRNAs of different coding region length are shown: RPL13a (ribosomal protein L13a), MAP2K2 (mitogen-activated protein kinase kinase 2) and NDUFB7 (NADH:ubiquinone oxidoreductase subunit B7). mRNA levels per fraction were normalised to the level of a spike-in control, rescaled as percentage of total signal across all fractions, and are shown as mean ± standard deviation across the three biological replicates. A representative absorbance trace (254nm) is shown at the top for reference. C: RNA quality of bsRNA-seq fractions prior to bisulfite treatment. RNA from each bsRNA-seq fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; an equal amount of RNA was loaded per well). Pseudo-gel images for each of the three biological replicates are shown. D: Microfluidic electrophograms for biological replicate E tracing the RNA quality at each step from input to the final library (from left to right). Data shown are exemplary for all biological replicates.

Techniques Used: Sample Prep, Electrophoresis, Chromatin Immunoprecipitation, Quantitative RT-PCR, Standard Deviation

7) Product Images from "An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)"

Article Title: An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

Journal: FEBS Open Bio

doi: 10.1002/2211-5463.12561

Electropherograms of total RNA from cassava obtained using our method showing 18S and 25S rRNA regions with RNA concentrations and RIN values; (A) to (C) correspond with RNA from leaves and storage roots, and (A) and (B) correspond with RNA from different stages of plant development (young and mature leaves). RNA were visualized in denaturing agarose gels stained with SYBR safe. RNA were analyzed using Agilent RNA 6000 Nano Assays in a 2100 Bioanalyzer (Agilent Technologies) and were then used for RNA sequencing.
Figure Legend Snippet: Electropherograms of total RNA from cassava obtained using our method showing 18S and 25S rRNA regions with RNA concentrations and RIN values; (A) to (C) correspond with RNA from leaves and storage roots, and (A) and (B) correspond with RNA from different stages of plant development (young and mature leaves). RNA were visualized in denaturing agarose gels stained with SYBR safe. RNA were analyzed using Agilent RNA 6000 Nano Assays in a 2100 Bioanalyzer (Agilent Technologies) and were then used for RNA sequencing.

Techniques Used: Staining, RNA Sequencing Assay

8) Product Images from "RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat"

Article Title: RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2018.01539

The quantity and quality of nucleic acids of wheat shoots. Total DNA (A) and RNA (B) yields extracted from Mace and RAC875 whole shoots ( Experiment 1 ) as determined by fluorescence assays (Quant-it dsDNA broad range kit and Quant-iT RNA Assay Kit, Life Technologies, United States). (C,D) RNA quality assessment via RNA smear analysis using an RNA 6000 Nano Kit (Agilent, United States) and the Agilent 2100 Bioanalyzer. The chromatograms (C,D) show the fluorescence ( y -axis fluorescent units, FU) of rRNA species over time ( x -axis, seconds, s) with the faster migrating 25S peak at 45.8 s and the slower 18S rRNA peak at 41.35 s. Representative image of a +N treated RAC875 shoot sample (C) and a -N treated RAC875 shoot sample (D) .
Figure Legend Snippet: The quantity and quality of nucleic acids of wheat shoots. Total DNA (A) and RNA (B) yields extracted from Mace and RAC875 whole shoots ( Experiment 1 ) as determined by fluorescence assays (Quant-it dsDNA broad range kit and Quant-iT RNA Assay Kit, Life Technologies, United States). (C,D) RNA quality assessment via RNA smear analysis using an RNA 6000 Nano Kit (Agilent, United States) and the Agilent 2100 Bioanalyzer. The chromatograms (C,D) show the fluorescence ( y -axis fluorescent units, FU) of rRNA species over time ( x -axis, seconds, s) with the faster migrating 25S peak at 45.8 s and the slower 18S rRNA peak at 41.35 s. Representative image of a +N treated RAC875 shoot sample (C) and a -N treated RAC875 shoot sample (D) .

Techniques Used: Fluorescence

9) Product Images from "mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets"

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

Journal: RNA Biology

doi: 10.1080/15476286.2018.1451723

Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.
Figure Legend Snippet: Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.

Techniques Used: Polyacrylamide Gel Electrophoresis, Electrophoresis, Multiple Displacement Amplification, Marker

Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.
Figure Legend Snippet: Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.

Techniques Used: Isolation, Multiple Displacement Amplification, Polyacrylamide Gel Electrophoresis, Electrophoresis, Marker

10) Product Images from "mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets"

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

Journal: RNA Biology

doi: 10.1080/15476286.2018.1451723

Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.
Figure Legend Snippet: Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.

Techniques Used: Polyacrylamide Gel Electrophoresis, Electrophoresis, Multiple Displacement Amplification, Marker

Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.
Figure Legend Snippet: Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.

Techniques Used: Isolation, Multiple Displacement Amplification, Polyacrylamide Gel Electrophoresis, Electrophoresis, Marker

11) Product Images from "RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat"

Article Title: RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2018.01539

The quantity and quality of nucleic acids of wheat shoots. Total DNA (A) and RNA (B) yields extracted from Mace and RAC875 whole shoots ( Experiment 1 ) as determined by fluorescence assays (Quant-it dsDNA broad range kit and Quant-iT RNA Assay Kit, Life Technologies, United States). (C,D) RNA quality assessment via RNA smear analysis using an RNA 6000 Nano Kit (Agilent, United States) and the Agilent 2100 Bioanalyzer. The chromatograms (C,D) show the fluorescence ( y -axis fluorescent units, FU) of rRNA species over time ( x -axis, seconds, s) with the faster migrating 25S peak at 45.8 s and the slower 18S rRNA peak at 41.35 s. Representative image of a +N treated RAC875 shoot sample (C) and a -N treated RAC875 shoot sample (D) .
Figure Legend Snippet: The quantity and quality of nucleic acids of wheat shoots. Total DNA (A) and RNA (B) yields extracted from Mace and RAC875 whole shoots ( Experiment 1 ) as determined by fluorescence assays (Quant-it dsDNA broad range kit and Quant-iT RNA Assay Kit, Life Technologies, United States). (C,D) RNA quality assessment via RNA smear analysis using an RNA 6000 Nano Kit (Agilent, United States) and the Agilent 2100 Bioanalyzer. The chromatograms (C,D) show the fluorescence ( y -axis fluorescent units, FU) of rRNA species over time ( x -axis, seconds, s) with the faster migrating 25S peak at 45.8 s and the slower 18S rRNA peak at 41.35 s. Representative image of a +N treated RAC875 shoot sample (C) and a -N treated RAC875 shoot sample (D) .

Techniques Used: Fluorescence

12) Product Images from "Multiple links between 5-methylcytosine content of mRNA and translation"

Article Title: Multiple links between 5-methylcytosine content of mRNA and translation

Journal: bioRxiv

doi: 10.1101/2020.02.04.933499

Quality controls for polysome profiling and bsRNA-seq sample preparation. Related to Figure 1. A: Distribution of tRNA and rRNA across gradients. Equal proportions of total RNA from each RNA fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; equal proportions of recovered RNA were loaded). Pseudo-gel images for each of the three biological replicates are shown. B: Distribution of additional representative mRNAs across gradients. mRNA levels in each RNA fraction were determined by RT-qPCR. Results for three mRNAs of different coding region length are shown: RPL13a (ribosomal protein L13a), MAP2K2 (mitogen-activated protein kinase kinase 2) and NDUFB7 (NADH:ubiquinone oxidoreductase subunit B7). mRNA levels per fraction were normalised to the level of a spike-in control, rescaled as percentage of total signal across all fractions, and are shown as mean ± standard deviation across the three biological replicates. A representative absorbance trace (254nm) is shown at the top for reference. C: RNA quality of bsRNA-seq fractions prior to bisulfite treatment. RNA from each bsRNA-seq fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; an equal amount of RNA was loaded per well). Pseudo-gel images for each of the three biological replicates are shown. D: Microfluidic electrophograms for biological replicate E tracing the RNA quality at each step from input to the final library (from left to right). Data shown are exemplary for all biological replicates.
Figure Legend Snippet: Quality controls for polysome profiling and bsRNA-seq sample preparation. Related to Figure 1. A: Distribution of tRNA and rRNA across gradients. Equal proportions of total RNA from each RNA fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; equal proportions of recovered RNA were loaded). Pseudo-gel images for each of the three biological replicates are shown. B: Distribution of additional representative mRNAs across gradients. mRNA levels in each RNA fraction were determined by RT-qPCR. Results for three mRNAs of different coding region length are shown: RPL13a (ribosomal protein L13a), MAP2K2 (mitogen-activated protein kinase kinase 2) and NDUFB7 (NADH:ubiquinone oxidoreductase subunit B7). mRNA levels per fraction were normalised to the level of a spike-in control, rescaled as percentage of total signal across all fractions, and are shown as mean ± standard deviation across the three biological replicates. A representative absorbance trace (254nm) is shown at the top for reference. C: RNA quality of bsRNA-seq fractions prior to bisulfite treatment. RNA from each bsRNA-seq fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; an equal amount of RNA was loaded per well). Pseudo-gel images for each of the three biological replicates are shown. D: Microfluidic electrophograms for biological replicate E tracing the RNA quality at each step from input to the final library (from left to right). Data shown are exemplary for all biological replicates.

Techniques Used: Sample Prep, Electrophoresis, Chromatin Immunoprecipitation, Quantitative RT-PCR, Standard Deviation

13) Product Images from "Multiple links between 5-methylcytosine content of mRNA and translation"

Article Title: Multiple links between 5-methylcytosine content of mRNA and translation

Journal: bioRxiv

doi: 10.1101/2020.02.04.933499

Quality controls for polysome profiling and bsRNA-seq sample preparation. Related to Figure 1. A: Distribution of tRNA and rRNA across gradients. Equal proportions of total RNA from each RNA fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; equal proportions of recovered RNA were loaded). Pseudo-gel images for each of the three biological replicates are shown. B: Distribution of additional representative mRNAs across gradients. mRNA levels in each RNA fraction were determined by RT-qPCR. Results for three mRNAs of different coding region length are shown: RPL13a (ribosomal protein L13a), MAP2K2 (mitogen-activated protein kinase kinase 2) and NDUFB7 (NADH:ubiquinone oxidoreductase subunit B7). mRNA levels per fraction were normalised to the level of a spike-in control, rescaled as percentage of total signal across all fractions, and are shown as mean ± standard deviation across the three biological replicates. A representative absorbance trace (254nm) is shown at the top for reference. C: RNA quality of bsRNA-seq fractions prior to bisulfite treatment. RNA from each bsRNA-seq fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; an equal amount of RNA was loaded per well). Pseudo-gel images for each of the three biological replicates are shown. D: Microfluidic electrophograms for biological replicate E tracing the RNA quality at each step from input to the final library (from left to right). Data shown are exemplary for all biological replicates.
Figure Legend Snippet: Quality controls for polysome profiling and bsRNA-seq sample preparation. Related to Figure 1. A: Distribution of tRNA and rRNA across gradients. Equal proportions of total RNA from each RNA fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; equal proportions of recovered RNA were loaded). Pseudo-gel images for each of the three biological replicates are shown. B: Distribution of additional representative mRNAs across gradients. mRNA levels in each RNA fraction were determined by RT-qPCR. Results for three mRNAs of different coding region length are shown: RPL13a (ribosomal protein L13a), MAP2K2 (mitogen-activated protein kinase kinase 2) and NDUFB7 (NADH:ubiquinone oxidoreductase subunit B7). mRNA levels per fraction were normalised to the level of a spike-in control, rescaled as percentage of total signal across all fractions, and are shown as mean ± standard deviation across the three biological replicates. A representative absorbance trace (254nm) is shown at the top for reference. C: RNA quality of bsRNA-seq fractions prior to bisulfite treatment. RNA from each bsRNA-seq fraction was analysed by microfluidic electrophoresis (Bioanalyzer RNA 6000 Nano Chip; an equal amount of RNA was loaded per well). Pseudo-gel images for each of the three biological replicates are shown. D: Microfluidic electrophograms for biological replicate E tracing the RNA quality at each step from input to the final library (from left to right). Data shown are exemplary for all biological replicates.

Techniques Used: Sample Prep, Electrophoresis, Chromatin Immunoprecipitation, Quantitative RT-PCR, Standard Deviation

14) Product Images from "mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets"

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

Journal: RNA Biology

doi: 10.1080/15476286.2018.1451723

Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.
Figure Legend Snippet: Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.

Techniques Used: Polyacrylamide Gel Electrophoresis, Electrophoresis, Multiple Displacement Amplification, Marker

Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.
Figure Legend Snippet: Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.

Techniques Used: Isolation, Multiple Displacement Amplification, Polyacrylamide Gel Electrophoresis, Electrophoresis, Marker

15) 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

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

16) Product Images from "Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis"

Article Title: Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis

Journal: Data in Brief

doi: 10.1016/j.dib.2019.105053

RNA isolation quality data and per base sequence quality of RNA-sequencing reads. (A) RNA quality of ribosome-free, monosome, polysome and total RNA from hASCs determined using the RNA 6000 Nano Chip. (B) Examples of electropherograms of ribosome-free, monosomal, polysomal and total RNA from hASCs as determined using the RNA 6000 Nano Chip. (C) Examples of per base sequence quality scores for ribosome-free, monosomal, polysomal and total RNA samples sequenced by FastQC (version 0.11.3). (D–E) MDS plot of polysomal and total RNA fractions for adipogenic (D) and osteogenic (E) differentiation. CT: control, hASCs treated with maintenance medium for 24 h; ADI: hASCs treated with adipogenic medium for 24 h; OST: hASCs treated with osteogenic medium for 24 h.
Figure Legend Snippet: RNA isolation quality data and per base sequence quality of RNA-sequencing reads. (A) RNA quality of ribosome-free, monosome, polysome and total RNA from hASCs determined using the RNA 6000 Nano Chip. (B) Examples of electropherograms of ribosome-free, monosomal, polysomal and total RNA from hASCs as determined using the RNA 6000 Nano Chip. (C) Examples of per base sequence quality scores for ribosome-free, monosomal, polysomal and total RNA samples sequenced by FastQC (version 0.11.3). (D–E) MDS plot of polysomal and total RNA fractions for adipogenic (D) and osteogenic (E) differentiation. CT: control, hASCs treated with maintenance medium for 24 h; ADI: hASCs treated with adipogenic medium for 24 h; OST: hASCs treated with osteogenic medium for 24 h.

Techniques Used: Isolation, Sequencing, RNA Sequencing Assay, Chromatin Immunoprecipitation

17) Product Images from "An ARF6-Exportin-5 Axis Delivers pre-miRNA Cargo to Tumor Microvesicles."

Article Title: An ARF6-Exportin-5 Axis Delivers pre-miRNA Cargo to Tumor Microvesicles.

Journal: Nature cell biology

doi: 10.1038/s41556-019-0345-y

TMVs are a distinct class of extracellular vesicles and contain pre-miRNA cargo. Whole LOX melanoma cells ( a ), isolated LOX TMVs ( b ), or isolated LOX exosomes ( c ) were analyzed by scanning electron microscopy. Representative images of each population shown. Images are representative of N=3 biological and n=2 technical replicates. d. 20 μg of total protein isolate from whole cells (LOX Cell) or isolated TMVs (LOX TMV) was separated by SDS-PAGE and protein cargo determined by western blotting. Blots are representative of N=3 independent biological experiments. e. Agilent bioanalyzer analysis of TMV RNA content using the RNA 6000 Nano kit shows cargo corresponding in size to pre-miRNA (green bar). f. Higher resolution analysis of TMV small RNA using the Bioanalyzer Small RNA 6–150 nt Analysis kit shows peak corresponding to mature miRNA (green bar). Representative images from N=3 independent biological samples shown. g. Bowtie analysis of small RNA content isolated from TMVs released from invasive tumor cell lines of melanoma (LOX), prostate (PC-3), and breast (MDA-MB-231) origin. For each cell type, N=3 independent biological samples. h. ARF6 activity was measured using an MT2 ARF6-GTP specific pulldown assay as described in methods. Data presented is representative of N=4 independent biological experiments-. ARF6 i. Analysis of small RNA content isolated from parental melanoma cells or those expressing constitutively active ARF6-GTP showed no difference in the quantity of detectable RNA with ARF6 activation. j. Sequencing analysis revealed a significant increase in the total read hits corresponding to miRNA upon expression of ARF6-Q67L. k. qRT-PCR analysis confirms the increase in pre-miRNA cargo content in TMVs released by tumor cells of melanoma (LOX), ovarian (OvCar3), and breast (MDA-MB-231) origins. l. qRT-PCR analysis of total cell pre-miRNA levels with expression of ARF6-Q67L. Data presented as mean±standard deviation. For panels b-e , statistical analysis was based on measurements obtained for 3 biological repeats (N=3). P-values determined by unpaired, two-tailed t-test between control and treatment reactions for each independent experimental condition. P-values
Figure Legend Snippet: TMVs are a distinct class of extracellular vesicles and contain pre-miRNA cargo. Whole LOX melanoma cells ( a ), isolated LOX TMVs ( b ), or isolated LOX exosomes ( c ) were analyzed by scanning electron microscopy. Representative images of each population shown. Images are representative of N=3 biological and n=2 technical replicates. d. 20 μg of total protein isolate from whole cells (LOX Cell) or isolated TMVs (LOX TMV) was separated by SDS-PAGE and protein cargo determined by western blotting. Blots are representative of N=3 independent biological experiments. e. Agilent bioanalyzer analysis of TMV RNA content using the RNA 6000 Nano kit shows cargo corresponding in size to pre-miRNA (green bar). f. Higher resolution analysis of TMV small RNA using the Bioanalyzer Small RNA 6–150 nt Analysis kit shows peak corresponding to mature miRNA (green bar). Representative images from N=3 independent biological samples shown. g. Bowtie analysis of small RNA content isolated from TMVs released from invasive tumor cell lines of melanoma (LOX), prostate (PC-3), and breast (MDA-MB-231) origin. For each cell type, N=3 independent biological samples. h. ARF6 activity was measured using an MT2 ARF6-GTP specific pulldown assay as described in methods. Data presented is representative of N=4 independent biological experiments-. ARF6 i. Analysis of small RNA content isolated from parental melanoma cells or those expressing constitutively active ARF6-GTP showed no difference in the quantity of detectable RNA with ARF6 activation. j. Sequencing analysis revealed a significant increase in the total read hits corresponding to miRNA upon expression of ARF6-Q67L. k. qRT-PCR analysis confirms the increase in pre-miRNA cargo content in TMVs released by tumor cells of melanoma (LOX), ovarian (OvCar3), and breast (MDA-MB-231) origins. l. qRT-PCR analysis of total cell pre-miRNA levels with expression of ARF6-Q67L. Data presented as mean±standard deviation. For panels b-e , statistical analysis was based on measurements obtained for 3 biological repeats (N=3). P-values determined by unpaired, two-tailed t-test between control and treatment reactions for each independent experimental condition. P-values

Techniques Used: Isolation, Electron Microscopy, SDS Page, Western Blot, Multiple Displacement Amplification, Activity Assay, Expressing, Activation Assay, Sequencing, Quantitative RT-PCR, Standard Deviation, Two Tailed Test

18) Product Images from "The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts"

Article Title: The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkx437

Elevated levels of the SmAPs increase the abundance of RNAs with A-rich tails. ( A ) Total RNA was isolated from strains PH1-16(pMJ05-SmAP1-His) and PH1-16(pMJO5-SmAP2-His) grown either in the presence of sucrose (−, non-induced) (lanes 1 and 3) or arabinose (+, induced) (lanes 2 and 4). Equal amounts of total RNA were used to isolate adenylated RNA with the Oligotex™ kit. Two microliter of each eluate was analyzed using with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies). ( B ) The sequence composition of the A-rich tails obtained after over-production of SmAP1 (top) and SmAP2 (bottom) was determined using WebLogo ( 51 ). Only 3΄ ends of the adaptor clipped reads, which do not map to the reference genome and which showed an overhang of longer than 15 nt were used for the analyzes. Only sites present in both replicas that are supported by at least five independent reads were analyzed. ( C ) Functional categorization of tailed RNAs. Functions, which are significant enriched (Fisher's exact test; α = 0.05) are marked with an asterisk. Genes are annotated according to ( 54 ).
Figure Legend Snippet: Elevated levels of the SmAPs increase the abundance of RNAs with A-rich tails. ( A ) Total RNA was isolated from strains PH1-16(pMJ05-SmAP1-His) and PH1-16(pMJO5-SmAP2-His) grown either in the presence of sucrose (−, non-induced) (lanes 1 and 3) or arabinose (+, induced) (lanes 2 and 4). Equal amounts of total RNA were used to isolate adenylated RNA with the Oligotex™ kit. Two microliter of each eluate was analyzed using with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies). ( B ) The sequence composition of the A-rich tails obtained after over-production of SmAP1 (top) and SmAP2 (bottom) was determined using WebLogo ( 51 ). Only 3΄ ends of the adaptor clipped reads, which do not map to the reference genome and which showed an overhang of longer than 15 nt were used for the analyzes. Only sites present in both replicas that are supported by at least five independent reads were analyzed. ( C ) Functional categorization of tailed RNAs. Functions, which are significant enriched (Fisher's exact test; α = 0.05) are marked with an asterisk. Genes are annotated according to ( 54 ).

Techniques Used: Isolation, Sequencing, Functional Assay

19) Product Images from "mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets"

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

Journal: RNA Biology

doi: 10.1080/15476286.2018.1451723

Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.
Figure Legend Snippet: Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.

Techniques Used: Polyacrylamide Gel Electrophoresis, Electrophoresis, Multiple Displacement Amplification, Marker

Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.
Figure Legend Snippet: Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.

Techniques Used: Isolation, Multiple Displacement Amplification, Polyacrylamide Gel Electrophoresis, Electrophoresis, Marker

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Article Snippet: .. RNA quality was assessed by microfluidic gel electrophoresis using an RNA 6000 Nano Kit (Agilent, United States) and an Agilent 2100 Bioanalyzer and performed at the David Gunn Genomics Facility (SAHMRI, Adelaide). ..

Spectrophotometry:

Article Title: Multiple links between 5-methylcytosine content of mRNA and translation
Article Snippet: .. RNA samples were analysed for quality using a Thermo Scientific™ NanoDrop™ One spectrophotometer (Thermo Fisher) and for integrity using the RNA 6000 Nano Kit on the 2100 Bioanalyzer (Agilent Technologies). .. RNA was treated using the TURBO DNA-free ™ Kit (Invitrogen) according to manufacturer’s instructions, purified by phenol/chloroform extraction and precipitated.

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    Agilent technologies rna 6000 nano kit
    RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the <t>RNA</t> 6000 <t>Nano-Kit</t> (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.
    Rna 6000 Nano Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 1508 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies bioanalyzer rna nano 6000 kit
    <t>Bioanalyzer</t> profiles of the large <t>RNA</t> fractions isolated from donors with the lowest and highest blood RNA level. The large RNA fractions (200 ng) from the low RNA level sample 180 (6.7 μg RNA/ml blood) and the high RNA level sample 162 (22.7 μg RNA/ml blood) were separated using the Bioanalyzer RNA <t>Nano</t> 6000 Kit. Shown are positions of: the (18S) and (28S) ribosomal RNA; the 600 nt globin region (G); and Bioanalyzer marker (M).
    Bioanalyzer Rna Nano 6000 Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.

    Journal: Scientific Reports

    Article Title: Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research

    doi: 10.1038/s41598-019-56509-5

    Figure Lengend Snippet: RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.

    Article Snippet: RNA quality was determined by the Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies).

    Techniques:

    Transcription levels of putative genes involved in conidiation and sexual potency. Total RNAs were extracted from 8 different experimental conditions as indicated. The quality of extracted RNA samples was further analyzed with the RNA 6000 Nano kit by Agilent 2100 Bioanalyzer (see Materials and Methods). ( A ) Northern blots analysis of act1 (actin) and env1 transcription. The denaturing RNA agarose gel was stained with ethidium bromide, the 18S rRNA and 28S rRNA bands were clearly visible in the intact RNA samples. ( B–H ) qRT-PCR. Relative transcript abundance of representative genes in sexually potent and impotent conditions. Data were given as relative quantitative (RQ) values to one of the eight conditions as indicated. The transcripts of the ribosome protein gene rpl6e were used for normalization of the qRT-PCR data [43] .

    Journal: PLoS ONE

    Article Title: Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei)

    doi: 10.1371/journal.pone.0044969

    Figure Lengend Snippet: Transcription levels of putative genes involved in conidiation and sexual potency. Total RNAs were extracted from 8 different experimental conditions as indicated. The quality of extracted RNA samples was further analyzed with the RNA 6000 Nano kit by Agilent 2100 Bioanalyzer (see Materials and Methods). ( A ) Northern blots analysis of act1 (actin) and env1 transcription. The denaturing RNA agarose gel was stained with ethidium bromide, the 18S rRNA and 28S rRNA bands were clearly visible in the intact RNA samples. ( B–H ) qRT-PCR. Relative transcript abundance of representative genes in sexually potent and impotent conditions. Data were given as relative quantitative (RQ) values to one of the eight conditions as indicated. The transcripts of the ribosome protein gene rpl6e were used for normalization of the qRT-PCR data [43] .

    Article Snippet: The quality of extracted RNA was further analyzed with the RNA 6000 Nano kit by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

    Techniques: Northern Blot, Agarose Gel Electrophoresis, Staining, Quantitative RT-PCR

    RNA integrity, protein levels and degradation, and cells size of stationary phase cells ( A–C, E–F ) Cell cultures at early stationary phase (t=6 h) were treated with 1mM KCN or transferred to an anaerobic chamber. At t=24 h, cells were pelleted for RNA, protein, and microscope analyses. For controls, untreated overnight cultures (t=24 h) and early stationary phase cultures (t=6 h) were used. ( A–B ) RNA quality was determined with a bioanalyzer using an RNA 6000 Nano kit. The degradation of rRNA was assessed with RNA integrity values which range from 10 (intact) to 1 (totally degraded). (C) Cells were sonicated and the protein content in the supernatant was determined with Bradford assays. (D) Before KCN treatment at t=6 h, the inducer for gfp expression was removed in the cultures with the cells carrying pQE-80L gfp-ssrA . After the KCN treatment, GFP levels were measured. Background fluorescence was determined using cells with empty vectors. (E–F) Phase contrast images of fixed cells were taken using a microscope, and cell size (fold change relative to 24 h untreated overnight cultures) were determined with ImageJ. (G–H) KCN treatment was performed at t=9 h. At t=24 h, microscope images were taken, and ampicillin and ofloxacin persister levels were determined. * signifies significant differences for comparisons to control groups (p-value

    Journal: Nature communications

    Article Title: Inhibition of stationary phase respiration impairs persister formation in E. coli

    doi: 10.1038/ncomms8983

    Figure Lengend Snippet: RNA integrity, protein levels and degradation, and cells size of stationary phase cells ( A–C, E–F ) Cell cultures at early stationary phase (t=6 h) were treated with 1mM KCN or transferred to an anaerobic chamber. At t=24 h, cells were pelleted for RNA, protein, and microscope analyses. For controls, untreated overnight cultures (t=24 h) and early stationary phase cultures (t=6 h) were used. ( A–B ) RNA quality was determined with a bioanalyzer using an RNA 6000 Nano kit. The degradation of rRNA was assessed with RNA integrity values which range from 10 (intact) to 1 (totally degraded). (C) Cells were sonicated and the protein content in the supernatant was determined with Bradford assays. (D) Before KCN treatment at t=6 h, the inducer for gfp expression was removed in the cultures with the cells carrying pQE-80L gfp-ssrA . After the KCN treatment, GFP levels were measured. Background fluorescence was determined using cells with empty vectors. (E–F) Phase contrast images of fixed cells were taken using a microscope, and cell size (fold change relative to 24 h untreated overnight cultures) were determined with ImageJ. (G–H) KCN treatment was performed at t=9 h. At t=24 h, microscope images were taken, and ampicillin and ofloxacin persister levels were determined. * signifies significant differences for comparisons to control groups (p-value

    Article Snippet: Quality of total RNA was assessed with a bioanalyzer using an RNA 6000 Nano kit (Agilent Technologies, Inc, Santa Clara, CA).

    Techniques: Microscopy, Sonication, Expressing, Fluorescence, Significance Assay

    Bioanalyzer profiles of the large RNA fractions isolated from donors with the lowest and highest blood RNA level. The large RNA fractions (200 ng) from the low RNA level sample 180 (6.7 μg RNA/ml blood) and the high RNA level sample 162 (22.7 μg RNA/ml blood) were separated using the Bioanalyzer RNA Nano 6000 Kit. Shown are positions of: the (18S) and (28S) ribosomal RNA; the 600 nt globin region (G); and Bioanalyzer marker (M).

    Journal: PLoS ONE

    Article Title: Inter-Individual Differences in RNA Levels in Human Peripheral Blood

    doi: 10.1371/journal.pone.0148260

    Figure Lengend Snippet: Bioanalyzer profiles of the large RNA fractions isolated from donors with the lowest and highest blood RNA level. The large RNA fractions (200 ng) from the low RNA level sample 180 (6.7 μg RNA/ml blood) and the high RNA level sample 162 (22.7 μg RNA/ml blood) were separated using the Bioanalyzer RNA Nano 6000 Kit. Shown are positions of: the (18S) and (28S) ribosomal RNA; the 600 nt globin region (G); and Bioanalyzer marker (M).

    Article Snippet: The isolated RNA samples were analyzed with the Agilent Bioanalyzer RNA Nano 6000 Kit (Agilent Technologies, Inc., Santa Clara, CA).

    Techniques: Isolation, Marker

    Characteristics of RNA isolated from healthy donors. a) Proportion of the large and small RNA fractions in relation to increasing quantities of total RNA in human peripheral blood. Samples of RNA from the 35 individuals are sequentially ranked in accord with the increasing amount of total RNA in the sample. For each sample, the amounts of the large RNA fraction (inverted triangle) and small RNA fraction (square) are depicted. b) The large RNA and small RNA fractions are expressed as a percentage of the total RNA in the sample. c) Bioanalyzer RIN values of the large RNA fractions from 35 samples.

    Journal: PLoS ONE

    Article Title: Inter-Individual Differences in RNA Levels in Human Peripheral Blood

    doi: 10.1371/journal.pone.0148260

    Figure Lengend Snippet: Characteristics of RNA isolated from healthy donors. a) Proportion of the large and small RNA fractions in relation to increasing quantities of total RNA in human peripheral blood. Samples of RNA from the 35 individuals are sequentially ranked in accord with the increasing amount of total RNA in the sample. For each sample, the amounts of the large RNA fraction (inverted triangle) and small RNA fraction (square) are depicted. b) The large RNA and small RNA fractions are expressed as a percentage of the total RNA in the sample. c) Bioanalyzer RIN values of the large RNA fractions from 35 samples.

    Article Snippet: The isolated RNA samples were analyzed with the Agilent Bioanalyzer RNA Nano 6000 Kit (Agilent Technologies, Inc., Santa Clara, CA).

    Techniques: Isolation