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Agilent technologies rna 6000 nano kit
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 <t>Nano</t> kit respectively.
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1) 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

2) 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

3) 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:

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

4) 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

5) 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

6) 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

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 "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

9) 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

Related Articles

Centrifugation:

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Article Snippet: After centrifugation, aqueous phase was carefully transferred to a new microcentrifuge tube and mixed with equal volume of 100% ethanol to precipitate RNA. .. The quality of extracted RNA was further analyzed with the RNA 6000 Nano kit by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

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Amplification:

Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
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Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: Total RNAs obtained from immature colonies and ALI differentiated structure were used for microarray preparation with WT Pico RNA Amplification System V2 for amplification of DNA and Encore Biotin Module for fragmentation and biotin labeling (NuGEN Technologies, USA). .. RNA quality (RNA integrity number, RIN) was measured by analysis using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA).

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Quantitative RT-PCR:

Article Title: Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei)
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Article Snippet: Only samples with RNA integrity number higher than 7 were used in these experiments (Agilent RNA 6000 Nano kit). .. Only samples with RNA integrity number higher than 7 were used in these experiments (Agilent RNA 6000 Nano kit).

Electrophoresis:

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
Article Snippet: Paragraph title: Electrophoresis of RNA fragments. ... The resultant RNA fragments were electrophoresed by either 1.5% agarose gels (Nusieve 3:1 agarose; BioWhittaker Molecular Applications) or the Agilent 2100 bioanalyzer with the RNA 6000 nano kit (Agilent).

Microarray:

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Article Snippet: Paragraph title: Expression microarray and bioinformatics ... RNA quality (RNA integrity number, RIN) was measured by analysis using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA).

Random Hexamer Labeling:

Article Title: Enhancer Redundancy Allows for Phenotypic Robustness in Mammalian Development
Article Snippet: For qPCR, RNA was treated with RNase-free DNase (Promega) and reverse transcribed using SuperScript III (Life Technologies) with random hexamer or poly-dT priming according to manufacturer instructions. qPCR was performed on a LightCycler 480 (Roche) using KAPA SYBR FAST qPCR Master Mix (Kapa Biosystems) according to manufacturer instructions. qPCR primers (listed in ) were designed in silico using Primer3 , and amplicons span exon-exon junctions in order to prevent amplification of genomic DNA. .. For RNA-seq, RNA samples were DNase treated (TURBO DNA-free Kit, Life Technologies), and RNA quality was verified using a 2100 Bioanalyzer (Agilent) with an RNA 6000 Nano Kit (Agilent).

In Silico:

Article Title: Enhancer Redundancy Allows for Phenotypic Robustness in Mammalian Development
Article Snippet: For qPCR, RNA was treated with RNase-free DNase (Promega) and reverse transcribed using SuperScript III (Life Technologies) with random hexamer or poly-dT priming according to manufacturer instructions. qPCR was performed on a LightCycler 480 (Roche) using KAPA SYBR FAST qPCR Master Mix (Kapa Biosystems) according to manufacturer instructions. qPCR primers (listed in ) were designed in silico using Primer3 , and amplicons span exon-exon junctions in order to prevent amplification of genomic DNA. .. For RNA-seq, RNA samples were DNase treated (TURBO DNA-free Kit, Life Technologies), and RNA quality was verified using a 2100 Bioanalyzer (Agilent) with an RNA 6000 Nano Kit (Agilent).

Expressing:

Article Title: Rare coding variants in Phospholipase D3 (PLD3) confer risk for Alzheimer's disease
Article Snippet: Total RNA was isolated from human post-mortem brain tissues using the miRNeasy 96 well kit (Qiagen, UK). .. The quality of total RNA was evaluated by the 2100 Bioanalyzer (Agilent, UK) and RNA 6000 Nano Kit (Agilent, UK) before processing with the Ambion® WT Expression Kit and Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay and hybridization to the Affymetrix Exon 1.0 ST. All arrays were pre-processed using Robust Multi-array Average using Partek Genomics Suite v6.6 (Partek Incorporated, USA). .. The resulting expression data was corrected for individual effects (within which are nested postmortem interval, brain pH, sex, age at death and cause of death) and experimental batch effects (date of hybridization).

Article Title: Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei)
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Article Title: Enhancer Redundancy Allows for Phenotypic Robustness in Mammalian Development
Article Snippet: Relative gene expression levels were calculated using the 2-ΔΔC T method , normalized to the Actb housekeeping gene, and the mean of wild-type control samples was set to 1. .. For RNA-seq, RNA samples were DNase treated (TURBO DNA-free Kit, Life Technologies), and RNA quality was verified using a 2100 Bioanalyzer (Agilent) with an RNA 6000 Nano Kit (Agilent).

Modification:

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets
Article Snippet: Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent. .. In addition, the breast cancer cell lines MDA-MB-231, LM2, and MCF7 were purchased from the American Type Culture Collection (Manassas).

Hybridization:

Article Title: Rare coding variants in Phospholipase D3 (PLD3) confer risk for Alzheimer's disease
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Article Title: Microparticle conferred microRNA profiles - implications in the transfer and dominance of cancer traits
Article Snippet: Total RNA integrity was analysed using the Agilent RNA 6000 Nano kit (Agilent Technologies Inc., Santa Clara, CA) and the result was analysed by Agilent 2100 Bioanalyzer (Agilent Technologies Inc.) as per the manufacturer’s recommendations; the RNA integrity number (RIN) of 10 represents the highest RNA integrity with minimal degradation and score of 1 is the lowest integrity [ ]. .. Nanodrop-1000 spectrophotometer (Nanodrop technologies, DE, USA) was used for the quantification of RNA and 500 ng of RNA from each sample was used for miRNA microarray analysis.

RIA Assay:

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Dissection:

Article Title: Rare coding variants in Phospholipase D3 (PLD3) confer risk for Alzheimer's disease
Article Snippet: All samples originated from individuals with no significant neurological history or neuropathological abnormality and were collected by the MRC Edinburgh Brain Bank ensuring a consistent dissection protocol and sample handling procedure. .. The quality of total RNA was evaluated by the 2100 Bioanalyzer (Agilent, UK) and RNA 6000 Nano Kit (Agilent, UK) before processing with the Ambion® WT Expression Kit and Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay and hybridization to the Affymetrix Exon 1.0 ST. All arrays were pre-processed using Robust Multi-array Average using Partek Genomics Suite v6.6 (Partek Incorporated, USA).

Northern Blot:

Article Title: Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei)
Article Snippet: Paragraph title: Quantification of Gene Expression by Northern Blot and qRT-PCR ... The quality of extracted RNA was further analyzed with the RNA 6000 Nano kit by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

Cell Culture:

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets
Article Snippet: Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent. .. In addition, the breast cancer cell lines MDA-MB-231, LM2, and MCF7 were purchased from the American Type Culture Collection (Manassas).

Generated:

Article Title: The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts
Article Snippet: Two microliter of the eluted A-rich RNAs were analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies) following the manufacturer's instructions. .. The cDNAs libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit.

Sequencing:

Article Title: The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts
Article Snippet: Two microliter of the eluted A-rich RNAs were analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies) following the manufacturer's instructions. .. Two microliter of the eluted A-rich RNAs were analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies) following the manufacturer's instructions.

Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: RNA quality (RNA integrity number, RIN) was measured by analysis Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA). .. RNAs having a RIN > 8 were used for microarray analysis.

DNA Extraction:

Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: RNA quality (RNA integrity number, RIN) was measured by analysis Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA). .. Genomic DNA was extracted with DNeasy Blood & Tissue kit (Qiagen, Netherlands) from intestinal and colonic stem cells for CNV analysis and exome capture sequencing.

Nucleic Acid Electrophoresis:

Article Title: RNA Catabolites Contribute to the Nitrogen Pool and Support Growth Recovery of Wheat
Article Snippet: Fluorescent signals were measured using a microplate reader (Optima, BMG LABTECH) with Excitation/Emission maxima of 640/690 nm. .. 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). .. The 25S to 18S ratio was determined to range from 1.16 to 1.24 which is within the theoretically desired range.

Article Title: Anxiety Associated Increased CpG Methylation in the Promoter of Asb1: A Translational Approach Evidenced by Epidemiological and Clinical Studies and a Murine Model
Article Snippet: For assessment of gene expression, 250 μl of trunk blood was placed in PAXgene Blood RNA Tubes (PreAnalytiX). .. RNA sample quality was qualitatively analyzed using capillary gel electrophoresis chip (RNA 6000 Nano Kit; Agilent, Boeblingen, Germany). .. RNA samples of sufficient quality (RIN⩾7.5) were then processed with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Austin, TX, USA) and hybridized onto MouseWG-6 v2 Expression BeadChips (Illumina, San Diego, CA, USA).

RNA Sequencing Assay:

Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
Article Snippet: RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. .. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit.

Article Title: Enhancer Redundancy Allows for Phenotypic Robustness in Mammalian Development
Article Snippet: Relative gene expression levels were calculated using the 2-ΔΔC T method , normalized to the Actb housekeeping gene, and the mean of wild-type control samples was set to 1. .. For RNA-seq, RNA samples were DNase treated (TURBO DNA-free Kit, Life Technologies), and RNA quality was verified using a 2100 Bioanalyzer (Agilent) with an RNA 6000 Nano Kit (Agilent). .. RNA-seq libraries were generated using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), following the manufacturer instructions, and purified, eluted, and quantified as described previously .

Article Title: Genetic determinants of co-accessible chromatin regions in activated T cells across humans
Article Snippet: Paragraph title: RNA-seq profiling ... RNA was isolated using Qiagen RNeasy Plus Mini Kit and RNA integrity was quantified by Agilent RNA 6000 Nano Kit using the Agilent Bioanalyzer.

Magnetic Beads:

Article Title: CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
Article Snippet: The quality of the RNA samples was assessed using an Agilent RNA 6000 Nano kit (RIN scores provided in Supplemental Table S1). .. The quality of the RNA samples was assessed using an Agilent RNA 6000 Nano kit (RIN scores provided in Supplemental Table S1).

Multiple Displacement Amplification:

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets
Article Snippet: Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent. .. StepOnePlus-Real Time PCR system (Applied Biosystems) was used for real time qPCR analysis.

Isolation:

Article Title: Inhibition of stationary phase respiration impairs persister formation in E. coli
Article Snippet: Paragraph title: RNA isolation ... Quality of total RNA was assessed with a bioanalyzer using an RNA 6000 Nano kit (Agilent Technologies, Inc, Santa Clara, CA).

Article Title: An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)
Article Snippet: Quantities and qualities of isolated RNA were evaluated spectrophotometrically by determining absorbance ratios of A 260 : A 280 and A 260 : A 230 using a Nanodrop® ND‐1000 spectrophotometer (Thermo Fisher Scientific). .. Gels were run at 90 V for about 45 min. RNA integrity was assessed using an Agilent RNA 6000 Nano Kit with an Agilent 2100 Bioanalyzer (Agilent Technologies; www.agilent.com/genomics/bioanalyzer ; Figs and ).

Article Title: The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts
Article Snippet: Paragraph title: Isolation of RNA and RNASeq ... Two microliter of the eluted A-rich RNAs were analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies) following the manufacturer's instructions.

Article Title: Rare coding variants in Phospholipase D3 (PLD3) confer risk for Alzheimer's disease
Article Snippet: Total RNA was isolated from human post-mortem brain tissues using the miRNeasy 96 well kit (Qiagen, UK). .. The quality of total RNA was evaluated by the 2100 Bioanalyzer (Agilent, UK) and RNA 6000 Nano Kit (Agilent, UK) before processing with the Ambion® WT Expression Kit and Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay and hybridization to the Affymetrix Exon 1.0 ST. All arrays were pre-processed using Robust Multi-array Average using Partek Genomics Suite v6.6 (Partek Incorporated, USA).

Article Title: DIE-RNA: A Reproducible Strategy for the Digestion of Normal and Injured Pancreas, Isolation of Pancreatic Cells from Genetically Engineered Mouse Models and Extraction of High Quality RNA
Article Snippet: Mice were sacrificed either at day 1 after the completion of the first series of injections or at day 4 following the second series of injections. .. - Agilent RNA 6000 Nano kit (5067-1512, Agilent Genomics, USA) - Bovine serum albumin (BSA) (160069 MP, Merck, Belgium) - Caerulein (C9026, Merck, Belgium) - Collagenase P 500 mg (1121386500, Merck, Belgium) - Deoxyribonucleotide (dNTP) (03622614001, Merck, Belgium) - Dulbecco's phosphate-buffered saline (DPBS) (BE17-512F, Lonza, Belgium) - High-capacity complementary deoxyribonucleic acid (cDNA) reverse transcription kit (4368814, Life technology Europe, Belgium) - KAPA SYBR FAST (KK4608, Merck, Belgium) - Nuclease-Free water (Promega, Netherlands) - Prepared solutions listed in Table - Pure Ethanol 100% (UN1170, VWR Chemicals, Belgium) - RNAqueous-Micro total RNA isolation kit (AM1931, Fisher Scientific, Belgium) - RNaseOut (10777019, Life technology Europe, Belgium) - Tamoxifen (T5648, Merck, Belgium) - Trypan blue (T8154, Merck, Belgium) .. - 0.22 μm-filter (430758, Fisher Scientific, Belgium) - 30-gauge needle (30400, BD Biosciences, Belgium) - 40 μm-cell strainer (431750, Fisher Scientific, Belgium) - 0.2, 0.5, and 1.5 mL-Sterile Eppendorf tubes (Eppendorf, Belgium) - 15 and 50 mL-Polypropylene Falcon tubes (Fisher Scientific, Belgium) - 250 and 500 mL-Pyrex bottles (Fisher Scientific, Belgium) - 96-well PCR plates (HSP9655, Bio-Rad, Belgium) - Automated cell counter (TC20, Bio-Rad, Belgium) - Cell sorter machine with water bath (FACS ARIAIII, BD Biosciences, Belgium) - CFX96 real-time PCR machine (C1000, Bio-Rad, Belgium) - Fluorescence microscope (Axiovert 200, Zeiss, Belgium) - Incubator at 37°C with a rotating plate (Eppendorf, Belgium) - Magnetic bar and agitator - Nanodrop spectrophotometer (ND-1000, Isogen, Belgium) - Nuclease-free tips and pipettes (Westburg, Netherlands) - Optical microscope (Axiovert 40C, Zeiss, Belgium) - Pyrex beaker (Fisher Scientific, Belgium) - RNA BioAnalyzer system (Agilent 2100, Agilent Genomics, Belgium) - Sterile dissection tools (i.e., scissors, forceps, and clamps) (Fine Science Tools, Germany) - Sterile Petri dishes (Fisher Scientific, Belgium) - Thermo-cycler machine (T100, Bio-Rad, Belgium)

Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: For ALI-differentiated epithelia, RNA was isolated using Trizol RNA Isolation Kit (Life Technologies, USA). .. RNA quality (RNA integrity number, RIN) was measured by analysis Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA).

Article Title: Anxiety Associated Increased CpG Methylation in the Promoter of Asb1: A Translational Approach Evidenced by Epidemiological and Clinical Studies and a Murine Model
Article Snippet: RNA sample quality was qualitatively analyzed using capillary gel electrophoresis chip (RNA 6000 Nano Kit; Agilent, Boeblingen, Germany). .. RNA sample quality was qualitatively analyzed using capillary gel electrophoresis chip (RNA 6000 Nano Kit; Agilent, Boeblingen, Germany).

Article Title: Enhancer Redundancy Allows for Phenotypic Robustness in Mammalian Development
Article Snippet: RNA was isolated from microdissected forelimbs or hindlimbs of mouse embryos at E11.5 using the Ambion RNAqueous Total RNA Isolation Kit (Life Technologies) according to manufacturer instructions. .. For RNA-seq, RNA samples were DNase treated (TURBO DNA-free Kit, Life Technologies), and RNA quality was verified using a 2100 Bioanalyzer (Agilent) with an RNA 6000 Nano Kit (Agilent).

Article Title: Genetic determinants of co-accessible chromatin regions in activated T cells across humans
Article Snippet: RNA-seq profiles were collected for 95 individuals, of which 92 have matching ATAC-seq profiles ( ). .. RNA was isolated using Qiagen RNeasy Plus Mini Kit and RNA integrity was quantified by Agilent RNA 6000 Nano Kit using the Agilent Bioanalyzer. .. Purified RNA were converted to RNA-seq libraries using a previously published protocol , where reverse transcription was carried out based on the SMART template switching method and the resulting cDNA was further tagmented and PCR amplified using Nextera XT DNA Sample kit (Illumina) to add the Illumina sequencing adaptors.

Labeling:

Article Title: Rare coding variants in Phospholipase D3 (PLD3) confer risk for Alzheimer's disease
Article Snippet: Total RNA was isolated from human post-mortem brain tissues using the miRNeasy 96 well kit (Qiagen, UK). .. The quality of total RNA was evaluated by the 2100 Bioanalyzer (Agilent, UK) and RNA 6000 Nano Kit (Agilent, UK) before processing with the Ambion® WT Expression Kit and Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay and hybridization to the Affymetrix Exon 1.0 ST. All arrays were pre-processed using Robust Multi-array Average using Partek Genomics Suite v6.6 (Partek Incorporated, USA). .. The resulting expression data was corrected for individual effects (within which are nested postmortem interval, brain pH, sex, age at death and cause of death) and experimental batch effects (date of hybridization).

Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: Total RNAs obtained from immature colonies and ALI differentiated structure were used for microarray preparation with WT Pico RNA Amplification System V2 for amplification of DNA and Encore Biotin Module for fragmentation and biotin labeling (NuGEN Technologies, USA). .. RNA quality (RNA integrity number, RIN) was measured by analysis using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA).

Purification:

Article Title: Inhibition of stationary phase respiration impairs persister formation in E. coli
Article Snippet: Total RNA was purified with RNeasy extraction kit using the manufacturer’s protocol (Qiagen). .. Quality of total RNA was assessed with a bioanalyzer using an RNA 6000 Nano kit (Agilent Technologies, Inc, Santa Clara, CA).

Article Title: The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts
Article Snippet: A total of 250 μg of total RNA of each sample (two biological replicates for each condition/strain) was used to isolate adenylated RNAs employing the poly(A) RNA purification kit Oligotex™ (Qiagen) following the manufacturer's instructions. .. Two microliter of the eluted A-rich RNAs were analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies) following the manufacturer's instructions.

Lysis:

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets
Article Snippet: The reagents and instruments used were as follows: QIAzol® lysis reagent (Qiagen, cat. no. 79306), isopropanol (Sigma Aldrich, cat. no. I9516-500ML), ethanol (Sigma Aldrich), UREA (Sigma Aldrich), Tris-Borate-EDTA 10X solution (Thermo Scientific), chloroform (Sigma Aldrich, cat. no. 288306), mirVana small RNA extraction kit (Invitrogen, cat. no. AM1560), TaqMan universal master mix II, no UNG (Applied Biosystems, cat. no. 4440040), hsa-miR-218–5p (Applied Biosystems, cat. no. 000521), hsa-miR-23a-3p (Applied Biosystems, cat. no. 000399), High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, cat. no. 4368814), U6 primer (Applied Biosystems, cat. no. 001973). .. Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent.

Mouse Assay:

Article Title: Anxiety Associated Increased CpG Methylation in the Promoter of Asb1: A Translational Approach Evidenced by Epidemiological and Clinical Studies and a Murine Model
Article Snippet: Exactly 4 h following stress/control exposure, mice were anesthetized with isoflurane and killed. .. RNA sample quality was qualitatively analyzed using capillary gel electrophoresis chip (RNA 6000 Nano Kit; Agilent, Boeblingen, Germany).

Chromatin Immunoprecipitation:

Article Title: Anxiety Associated Increased CpG Methylation in the Promoter of Asb1: A Translational Approach Evidenced by Epidemiological and Clinical Studies and a Murine Model
Article Snippet: For assessment of gene expression, 250 μl of trunk blood was placed in PAXgene Blood RNA Tubes (PreAnalytiX). .. RNA sample quality was qualitatively analyzed using capillary gel electrophoresis chip (RNA 6000 Nano Kit; Agilent, Boeblingen, Germany). .. RNA samples of sufficient quality (RIN⩾7.5) were then processed with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Austin, TX, USA) and hybridized onto MouseWG-6 v2 Expression BeadChips (Illumina, San Diego, CA, USA).

Software:

Article Title: Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei)
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). .. For qRT-PCR, total RNAs were converted into cDNAs using the oligo(dT)20 primers and the SuperScript III Fist-Strand Synthesis System (Invitrogen, Carlsbad, CA).

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
Article Snippet: The resultant RNA fragments were electrophoresed by either 1.5% agarose gels (Nusieve 3:1 agarose; BioWhittaker Molecular Applications) or the Agilent 2100 bioanalyzer with the RNA 6000 nano kit (Agilent). .. For electrophoresis with the Agilent 2100 bioanalyzer, the RNA samples and electrophoresis medium (microchips) were prepared according to the manufacturer's instructions.

Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: RNA quality (RNA integrity number, RIN) was measured by analysis using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA). .. RNA quality (RNA integrity number, RIN) was measured by analysis using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA).

Real-time Polymerase Chain Reaction:

Article Title: Enhancer Redundancy Allows for Phenotypic Robustness in Mammalian Development
Article Snippet: Paragraph title: Quantitative real-time PCR (qPCR) and RNA-seq ... For RNA-seq, RNA samples were DNase treated (TURBO DNA-free Kit, Life Technologies), and RNA quality was verified using a 2100 Bioanalyzer (Agilent) with an RNA 6000 Nano Kit (Agilent).

RNA Extraction:

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets
Article Snippet: The reagents and instruments used were as follows: QIAzol® lysis reagent (Qiagen, cat. no. 79306), isopropanol (Sigma Aldrich, cat. no. I9516-500ML), ethanol (Sigma Aldrich), UREA (Sigma Aldrich), Tris-Borate-EDTA 10X solution (Thermo Scientific), chloroform (Sigma Aldrich, cat. no. 288306), mirVana small RNA extraction kit (Invitrogen, cat. no. AM1560), TaqMan universal master mix II, no UNG (Applied Biosystems, cat. no. 4440040), hsa-miR-218–5p (Applied Biosystems, cat. no. 000521), hsa-miR-23a-3p (Applied Biosystems, cat. no. 000399), High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, cat. no. 4368814), U6 primer (Applied Biosystems, cat. no. 001973). .. Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent.

Article Title: An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)
Article Snippet: Paragraph title: RNA extraction for mini and maxi preparations ... Gels were run at 90 V for about 45 min. RNA integrity was assessed using an Agilent RNA 6000 Nano Kit with an Agilent 2100 Bioanalyzer (Agilent Technologies; www.agilent.com/genomics/bioanalyzer ; Figs and ).

Sample Prep:

Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
Article Snippet: Paragraph title: NGS Sample Preparation ... Input RNA quality was validated using the Agilent RNA 6000 Nano Kit.

Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: Paragraph title: RNA and genomic DNA sample preparation ... RNA quality (RNA integrity number, RIN) was measured by analysis Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA).

Next-Generation Sequencing:

Article Title: The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts
Article Snippet: Two microliter of the eluted A-rich RNAs were analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies) and the RNA 6000 Nano Kit (Agilent Technologies) following the manufacturer's instructions. .. The cDNAs libraries were constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit.

Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
Article Snippet: Paragraph title: NGS Sample Preparation ... Input RNA quality was validated using the Agilent RNA 6000 Nano Kit.

Spectrophotometry:

Article Title: An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)
Article Snippet: Quantities and qualities of isolated RNA were evaluated spectrophotometrically by determining absorbance ratios of A 260 : A 280 and A 260 : A 230 using a Nanodrop® ND‐1000 spectrophotometer (Thermo Fisher Scientific). .. Gels were run at 90 V for about 45 min. RNA integrity was assessed using an Agilent RNA 6000 Nano Kit with an Agilent 2100 Bioanalyzer (Agilent Technologies; www.agilent.com/genomics/bioanalyzer ; Figs and ).

Concentration Assay:

Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets
Article Snippet: Concentration of RNA is measured by Nanodrop device (Thermo Fisher Scientific). .. Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent.

Article Title: Cloning and Variation of Ground State Intestinal Stem Cells
Article Snippet: RNA quality (RNA integrity number, RIN) was measured by analysis Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano Kit (Agilent Technologies, USA). .. For genomic DNA extraction, human intestinal and colonic stem cells were isolated from mouse 3T3 feeder layer using QuadroMACS Starting Kit (Miltenyi Biotec, Germany).

Staining:

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
Article Snippet: The resultant RNA fragments were electrophoresed by either 1.5% agarose gels (Nusieve 3:1 agarose; BioWhittaker Molecular Applications) or the Agilent 2100 bioanalyzer with the RNA 6000 nano kit (Agilent). .. For electrophoresis with agarose gels, digested RNA fragments were denatured at 70°C for 2 min, rapidly cooled on ice, and subjected to electrophoresis.

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  • 99
    Agilent technologies rna 6000 nano kit
    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 <t>Nano</t> kit respectively.
    Rna 6000 Nano Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 392 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna 6000 nano kit/product/Agilent technologies
    Average 99 stars, based on 392 article reviews
    Price from $9.99 to $1999.99
    rna 6000 nano kit - by Bioz Stars, 2019-11
    99/100 stars
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    78
    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 Nano 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: 78/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioanalyzer rna nano 6000 kit/product/Agilent technologies
    Average 78 stars, based on 1 article reviews
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    bioanalyzer rna nano 6000 kit - by Bioz Stars, 2019-11
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    99
    Agilent technologies bioanalyser
    Microsampling protocol design and reproducibility. a In terminal blood sampling, at each time point, groups of mice are exsanguinated to obtain 0.5–0.6 mL blood volumes, which are then subject to leukocyte depletion and saponin lysis before TRIzol treatment. Thus, the number of mice increases proportionally with the number of biological replicates and time points in the study design (number of mice per timepoint X number of timepoints; NT). Microsampling involves obtaining sample volumes as low as 20 μL from the same mouse at different time points, thus confining the number of mice to just biological replicates (N) and significantly lowering costs and biological variability. Leukocyte depletion and saponin lysis are also not performed on the low volume samples, thus saving time and manpower. b Heatmap shows pair-wise Pearson correlation coefficients and the inset shows multidimensional scaling to visualize the level of similarity between the P. vinckei microsamples. Microsamples show low degree of variability and are highly reproducible as proved by tight correlations between biological replicates. c High Pearson correlations were observed between normalized gene expression values (shown as logarithm of fragments per kilobase of transcript per million mapped reads) from microsampling (x-axis) and terminal blood sampling (y-axis) methods. d <t>Bioanalyser</t> electrophoregrams of total RNA from Plasmodium vinckei vinckei CY microsamples show that high quality RNA could be extracted consistently from 20 μL microsamples
    Bioanalyser, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioanalyser/product/Agilent technologies
    Average 99 stars, based on 122 article reviews
    Price from $9.99 to $1999.99
    bioanalyser - by Bioz Stars, 2019-11
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    Image Search Results


    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.

    Journal: RNA Biology

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

    doi: 10.1080/15476286.2018.1451723

    Figure Lengend 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.

    Article Snippet: Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent.

    Techniques: 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.

    Journal: RNA Biology

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

    doi: 10.1080/15476286.2018.1451723

    Figure Lengend 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.

    Article Snippet: Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent.

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

    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

    Microsampling protocol design and reproducibility. a In terminal blood sampling, at each time point, groups of mice are exsanguinated to obtain 0.5–0.6 mL blood volumes, which are then subject to leukocyte depletion and saponin lysis before TRIzol treatment. Thus, the number of mice increases proportionally with the number of biological replicates and time points in the study design (number of mice per timepoint X number of timepoints; NT). Microsampling involves obtaining sample volumes as low as 20 μL from the same mouse at different time points, thus confining the number of mice to just biological replicates (N) and significantly lowering costs and biological variability. Leukocyte depletion and saponin lysis are also not performed on the low volume samples, thus saving time and manpower. b Heatmap shows pair-wise Pearson correlation coefficients and the inset shows multidimensional scaling to visualize the level of similarity between the P. vinckei microsamples. Microsamples show low degree of variability and are highly reproducible as proved by tight correlations between biological replicates. c High Pearson correlations were observed between normalized gene expression values (shown as logarithm of fragments per kilobase of transcript per million mapped reads) from microsampling (x-axis) and terminal blood sampling (y-axis) methods. d Bioanalyser electrophoregrams of total RNA from Plasmodium vinckei vinckei CY microsamples show that high quality RNA could be extracted consistently from 20 μL microsamples

    Journal: Malaria Journal

    Article Title: A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites

    doi: 10.1186/s12936-019-2659-4

    Figure Lengend Snippet: Microsampling protocol design and reproducibility. a In terminal blood sampling, at each time point, groups of mice are exsanguinated to obtain 0.5–0.6 mL blood volumes, which are then subject to leukocyte depletion and saponin lysis before TRIzol treatment. Thus, the number of mice increases proportionally with the number of biological replicates and time points in the study design (number of mice per timepoint X number of timepoints; NT). Microsampling involves obtaining sample volumes as low as 20 μL from the same mouse at different time points, thus confining the number of mice to just biological replicates (N) and significantly lowering costs and biological variability. Leukocyte depletion and saponin lysis are also not performed on the low volume samples, thus saving time and manpower. b Heatmap shows pair-wise Pearson correlation coefficients and the inset shows multidimensional scaling to visualize the level of similarity between the P. vinckei microsamples. Microsamples show low degree of variability and are highly reproducible as proved by tight correlations between biological replicates. c High Pearson correlations were observed between normalized gene expression values (shown as logarithm of fragments per kilobase of transcript per million mapped reads) from microsampling (x-axis) and terminal blood sampling (y-axis) methods. d Bioanalyser electrophoregrams of total RNA from Plasmodium vinckei vinckei CY microsamples show that high quality RNA could be extracted consistently from 20 μL microsamples

    Article Snippet: The RNA pellet was resuspended in 15 μL nuclease-free water, RNA quantity measured by Qubit fluorometer and RNA integrity measured by Agilent Bioanalyser (Agilent RNA 6000 Nano kit Cat#5067-1511).

    Techniques: Sampling, Mouse Assay, Lysis, Expressing