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Agilent technologies rna
Rna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 2871 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rna - by Bioz Stars, 2020-02
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Amplification:

Article Title: Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle
Article Snippet: Paragraph title: RNA extraction and amplification ... RNA quality and concentration were verified with a 2100 Bioanalyzer (Agilent, Santa Clara, CA), using RNA 6000 Nano reagents (Agilent).

Article Title: RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Article Snippet: Successful removal of DNA contaminants was verified by the absence of PCR amplification of the MC1R gene (GenBank accession number X98012, primers as described by Rieder and colleagues ). mRNA was further isolated with the GeneElute mRNA isolation kit (Sigma, St. Louis, MO, USA). .. The quality of the ribonucleic acid was checked with a microfluidic electrophoresis on the BioAnalyzer (Agilent, Santa Clara, CA, USA).

Article Title: Puberty is a critical window for the impact of diet on mammary gland development in the rabbit, et al. Puberty is a critical window for the impact of diet on mammary gland development in the rabbit
Article Snippet: The integrity of ribonucleic acid was assessed using an Agilent Bioanalyzer. .. After the optimization of qPCR systems (efficiency ranging from −3.25 to −3.45), amplification reactions were run in triplicate under the following conditions: 95°C for 15 minutes, 45 cycles of 95°C for 15 seconds and 60°C for 1 minute.

Synthesized:

Article Title: Gene Expression and Genetic Variation Data Implicate PCLO in Bipolar Disorder
Article Snippet: Total RNA was re-extracted from the PFC of the same subjects that were used in the microarray experiments, and the quality of RNA was assessed with the Bioanalyzer 2100 (Agilent, Foster City, California). .. RNA was purified using the PureLink Total RNA Purification System (Invitrogen, Carlsbad, California), and complementary DNA was synthesized using reverse-transcriptase polymerase chain reaction (PCR) with oligo dT primers as previously described ( ).

Article Title: Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
Article Snippet: RNA quality and quantity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA) and Nanodrop ND1000 (NanoDrop Technologies Wilmington, USA) respectively. .. First-strand cDNA synthesis was primed with a N6 randomized primer and second-strand cDNA was synthesized according to the Gubler-Hoffman protocol.

Quantitative RT-PCR:

Article Title: Puberty is a critical window for the impact of diet on mammary gland development in the rabbit, et al. Puberty is a critical window for the impact of diet on mammary gland development in the rabbit
Article Snippet: Paragraph title: RNA extraction and RT‐qPCR ... The integrity of ribonucleic acid was assessed using an Agilent Bioanalyzer.

SYBR Green Assay:

Article Title: Puberty is a critical window for the impact of diet on mammary gland development in the rabbit, et al. Puberty is a critical window for the impact of diet on mammary gland development in the rabbit
Article Snippet: The integrity of ribonucleic acid was assessed using an Agilent Bioanalyzer. .. For gene assays by quantitative PCR (qPCR), reverse transcription (RT) was performed on 200 ng of total RNA using the SuperScript VILO cDNA Synthesis kit according to the manufacturer's instructions (Invitrogen) and under the following conditions: 42°C for 60 minutes and 85°C for 5 minutes. qPCR runs were achieved using Applied Biosystems SYBR Green PCR Mastermix (Thermo Scientific) according to the manufacturer's instructions, on a QuantStudio system (Thermo Scientific).

Microarray:

Article Title: NOTCH pathway inactivation promotes bladder cancer progression
Article Snippet: Paragraph title: Microarray analysis. ... RNA was purified as described above and analyzed with an Agilent 2100 Bioanalyzer.

Article Title: Gene Expression and Genetic Variation Data Implicate PCLO in Bipolar Disorder
Article Snippet: .. Total RNA was re-extracted from the PFC of the same subjects that were used in the microarray experiments, and the quality of RNA was assessed with the Bioanalyzer 2100 (Agilent, Foster City, California). .. RNA was purified using the PureLink Total RNA Purification System (Invitrogen, Carlsbad, California), and complementary DNA was synthesized using reverse-transcriptase polymerase chain reaction (PCR) with oligo dT primers as previously described ( ).

Article Title: Molecular signatures of neurodegeneration in the cortex of PS1/PS2 double knockout mice
Article Snippet: RNA quality was assessed using the Agilent Bioanalyzer. .. FC and HC samples for microarray analysis were generated by pooling RNA from 3 animals from appropriate genotypes and ages.

Article Title: Prognostic Molecular Subtypes of Low-Grade Cancer of the Appendix
Article Snippet: .. Ribonucleic acid quality and quantity was assessed on an Agilent Bioanalyzer and samples with RNA Integrity values > 6.0 were carried forward for microarray profiling. .. Ribonucleic acid samples of the original tumor series were profiled on the Affymetrix U133A GeneChip system as described previously.

Expressing:

Article Title: Macrophage‐specific hypoxia‐inducible factor‐1α deletion suppresses the development of liver tumors in high‐fat diet‐fed obese and diabetic mice
Article Snippet: .. After extracting total ribonucleic acid from F4/80‐positive liver macrophages, gene expression was analyzed by using the Mx3000P QPCR System (Agilent Technologies, Santa Clara, CA, USA) as previously described , , . .. Messenger ribonucleic acid expressions of the genes were calculated relative to 18S, and they were presented as values relative to those for control mice.

Genome Wide:

Article Title: NOTCH pathway inactivation promotes bladder cancer progression
Article Snippet: RNA was purified as described above and analyzed with an Agilent 2100 Bioanalyzer. .. Genome-wide transcriptome experiments were performed using the Affymetrix HuGene-1_0-st-v1 microarray at the Genomics Facility of the Cancer Research Center (Salamanca, Spain) using standard procedures.

Real-time Polymerase Chain Reaction:

Article Title: S100A9-induced overexpression of PD-1/PD-L1 contributes to ineffective hematopoiesis in myelodysplastic syndromes
Article Snippet: RNA was quantified in a NanoDrop 1000 and RNA quality was assessed by Agilent 2100 Bioanalyzer. .. Quality control steps included BioAnalyzer library assessment and quantitative PCR for library quantification.

Article Title: Gene Expression and Genetic Variation Data Implicate PCLO in Bipolar Disorder
Article Snippet: Paragraph title: Quantitative Polymerase Chain Reaction ... Total RNA was re-extracted from the PFC of the same subjects that were used in the microarray experiments, and the quality of RNA was assessed with the Bioanalyzer 2100 (Agilent, Foster City, California).

Article Title: Puberty is a critical window for the impact of diet on mammary gland development in the rabbit, et al. Puberty is a critical window for the impact of diet on mammary gland development in the rabbit
Article Snippet: The integrity of ribonucleic acid was assessed using an Agilent Bioanalyzer. .. For gene assays by quantitative PCR (qPCR), reverse transcription (RT) was performed on 200 ng of total RNA using the SuperScript VILO cDNA Synthesis kit according to the manufacturer's instructions (Invitrogen) and under the following conditions: 42°C for 60 minutes and 85°C for 5 minutes. qPCR runs were achieved using Applied Biosystems SYBR Green PCR Mastermix (Thermo Scientific) according to the manufacturer's instructions, on a QuantStudio system (Thermo Scientific).

Article Title: Macrophage‐specific hypoxia‐inducible factor‐1α deletion suppresses the development of liver tumors in high‐fat diet‐fed obese and diabetic mice
Article Snippet: .. After extracting total ribonucleic acid from F4/80‐positive liver macrophages, gene expression was analyzed by using the Mx3000P QPCR System (Agilent Technologies, Santa Clara, CA, USA) as previously described , , . .. Messenger ribonucleic acid expressions of the genes were calculated relative to 18S, and they were presented as values relative to those for control mice.

Hybridization:

Article Title: Molecular signatures of neurodegeneration in the cortex of PS1/PS2 double knockout mice
Article Snippet: Paragraph title: B. Sample preparation and hybridization ... RNA quality was assessed using the Agilent Bioanalyzer.

Cell Culture:

Article Title: Deciphering the RNA landscape by RNAome sequencing
Article Snippet: Total RNA isolation Mouse embryonic stem (mES) cells (HM1) were cultured as described. .. The integrity (scores > 9.0) of the RNA was determined on the Agilent 2100 Bioanalyzer (Agilent) according to manufacturer's protocol.

Generated:

Article Title: Molecular signatures of neurodegeneration in the cortex of PS1/PS2 double knockout mice
Article Snippet: RNA quality was assessed using the Agilent Bioanalyzer. .. FC and HC samples for microarray analysis were generated by pooling RNA from 3 animals from appropriate genotypes and ages.

Sequencing:

Article Title: Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis
Article Snippet: Ribonucleic acid quality and quantity was assessed on an Agilent bioanalyser (Agilent, Edinburgh, UK). .. One hundred bp paired‐end sequencing was carried out on an Illumina HiSeq 2500 platform (Illumina, Little Chesterfield, UK).

Article Title: Deciphering the RNA landscape by RNAome sequencing
Article Snippet: The integrity (scores > 9.0) of the RNA was determined on the Agilent 2100 Bioanalyzer (Agilent) according to manufacturer's protocol. .. Subsequent sequencing and array protocols were performed on the total RNA from the same biological samples.

Article Title: Gamma Interferon Alters Junctional Integrity via Rho Kinase, Resulting in Blood-Brain Barrier Leakage in Experimental Viral Encephalitis
Article Snippet: RNA quality was analyzed using a Agilent 2100 Bioanalyzer and a 2200 Tape Station. .. The mRNA template libraries were then sequenced as single-pass 50-bp reads on the Illumina HiSeq4000 platform at the University of Colorado’s Genomics and Sequencing Core Facility.

RNA Sequencing Assay:

Article Title: S100A9-induced overexpression of PD-1/PD-L1 contributes to ineffective hematopoiesis in myelodysplastic syndromes
Article Snippet: Paragraph title: RNA-seq and bioinformatics analysis ... RNA was quantified in a NanoDrop 1000 and RNA quality was assessed by Agilent 2100 Bioanalyzer.

Article Title: Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis
Article Snippet: Ribonucleic acid quality and quantity was assessed on an Agilent bioanalyser (Agilent, Edinburgh, UK). .. Complementary DNA Libraries were prepared using ScriptSeq v2 RNA‐Seq Library Preparation Kit (Epicentre, Cambio, UK).

Article Title: Gamma Interferon Alters Junctional Integrity via Rho Kinase, Resulting in Blood-Brain Barrier Leakage in Experimental Viral Encephalitis
Article Snippet: Paragraph title: RNA-seq and transcriptome analysis on brain endothelial cells. ... RNA quality was analyzed using a Agilent 2100 Bioanalyzer and a 2200 Tape Station.

Fluorescence:

Article Title: Gamma Interferon Alters Junctional Integrity via Rho Kinase, Resulting in Blood-Brain Barrier Leakage in Experimental Viral Encephalitis
Article Snippet: After fluorescence-activated cell sorting of the brain endothelial cells, the samples were lysed, and RNA was isolated using an RNeasy microkit (Qiagen). .. RNA quality was analyzed using a Agilent 2100 Bioanalyzer and a 2200 Tape Station.

Isolation:

Article Title: S100A9-induced overexpression of PD-1/PD-L1 contributes to ineffective hematopoiesis in myelodysplastic syndromes
Article Snippet: RNA-seq and bioinformatics analysis Total RNA from isolated CD34+ cells (isolated using StemExpress) from both healthy and MDS BM specimens was obtained using the RNeasy Mini Kit (Qiagen). .. RNA was quantified in a NanoDrop 1000 and RNA quality was assessed by Agilent 2100 Bioanalyzer.

Article Title: Molecular characterization of numr-1 and numr-2: genes that increase both resistance to metal-induced stress and lifespan in Caenorhabditis elegans
Article Snippet: Paragraph title: Isolation of total RNA ... The quality of the purified RNA was assessed with an Agilent 2100 Bioanalyzer using RNA 6000 Nano LabChip kits (Agilent Technologies, Santa Clara, CA).

Article Title: Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis
Article Snippet: Paragraph title: Ribonucleic acid isolation and transcriptome analysis by RNA ‐ S eq ... Ribonucleic acid quality and quantity was assessed on an Agilent bioanalyser (Agilent, Edinburgh, UK).

Article Title: Deciphering the RNA landscape by RNAome sequencing
Article Snippet: Paragraph title: Total RNA isolation ... The integrity (scores > 9.0) of the RNA was determined on the Agilent 2100 Bioanalyzer (Agilent) according to manufacturer's protocol.

Article Title: Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle
Article Snippet: RNA extraction and amplification Total RNA extraction was performed using the PicoPure RNA Isolation kit, (Life Technologies Inc., Burlington, ON) under an RNase-free environment and including a DNase digestion (Qiagen, Toronto, ON) step. .. RNA quality and concentration were verified with a 2100 Bioanalyzer (Agilent, Santa Clara, CA), using RNA 6000 Nano reagents (Agilent).

Article Title: Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
Article Snippet: cDNA synthesis Total RNA was isolated by homogenization of liver samples in TRIzol (Invitrogen, Carlsbad, USA)/chloroform followed by RNeasy mini kit (Qiagen, Chatsworth, USA) for DNAse treatment and cleaning. .. RNA quality and quantity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA) and Nanodrop ND1000 (NanoDrop Technologies Wilmington, USA) respectively.

Article Title: Molecular signatures of neurodegeneration in the cortex of PS1/PS2 double knockout mice
Article Snippet: Total RNA was isolated using the Trizol reagent. .. RNA quality was assessed using the Agilent Bioanalyzer.

Article Title: RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Article Snippet: Successful removal of DNA contaminants was verified by the absence of PCR amplification of the MC1R gene (GenBank accession number X98012, primers as described by Rieder and colleagues ). mRNA was further isolated with the GeneElute mRNA isolation kit (Sigma, St. Louis, MO, USA). .. The quality of the ribonucleic acid was checked with a microfluidic electrophoresis on the BioAnalyzer (Agilent, Santa Clara, CA, USA).

Article Title: Gamma Interferon Alters Junctional Integrity via Rho Kinase, Resulting in Blood-Brain Barrier Leakage in Experimental Viral Encephalitis
Article Snippet: After fluorescence-activated cell sorting of the brain endothelial cells, the samples were lysed, and RNA was isolated using an RNeasy microkit (Qiagen). .. RNA quality was analyzed using a Agilent 2100 Bioanalyzer and a 2200 Tape Station.

Article Title: Puberty is a critical window for the impact of diet on mammary gland development in the rabbit, et al. Puberty is a critical window for the impact of diet on mammary gland development in the rabbit
Article Snippet: 4.6 RNA extraction and RT‐qPCR Total RNA from captured mammary epithelial tissue was isolated from each sample using the RNA NOW kit (Ozyme) according to the manufacturer's protocol. .. The integrity of ribonucleic acid was assessed using an Agilent Bioanalyzer.

Article Title: Prognostic Molecular Subtypes of Low-Grade Cancer of the Appendix
Article Snippet: Paragraph title: Ribonucleic acid isolation and microarray analysis ... Ribonucleic acid quality and quantity was assessed on an Agilent Bioanalyzer and samples with RNA Integrity values > 6.0 were carried forward for microarray profiling.

Multiplex Assay:

Article Title: S100A9-induced overexpression of PD-1/PD-L1 contributes to ineffective hematopoiesis in myelodysplastic syndromes
Article Snippet: RNA was quantified in a NanoDrop 1000 and RNA quality was assessed by Agilent 2100 Bioanalyzer. .. Samples were then processed for RNA-Sequencing (RNA-seq) using the NuGen Ovation Human RNA-Seq Multiplex System (NuGEN Technologies).

Labeling:

Article Title: Prognostic Molecular Subtypes of Low-Grade Cancer of the Appendix
Article Snippet: Ribonucleic acid quality and quantity was assessed on an Agilent Bioanalyzer and samples with RNA Integrity values > 6.0 were carried forward for microarray profiling. .. Briefly, 250 ng total RNA was used to generate labeled in vitro transcription products (complementary RNA).

Purification:

Article Title: NOTCH pathway inactivation promotes bladder cancer progression
Article Snippet: .. RNA was purified as described above and analyzed with an Agilent 2100 Bioanalyzer. .. Samples showing RNA integrity number above 8 were selected for microarray analysis.

Article Title: Molecular characterization of numr-1 and numr-2: genes that increase both resistance to metal-induced stress and lifespan in Caenorhabditis elegans
Article Snippet: .. The quality of the purified RNA was assessed with an Agilent 2100 Bioanalyzer using RNA 6000 Nano LabChip kits (Agilent Technologies, Santa Clara, CA). .. To obtain full-length cDNAs corresponding to numr-1 and numr-2 ,3′- and 5′-RACE were performed following the manufacturer's protocol (Invitrogen Corp., Carlsbad, CA).

Article Title: Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis
Article Snippet: Purified RNA was re‐suspended in 60 μl RNase‐free water. .. Ribonucleic acid quality and quantity was assessed on an Agilent bioanalyser (Agilent, Edinburgh, UK).

Article Title: Deciphering the RNA landscape by RNAome sequencing
Article Snippet: After 8 h continuous exposure total RNA was isolated using Qiazol Lysis Reagent (Qiagen) and total RNA was purified with the miRNeasy kit (Qiagen), according to manufacturer's protocols. .. The integrity (scores > 9.0) of the RNA was determined on the Agilent 2100 Bioanalyzer (Agilent) according to manufacturer's protocol.

Article Title: Gene Expression and Genetic Variation Data Implicate PCLO in Bipolar Disorder
Article Snippet: Total RNA was re-extracted from the PFC of the same subjects that were used in the microarray experiments, and the quality of RNA was assessed with the Bioanalyzer 2100 (Agilent, Foster City, California). .. RNA was purified using the PureLink Total RNA Purification System (Invitrogen, Carlsbad, California), and complementary DNA was synthesized using reverse-transcriptase polymerase chain reaction (PCR) with oligo dT primers as previously described ( ).

Polymerase Chain Reaction:

Article Title: A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle
Article Snippet: The quality and concentration of total RNA was analysed using Agilent’s 2100 Bioanalyzer and the Nanodrop ND-2000 spectrophotometer (Thermo Scientific). .. PCR reactions were done with the DyNAzyme II DNA Polymerase (Thermo Fisher, MA, US) in a 30 μl volume of 1 x PCR buffer, 0.2 mM dNTPs, 10 pmol primer mix (forward 5′-ACTGAGGAGATGAGGGAGGT-3′ and reverse primer: reverse 5′- TAGAGCTTGAAGTGGCGGAA-3′) and 50 ng of cDNA.

Article Title: Gene Expression and Genetic Variation Data Implicate PCLO in Bipolar Disorder
Article Snippet: Total RNA was re-extracted from the PFC of the same subjects that were used in the microarray experiments, and the quality of RNA was assessed with the Bioanalyzer 2100 (Agilent, Foster City, California). .. RNA was purified using the PureLink Total RNA Purification System (Invitrogen, Carlsbad, California), and complementary DNA was synthesized using reverse-transcriptase polymerase chain reaction (PCR) with oligo dT primers as previously described ( ).

Article Title: RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Article Snippet: Successful removal of DNA contaminants was verified by the absence of PCR amplification of the MC1R gene (GenBank accession number X98012, primers as described by Rieder and colleagues ). mRNA was further isolated with the GeneElute mRNA isolation kit (Sigma, St. Louis, MO, USA). .. The quality of the ribonucleic acid was checked with a microfluidic electrophoresis on the BioAnalyzer (Agilent, Santa Clara, CA, USA).

Article Title: Puberty is a critical window for the impact of diet on mammary gland development in the rabbit, et al. Puberty is a critical window for the impact of diet on mammary gland development in the rabbit
Article Snippet: The integrity of ribonucleic acid was assessed using an Agilent Bioanalyzer. .. For gene assays by quantitative PCR (qPCR), reverse transcription (RT) was performed on 200 ng of total RNA using the SuperScript VILO cDNA Synthesis kit according to the manufacturer's instructions (Invitrogen) and under the following conditions: 42°C for 60 minutes and 85°C for 5 minutes. qPCR runs were achieved using Applied Biosystems SYBR Green PCR Mastermix (Thermo Scientific) according to the manufacturer's instructions, on a QuantStudio system (Thermo Scientific).

Lysis:

Article Title: Molecular characterization of numr-1 and numr-2: genes that increase both resistance to metal-induced stress and lifespan in Caenorhabditis elegans
Article Snippet: Frozen nematode pellets were ground into a fine powder using a liquid-nitrogen-cooled mortar and pestle before being homogenized in RNeasy Lysis buffer and total RNA was then isolated using RNeasy Midi kits (Qiagen Inc., Valencia, CA). .. The quality of the purified RNA was assessed with an Agilent 2100 Bioanalyzer using RNA 6000 Nano LabChip kits (Agilent Technologies, Santa Clara, CA).

Article Title: Deciphering the RNA landscape by RNAome sequencing
Article Snippet: After 8 h continuous exposure total RNA was isolated using Qiazol Lysis Reagent (Qiagen) and total RNA was purified with the miRNeasy kit (Qiagen), according to manufacturer's protocols. .. The integrity (scores > 9.0) of the RNA was determined on the Agilent 2100 Bioanalyzer (Agilent) according to manufacturer's protocol.

Mouse Assay:

Article Title: Macrophage‐specific hypoxia‐inducible factor‐1α deletion suppresses the development of liver tumors in high‐fat diet‐fed obese and diabetic mice
Article Snippet: After extracting total ribonucleic acid from F4/80‐positive liver macrophages, gene expression was analyzed by using the Mx3000P QPCR System (Agilent Technologies, Santa Clara, CA, USA) as previously described , , . .. Messenger ribonucleic acid expressions of the genes were calculated relative to 18S, and they were presented as values relative to those for control mice.

Electrophoresis:

Article Title: RNA Sequencing of the Exercise Transcriptome in Equine Athletes
Article Snippet: .. The quality of the ribonucleic acid was checked with a microfluidic electrophoresis on the BioAnalyzer (Agilent, Santa Clara, CA, USA). .. Library preparation Samples were prepared for ligation sequencing according to the protocol provided with the SOLiD whole transcriptome library kit (Applied Biosystems, SOLiD™ Whole Transcriptome Analysis Kit, PN 4409491 Rev E).

RNA Extraction:

Article Title: Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle
Article Snippet: Paragraph title: RNA extraction and amplification ... RNA quality and concentration were verified with a 2100 Bioanalyzer (Agilent, Santa Clara, CA), using RNA 6000 Nano reagents (Agilent).

Article Title: Puberty is a critical window for the impact of diet on mammary gland development in the rabbit, et al. Puberty is a critical window for the impact of diet on mammary gland development in the rabbit
Article Snippet: Paragraph title: RNA extraction and RT‐qPCR ... The integrity of ribonucleic acid was assessed using an Agilent Bioanalyzer.

Sample Prep:

Article Title: Molecular signatures of neurodegeneration in the cortex of PS1/PS2 double knockout mice
Article Snippet: Paragraph title: B. Sample preparation and hybridization ... RNA quality was assessed using the Agilent Bioanalyzer.

In Vitro:

Article Title: Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle
Article Snippet: RNA quality and concentration were verified with a 2100 Bioanalyzer (Agilent, Santa Clara, CA), using RNA 6000 Nano reagents (Agilent). .. Using 5 ng of extracted total RNA as starting material, linear amplification of the mRNA fraction was performed using the RiboAmp HSPlus RNA Amplification Kit (Life Technologies Inc., Burlington, ON) which relies on T7 RNA polymerase in vitro transcription (IVT) to yield antisense RNA (aRNA).

Article Title: Prognostic Molecular Subtypes of Low-Grade Cancer of the Appendix
Article Snippet: Ribonucleic acid quality and quantity was assessed on an Agilent Bioanalyzer and samples with RNA Integrity values > 6.0 were carried forward for microarray profiling. .. Briefly, 250 ng total RNA was used to generate labeled in vitro transcription products (complementary RNA).

Homogenization:

Article Title: Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
Article Snippet: cDNA synthesis Total RNA was isolated by homogenization of liver samples in TRIzol (Invitrogen, Carlsbad, USA)/chloroform followed by RNeasy mini kit (Qiagen, Chatsworth, USA) for DNAse treatment and cleaning. .. RNA quality and quantity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA) and Nanodrop ND1000 (NanoDrop Technologies Wilmington, USA) respectively.

Spectrophotometry:

Article Title: A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle
Article Snippet: .. The quality and concentration of total RNA was analysed using Agilent’s 2100 Bioanalyzer and the Nanodrop ND-2000 spectrophotometer (Thermo Scientific). .. An amount of 500 ng of total RNA from each sample was reversely transcribed using QuantiTech Rev.

Concentration Assay:

Article Title: A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle
Article Snippet: .. The quality and concentration of total RNA was analysed using Agilent’s 2100 Bioanalyzer and the Nanodrop ND-2000 spectrophotometer (Thermo Scientific). .. An amount of 500 ng of total RNA from each sample was reversely transcribed using QuantiTech Rev.

Article Title: Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle
Article Snippet: .. RNA quality and concentration were verified with a 2100 Bioanalyzer (Agilent, Santa Clara, CA), using RNA 6000 Nano reagents (Agilent). .. Using 5 ng of extracted total RNA as starting material, linear amplification of the mRNA fraction was performed using the RiboAmp HSPlus RNA Amplification Kit (Life Technologies Inc., Burlington, ON) which relies on T7 RNA polymerase in vitro transcription (IVT) to yield antisense RNA (aRNA).

FACS:

Article Title: Gamma Interferon Alters Junctional Integrity via Rho Kinase, Resulting in Blood-Brain Barrier Leakage in Experimental Viral Encephalitis
Article Snippet: After fluorescence-activated cell sorting of the brain endothelial cells, the samples were lysed, and RNA was isolated using an RNeasy microkit (Qiagen). .. RNA quality was analyzed using a Agilent 2100 Bioanalyzer and a 2200 Tape Station.

Article Title: Macrophage‐specific hypoxia‐inducible factor‐1α deletion suppresses the development of liver tumors in high‐fat diet‐fed obese and diabetic mice
Article Snippet: Paragraph title: Magnetic activated cell sorting and quantitative real‐time polymerase chain reaction ... After extracting total ribonucleic acid from F4/80‐positive liver macrophages, gene expression was analyzed by using the Mx3000P QPCR System (Agilent Technologies, Santa Clara, CA, USA) as previously described , , .

Variant Assay:

Article Title: A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle
Article Snippet: Transcription analysis Total RNA from two bulls homozygous for the CCDC189 splice donor variant (GCA_000003055.3:Chr25:g.27138357C > T) and two control bulls that were homozygous for the wild type allele was extracted from testis tissues using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. .. The quality and concentration of total RNA was analysed using Agilent’s 2100 Bioanalyzer and the Nanodrop ND-2000 spectrophotometer (Thermo Scientific).

Fluorescence In Situ Hybridization:

Article Title: Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing
Article Snippet: RNA quality and quantity was analysed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA) and Nanodrop ND1000 (NanoDrop Technologies Wilmington, USA) respectively. .. Equal amount of total RNA from each of the 31 fish samples was pooled and used for cDNA synthesis. cDNA synthesis and normalization was performed by Vertis Biotechnologie AG (Freising, Germany) as follows.

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    Agilent technologies rna
    Bias in miRNA detection using various <t>small-RNA</t> library preparation kits. For each kit, sequencing libraries were prepared from the miRXplore™ pool and sequenced; the sequence data were then used to calculate fold-deviations from the equimolar input and plotted as log 2 values. Densities of miRNAs within a two-fold deviation from the expected values (between vertical lines ) are considered unbiased according to [ 8 ]. Under-represented, over-represented, and accurately quantified percentages of miRNAs are shown in red font . Results for two-adapter schemes are a <t>TruSeq®</t> Small RNA, b NEBNext®, and c QIAseq. d NEXTFlex™, a scheme using two adapters with randomized sequences. e SMARTer, which uses template switching. f RealSeq®-AC, which uses a single-adapter and circularization (* p value vs other kits
    Rna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 2871 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna/product/Agilent technologies
    Average 94 stars, based on 2871 article reviews
    Price from $9.99 to $1999.99
    rna - by Bioz Stars, 2020-02
    94/100 stars
      Buy from Supplier

    85
    Agilent technologies mirnas total rna
    Identification of miR-29b-1-5p-regulated genes. a Expression profiles of messenger RNAs (mRNAs) in K562 cells transfected with miR-29b-1-5p mimic or scramble oligonucleotides then cultured with medium for 48 h were evaluated using <t>RNA-Seq</t> transcriptome analysis. Each scatter spot represents the mean raw signals of microRNA <t>(miRNA)</t> in three repeats of each treatment. b The RNA expression levels of 16 genes were significantly higher, whereas the RNA expression levels of 10 genes were significantly lower, in K562 cells after being transfected with miR-29b-1-5p mimic for 48 h. c Four genes potentially involved in the inflammatory responses were selected for further analysis. The mRNA expression levels of ANG were significantly elevated in K562 cells after coculture with interleukin (IL)-23 (20 ng/ml) for 3 days (Fig. 3 c)
    Mirnas Total Rna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mirnas total rna/product/Agilent technologies
    Average 85 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    mirnas total rna - by Bioz Stars, 2020-02
    85/100 stars
      Buy from Supplier

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    Bias in miRNA detection using various small-RNA library preparation kits. For each kit, sequencing libraries were prepared from the miRXplore™ pool and sequenced; the sequence data were then used to calculate fold-deviations from the equimolar input and plotted as log 2 values. Densities of miRNAs within a two-fold deviation from the expected values (between vertical lines ) are considered unbiased according to [ 8 ]. Under-represented, over-represented, and accurately quantified percentages of miRNAs are shown in red font . Results for two-adapter schemes are a TruSeq® Small RNA, b NEBNext®, and c QIAseq. d NEXTFlex™, a scheme using two adapters with randomized sequences. e SMARTer, which uses template switching. f RealSeq®-AC, which uses a single-adapter and circularization (* p value vs other kits

    Journal: Genome Biology

    Article Title: Decreasing miRNA sequencing bias using a single adapter and circularization approach

    doi: 10.1186/s13059-018-1488-z

    Figure Lengend Snippet: Bias in miRNA detection using various small-RNA library preparation kits. For each kit, sequencing libraries were prepared from the miRXplore™ pool and sequenced; the sequence data were then used to calculate fold-deviations from the equimolar input and plotted as log 2 values. Densities of miRNAs within a two-fold deviation from the expected values (between vertical lines ) are considered unbiased according to [ 8 ]. Under-represented, over-represented, and accurately quantified percentages of miRNAs are shown in red font . Results for two-adapter schemes are a TruSeq® Small RNA, b NEBNext®, and c QIAseq. d NEXTFlex™, a scheme using two adapters with randomized sequences. e SMARTer, which uses template switching. f RealSeq®-AC, which uses a single-adapter and circularization (* p value vs other kits

    Article Snippet: Using RealSeq®-AC and TruSeq®, we prepared sequencing libraries from a reference sample of total RNA (Agilent) obtained from nine different human tissues and cell lines.

    Techniques: Sequencing

    Differential quantification of brain samples between different small RNA library preparation kits. Data obtained with either a TruSeq®, b NEBNext®, c NEXTFlex™, d QIAseq, or e SMARTer kits were compared with data obtained with RealSeq®-AC to obtain differential quantification (log 2 ) values for 276 high-confidence miRNAs. These values were plotted against the accuracy of detection of that miRNA when profiling the equimolar pool of synthetic miRNAs (Fig. 2 a–c). f–j The reverse comparison, with the differential quantification of RealSeq®-AC versus each of the other kits plotted against the accuracy of RealSeq®-AC when quantifying the synthetic pool of miRNAs. FN false negative, FP false positive. See Methods for more details

    Journal: Genome Biology

    Article Title: Decreasing miRNA sequencing bias using a single adapter and circularization approach

    doi: 10.1186/s13059-018-1488-z

    Figure Lengend Snippet: Differential quantification of brain samples between different small RNA library preparation kits. Data obtained with either a TruSeq®, b NEBNext®, c NEXTFlex™, d QIAseq, or e SMARTer kits were compared with data obtained with RealSeq®-AC to obtain differential quantification (log 2 ) values for 276 high-confidence miRNAs. These values were plotted against the accuracy of detection of that miRNA when profiling the equimolar pool of synthetic miRNAs (Fig. 2 a–c). f–j The reverse comparison, with the differential quantification of RealSeq®-AC versus each of the other kits plotted against the accuracy of RealSeq®-AC when quantifying the synthetic pool of miRNAs. FN false negative, FP false positive. See Methods for more details

    Article Snippet: Using RealSeq®-AC and TruSeq®, we prepared sequencing libraries from a reference sample of total RNA (Agilent) obtained from nine different human tissues and cell lines.

    Techniques:

    TRP53-regulated EndMT modulates the M1 and M2 populations of increased TAMs after radiotherapy. a RNA-seq data analysis of the samples represented in Fig. 4a . Venn diagram depicting differentially expressed genes in irradiated HUVECs. Reverse-regulated genes ( > 1.2-fold) between TGFβR2 knockdown+IR and Trp53 -knockdown (with and without TGFβR2 knockdown)+IR conditions (compared with IR alone) were selected (subgroup A). Only matrisome- and surface-associated genes in subset A are shown in the heatmap generated by k-means clustering (subgroup B). b GeneMANIA network analysis of subset B showing significant enrichment for the GO term ‘leukocyte migration’. Red-filled circles represent genes upregulated in the Trp53 siRNA+IR group vs. the IR-alone group. Blue-filled circles represent genes upregulated in the TGFβR2 siRNA+IR group vs. the IR-alone group. The names of leukocyte migration-related genes are indicated in red. c Immunofluorescence detection of F4/80, CD31, and Arg1, or iNOS, CD31, and F4/80 in KP tumours from WT and EC-p53KO mice, with or without irradiation (23 days after irradiation). Scale bar = 20 μm. d Quantification of F4/80 + Arg1 + and F4/80 + iNOS + cells/field (magnification, ×200) using immunofluorescence images of KP tumours from WT, EC-p53KO, and TGFβR2KD mice, with or without irradiation (23 days after irradiation). e Ratio of CD206 + in F4/80 + cells from WT and EC-p53KO tumours 7 days after irradiation, as determined by flow cytometry. f Immunofluorescence staining of F4/80 and Arg1 in WT bone marrow-derived macrophages after coculture with KP tumour-derived ECs from WT and EC-p53KO mice for 48 h after irradiation. Scale bar = 50 μm (crop, 20 μm). Flow-cytometric analysis of CD206 + , iNOS + , and EdU + cells among F4/80 + cells (magnification, ×200) is shown. For ( d – f ), error bars indicate SEM; * p

    Journal: Nature Communications

    Article Title: Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization

    doi: 10.1038/s41467-018-07470-w

    Figure Lengend Snippet: TRP53-regulated EndMT modulates the M1 and M2 populations of increased TAMs after radiotherapy. a RNA-seq data analysis of the samples represented in Fig. 4a . Venn diagram depicting differentially expressed genes in irradiated HUVECs. Reverse-regulated genes ( > 1.2-fold) between TGFβR2 knockdown+IR and Trp53 -knockdown (with and without TGFβR2 knockdown)+IR conditions (compared with IR alone) were selected (subgroup A). Only matrisome- and surface-associated genes in subset A are shown in the heatmap generated by k-means clustering (subgroup B). b GeneMANIA network analysis of subset B showing significant enrichment for the GO term ‘leukocyte migration’. Red-filled circles represent genes upregulated in the Trp53 siRNA+IR group vs. the IR-alone group. Blue-filled circles represent genes upregulated in the TGFβR2 siRNA+IR group vs. the IR-alone group. The names of leukocyte migration-related genes are indicated in red. c Immunofluorescence detection of F4/80, CD31, and Arg1, or iNOS, CD31, and F4/80 in KP tumours from WT and EC-p53KO mice, with or without irradiation (23 days after irradiation). Scale bar = 20 μm. d Quantification of F4/80 + Arg1 + and F4/80 + iNOS + cells/field (magnification, ×200) using immunofluorescence images of KP tumours from WT, EC-p53KO, and TGFβR2KD mice, with or without irradiation (23 days after irradiation). e Ratio of CD206 + in F4/80 + cells from WT and EC-p53KO tumours 7 days after irradiation, as determined by flow cytometry. f Immunofluorescence staining of F4/80 and Arg1 in WT bone marrow-derived macrophages after coculture with KP tumour-derived ECs from WT and EC-p53KO mice for 48 h after irradiation. Scale bar = 50 μm (crop, 20 μm). Flow-cytometric analysis of CD206 + , iNOS + , and EdU + cells among F4/80 + cells (magnification, ×200) is shown. For ( d – f ), error bars indicate SEM; * p

    Article Snippet: RNA-seq analysis Total RNA was isolated from HUVECs, and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

    Techniques: RNA Sequencing Assay, Irradiation, Generated, Migration, Immunofluorescence, Mouse Assay, Flow Cytometry, Cytometry, Staining, Derivative Assay

    Increased OPN expression during radiation-induced EndMT correlates with proliferating CD44v6 + cancer cells in hypoxic areas. a – c HUVECs were transfected with siRNAs targeting TGFβR2 , Trp53 , or TGF β R2 + Trp53 for 48 h and irradiated (10 Gy). After 48 h in culture, total RNA was isolated for RNA-seq and RT-qPCR analyses. a Heat map of RNA-seq analysis showing inhibition of radiation-induced EndMT and the mesenchymal phenotype in HUVECs by Trp53 knockdown. b RT-qPCR analysis of EC-adhesion molecules, collagen, and fibroblastic markers in HUVECs. c RT-qPCR analysis of OPN in HUVECs. d Human soluble-receptor array analysis of conditioned medium from human pulmonary microvascular endothelial cells at 8 days after 5 Gy irradiation. The cyan boxes mark the spots corresponding to OPN. e , f Immunofluorescence detection of CD31 and OPN ( e ) or CD44v6, OPN, and CD31 ( f ) in KP tumours from irradiated WT and EC-p53KO mice (23 dpi). Scale bar = 20 μm. g Quantification of OPN + αSMA + CD31 + cells in the total CD31 + area (left) and OPN + CD44v6 + cells in the total CD44v6 + area (right) (magnification, ×200; n > 5). Mouse strain designations are the same as in Figs 1 and 2 . IR irradiation (20 Gy). h , i KP tumour cells were cultured under normoxia, 1% O 2 (mild hypoxia), or 0.5% O 2 (severe hypoxia) and irradiated with or without OPN. Data are representative of three independent experiments. h Immunofluorescence detection of CD44v6 and Ki67 in KP tumour cells 11 days after irradiation (left) and quantification of CD44v6 + Ki67 + cells in total CD44v6 + cells (right) (magnification, ×200; n > 5). Scale bar = 50 μm. i Flow-cytometric analysis of EdU incorporation and CD44v6 expression in KP tumour cells 11 days after irradiation. For ( b – d ), the error bars indicate SD of three independent experiments. For ( g – i ), the error bars indicate SEM; For ( b, c ), si-TGFβR2 + IR or si-Control + IR versus si-Control group, # p

    Journal: Nature Communications

    Article Title: Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization

    doi: 10.1038/s41467-018-07470-w

    Figure Lengend Snippet: Increased OPN expression during radiation-induced EndMT correlates with proliferating CD44v6 + cancer cells in hypoxic areas. a – c HUVECs were transfected with siRNAs targeting TGFβR2 , Trp53 , or TGF β R2 + Trp53 for 48 h and irradiated (10 Gy). After 48 h in culture, total RNA was isolated for RNA-seq and RT-qPCR analyses. a Heat map of RNA-seq analysis showing inhibition of radiation-induced EndMT and the mesenchymal phenotype in HUVECs by Trp53 knockdown. b RT-qPCR analysis of EC-adhesion molecules, collagen, and fibroblastic markers in HUVECs. c RT-qPCR analysis of OPN in HUVECs. d Human soluble-receptor array analysis of conditioned medium from human pulmonary microvascular endothelial cells at 8 days after 5 Gy irradiation. The cyan boxes mark the spots corresponding to OPN. e , f Immunofluorescence detection of CD31 and OPN ( e ) or CD44v6, OPN, and CD31 ( f ) in KP tumours from irradiated WT and EC-p53KO mice (23 dpi). Scale bar = 20 μm. g Quantification of OPN + αSMA + CD31 + cells in the total CD31 + area (left) and OPN + CD44v6 + cells in the total CD44v6 + area (right) (magnification, ×200; n > 5). Mouse strain designations are the same as in Figs 1 and 2 . IR irradiation (20 Gy). h , i KP tumour cells were cultured under normoxia, 1% O 2 (mild hypoxia), or 0.5% O 2 (severe hypoxia) and irradiated with or without OPN. Data are representative of three independent experiments. h Immunofluorescence detection of CD44v6 and Ki67 in KP tumour cells 11 days after irradiation (left) and quantification of CD44v6 + Ki67 + cells in total CD44v6 + cells (right) (magnification, ×200; n > 5). Scale bar = 50 μm. i Flow-cytometric analysis of EdU incorporation and CD44v6 expression in KP tumour cells 11 days after irradiation. For ( b – d ), the error bars indicate SD of three independent experiments. For ( g – i ), the error bars indicate SEM; For ( b, c ), si-TGFβR2 + IR or si-Control + IR versus si-Control group, # p

    Article Snippet: RNA-seq analysis Total RNA was isolated from HUVECs, and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).

    Techniques: Expressing, Transfection, Irradiation, Isolation, RNA Sequencing Assay, Quantitative RT-PCR, Inhibition, Immunofluorescence, Mouse Assay, Cell Culture, Flow Cytometry

    Comprehensive genomic analyses of single-cell clones. ( A ) Genomic proportion of copy number alteration. For clonal samples B–F, > 84% of their genome is between copy number 3 and 4 (ranging from 84.82% to 85.9%, shown as dark grey bars) as compared to ≤3% for the other samples. This global whole genome duplication typically affected both alleles, preserving heterozygosity in these samples. ( B ) Number of somatic structural variants identified per sample with the type indicated by colours. ( C ) Hierarchical clustering of somatic substitution variant allele frequencies across tumour and clonal samples. The absence of a variant in the normal control cortex sample is demonstrated by a variant allele frequency of zero (dark blue). ( D ) Hierarchical clustering of Log2-normalised and gene-scaled RNA seq gene expression of genes with most variable expression as identified as contributing to the first principle component. Positive values indicate a sample with the highest expression and negative values with the lowest expression. ( E ) Hierarchical clustering of 1000 most variable β-values from DNA methylation sequencing data. Β-value of 1 indicates completely methylated and 0 unmethylated CpGs.

    Journal: Cancers

    Article Title: Intratumoural Heterogeneity Underlies Distinct Therapy Responses and Treatment Resistance in Glioblastoma

    doi: 10.3390/cancers11020190

    Figure Lengend Snippet: Comprehensive genomic analyses of single-cell clones. ( A ) Genomic proportion of copy number alteration. For clonal samples B–F, > 84% of their genome is between copy number 3 and 4 (ranging from 84.82% to 85.9%, shown as dark grey bars) as compared to ≤3% for the other samples. This global whole genome duplication typically affected both alleles, preserving heterozygosity in these samples. ( B ) Number of somatic structural variants identified per sample with the type indicated by colours. ( C ) Hierarchical clustering of somatic substitution variant allele frequencies across tumour and clonal samples. The absence of a variant in the normal control cortex sample is demonstrated by a variant allele frequency of zero (dark blue). ( D ) Hierarchical clustering of Log2-normalised and gene-scaled RNA seq gene expression of genes with most variable expression as identified as contributing to the first principle component. Positive values indicate a sample with the highest expression and negative values with the lowest expression. ( E ) Hierarchical clustering of 1000 most variable β-values from DNA methylation sequencing data. Β-value of 1 indicates completely methylated and 0 unmethylated CpGs.

    Article Snippet: DNA and RNA samples were quantified using Qubit Fluorometric Quantification instrument, and RNA integrity was assessed using RNA 6000 Nano Eukaryote Total RNA kit (Agilent Technologies cat. 5067-1511, Santa Clara, CA, USA) and Bioanalyzer 2100 instrument (Thermo Fisher Scientific, Waltham, MA, USA).

    Techniques: Clone Assay, Preserving, Variant Assay, RNA Sequencing Assay, Expressing, DNA Methylation Assay, Sequencing, Methylation

    Identification of miR-29b-1-5p-regulated genes. a Expression profiles of messenger RNAs (mRNAs) in K562 cells transfected with miR-29b-1-5p mimic or scramble oligonucleotides then cultured with medium for 48 h were evaluated using RNA-Seq transcriptome analysis. Each scatter spot represents the mean raw signals of microRNA (miRNA) in three repeats of each treatment. b The RNA expression levels of 16 genes were significantly higher, whereas the RNA expression levels of 10 genes were significantly lower, in K562 cells after being transfected with miR-29b-1-5p mimic for 48 h. c Four genes potentially involved in the inflammatory responses were selected for further analysis. The mRNA expression levels of ANG were significantly elevated in K562 cells after coculture with interleukin (IL)-23 (20 ng/ml) for 3 days (Fig. 3 c)

    Journal: Arthritis Research & Therapy

    Article Title: Aberrant expression of interleukin-23-regulated miRNAs in T cells from patients with ankylosing spondylitis

    doi: 10.1186/s13075-018-1754-1

    Figure Lengend Snippet: Identification of miR-29b-1-5p-regulated genes. a Expression profiles of messenger RNAs (mRNAs) in K562 cells transfected with miR-29b-1-5p mimic or scramble oligonucleotides then cultured with medium for 48 h were evaluated using RNA-Seq transcriptome analysis. Each scatter spot represents the mean raw signals of microRNA (miRNA) in three repeats of each treatment. b The RNA expression levels of 16 genes were significantly higher, whereas the RNA expression levels of 10 genes were significantly lower, in K562 cells after being transfected with miR-29b-1-5p mimic for 48 h. c Four genes potentially involved in the inflammatory responses were selected for further analysis. The mRNA expression levels of ANG were significantly elevated in K562 cells after coculture with interleukin (IL)-23 (20 ng/ml) for 3 days (Fig. 3 c)

    Article Snippet: Microarray analysis of miRNAs Total RNA (0.1 μg) was dephosphorylated and labeled with pCp-Cy3 by using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies).

    Techniques: Expressing, Transfection, Cell Culture, RNA Sequencing Assay, RNA Expression