mirneasy mini kit  (Qiagen)


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    miRNeasy mini kit
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    Structured Review

    Qiagen mirneasy mini kit
    Correlations between mean “fold recovery” (FR) values of miRNAs and base 10 logarithm of miRNA relative abundance in sample (SRA), using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, <t>miRNeasy</t> Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; SRA, the mean relative abundance of each miRNA on samples isolated without carrier.

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    Images

    1) Product Images from "Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation"

    Article Title: Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0187005

    Correlations between mean “fold recovery” (FR) values of miRNAs and base 10 logarithm of miRNA relative abundance in sample (SRA), using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; SRA, the mean relative abundance of each miRNA on samples isolated without carrier.
    Figure Legend Snippet: Correlations between mean “fold recovery” (FR) values of miRNAs and base 10 logarithm of miRNA relative abundance in sample (SRA), using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; SRA, the mean relative abundance of each miRNA on samples isolated without carrier.

    Techniques Used: Isolation, Modification

    Raw Cq values. Evaluation of Cq values of UniSp2, miR-103a-3p and miR-451a in four samples using different isolation protocols and RNA carriers. y, yeast RNA carrier; m, MS2 RNA carrier; w, without carrier; Q, miRNeasy Mini kit modified protocol; E, miRCURY RNA isolation kit Biofluids modified protocol. Mean and standard deviation values are indicated under each box plot diagram.
    Figure Legend Snippet: Raw Cq values. Evaluation of Cq values of UniSp2, miR-103a-3p and miR-451a in four samples using different isolation protocols and RNA carriers. y, yeast RNA carrier; m, MS2 RNA carrier; w, without carrier; Q, miRNeasy Mini kit modified protocol; E, miRCURY RNA isolation kit Biofluids modified protocol. Mean and standard deviation values are indicated under each box plot diagram.

    Techniques Used: Isolation, Modification, Standard Deviation

    Correlations between mean “fold recovery” (FR) values of miRNAs and ΔG of each miRNA, using yE protocol (A) and yQ protocol (B). To avoid the influence of GC content in the analysis of ΔG, for these correlations we used only miRNAs with a GC content between 25% and 75% percentile. yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; ΔG, the free energy of the most stable secondary structure of each miRNA.
    Figure Legend Snippet: Correlations between mean “fold recovery” (FR) values of miRNAs and ΔG of each miRNA, using yE protocol (A) and yQ protocol (B). To avoid the influence of GC content in the analysis of ΔG, for these correlations we used only miRNAs with a GC content between 25% and 75% percentile. yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; ΔG, the free energy of the most stable secondary structure of each miRNA.

    Techniques Used: Gas Chromatography, Isolation, Modification

    Correlations between mean “fold recovery” (FR) values of miRNAs and GC content of each miRNA, using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier.
    Figure Legend Snippet: Correlations between mean “fold recovery” (FR) values of miRNAs and GC content of each miRNA, using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier.

    Techniques Used: Gas Chromatography, Isolation, Modification

    miRNA levels normalized by plasma volume and by an endogenous miRNA. Fold abundance of miRNAs normalized by plasma volume (FR of miRNAs, left column) and normalized by hsa-miR-103a-3p (apFC of miRNAs, right column) and referred to control plasma samples isolated with the E protocol without carrier (in gray). Data were determined in plasma RNA-derived samples isolated with Q and E modified protocols with yeast RNA as carrier (y) or without RNA carrier (w). E, miRCURY RNA isolation kit Biofluids modified protocol; Q, miRNeasy Mini kit modified protocol; FR, fold recovery of miRNAs vs wE protocol; apFC, apparent fold change of miRNAs vs wE protocol. P -values were calculated using Wilcoxon Signed Rank Test, Exact Signification two-tailed, with the IBM SPSS Statistics 20 software. ϕ P
    Figure Legend Snippet: miRNA levels normalized by plasma volume and by an endogenous miRNA. Fold abundance of miRNAs normalized by plasma volume (FR of miRNAs, left column) and normalized by hsa-miR-103a-3p (apFC of miRNAs, right column) and referred to control plasma samples isolated with the E protocol without carrier (in gray). Data were determined in plasma RNA-derived samples isolated with Q and E modified protocols with yeast RNA as carrier (y) or without RNA carrier (w). E, miRCURY RNA isolation kit Biofluids modified protocol; Q, miRNeasy Mini kit modified protocol; FR, fold recovery of miRNAs vs wE protocol; apFC, apparent fold change of miRNAs vs wE protocol. P -values were calculated using Wilcoxon Signed Rank Test, Exact Signification two-tailed, with the IBM SPSS Statistics 20 software. ϕ P

    Techniques Used: Isolation, Derivative Assay, Modification, Two Tailed Test, Software

    2) Product Images from "Optimized microRNA purification from TRIzol-treated plasma"

    Article Title: Optimized microRNA purification from TRIzol-treated plasma

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-1299-5

    MiRNA recovery from decreasing amounts of plasma input. The impact of plasma volume on the recovery of (A) exogenous RNA sequences and (B) endogenous miRNAs was evaluated using real-time RT-PCR. Plasma samples were diluted in water to 50 μL and processed with the QIAGEN miRNeasy Mini Kit. In (A) , three synthetic sequences of different amounts were spiked into the samples and measured in six technical replicates. Significance compared to the water-only control was determined using a linear mixed effects model, **** = p
    Figure Legend Snippet: MiRNA recovery from decreasing amounts of plasma input. The impact of plasma volume on the recovery of (A) exogenous RNA sequences and (B) endogenous miRNAs was evaluated using real-time RT-PCR. Plasma samples were diluted in water to 50 μL and processed with the QIAGEN miRNeasy Mini Kit. In (A) , three synthetic sequences of different amounts were spiked into the samples and measured in six technical replicates. Significance compared to the water-only control was determined using a linear mixed effects model, **** = p

    Techniques Used: Quantitative RT-PCR

    MiRNA recovery with 5 μg glycogen or linear acrylamide as a co-precipitant during RNA extraction. A . The effect of glycogen or linear acrylamide (LA) on miRNA recovery was determined for the RNeasy and miRNeasy kits. Boxplot whiskers indicate minimum and maximum values, with the line drawn at the median. Individual datapoints show the spread (n = 6 for each sequence; total n = 18). Extraction efficiencies were compared to the no carrier control sample, and significance was calculated using a linear mixed effects model. **** indicates p
    Figure Legend Snippet: MiRNA recovery with 5 μg glycogen or linear acrylamide as a co-precipitant during RNA extraction. A . The effect of glycogen or linear acrylamide (LA) on miRNA recovery was determined for the RNeasy and miRNeasy kits. Boxplot whiskers indicate minimum and maximum values, with the line drawn at the median. Individual datapoints show the spread (n = 6 for each sequence; total n = 18). Extraction efficiencies were compared to the no carrier control sample, and significance was calculated using a linear mixed effects model. **** indicates p

    Techniques Used: RNA Extraction, Sequencing

    3) Product Images from "MicroRNA-205 Directly Regulates the Tumor Suppressor, Interleukin-24, in Human KB Oral Cancer Cells"

    Article Title: MicroRNA-205 Directly Regulates the Tumor Suppressor, Interleukin-24, in Human KB Oral Cancer Cells

    Journal:

    doi: 10.1007/s10059-013-2154-7

    MicroRNA array in KB cells compared with NHOK cells. Total RNA from both KB cells and NHOK were isolated with miRNeasy mini kit following the manufacturer’s instructions. The concentration, purity, and amount of total RNA were quantified using
    Figure Legend Snippet: MicroRNA array in KB cells compared with NHOK cells. Total RNA from both KB cells and NHOK were isolated with miRNeasy mini kit following the manufacturer’s instructions. The concentration, purity, and amount of total RNA were quantified using

    Techniques Used: Isolation, Concentration Assay

    4) Product Images from "Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material"

    Article Title: Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material

    Journal: Scientific Reports

    doi: 10.1038/srep19529

    Efficiency of RNA extraction methods for miRNA detection by RT-qPCR in different cell density conditions, using a fixed RNA quantity. The results represent average Cq values obtained for ( a ) mir-106a, ( b ) mir-222 and ( c ) U6 snRNA. RNA samples from 25 × 10 3 , 200 × 10 3 and 800 × 10 3 A549 cells were obtained by extraction with either Trizol ® LS, miRNeasy ® , or miRCURY™, in the presence or absence of MS2 carrier. The detection of miRNA was performed by RT-qPCR starting with 5 ng of total RNA/RT reaction. The mean values ± SD of 3 independent experiments are shown. * P
    Figure Legend Snippet: Efficiency of RNA extraction methods for miRNA detection by RT-qPCR in different cell density conditions, using a fixed RNA quantity. The results represent average Cq values obtained for ( a ) mir-106a, ( b ) mir-222 and ( c ) U6 snRNA. RNA samples from 25 × 10 3 , 200 × 10 3 and 800 × 10 3 A549 cells were obtained by extraction with either Trizol ® LS, miRNeasy ® , or miRCURY™, in the presence or absence of MS2 carrier. The detection of miRNA was performed by RT-qPCR starting with 5 ng of total RNA/RT reaction. The mean values ± SD of 3 independent experiments are shown. * P

    Techniques Used: RNA Extraction, Quantitative RT-PCR

    Efficiency of RNA extraction methods for miRNA detection by RT-qPCR in different cell density conditions, using fixed RNA volumes. RNA samples from ( a,b,c,f ) 25 × 10 3 , 200 × 10 3 and 800 × 10 3 A549 cells (n = 3) and ( d,e,g ) 100, 1000 and 10 × 10 3 A549 cells (n = 3) were obtained by extraction with either Trizol ® LS, miRNeasy ® , or miRCURY™, in the presence or absence of MS2 carrier. The results represent average Cq values obtained for ( a,d ) mir-106a, ( b,e ) mir-222, ( c ) mir-141 and ( f,g ) U6 snRNA. The detection of miRNA was performed by RT-qPCR using a fixed volume of RNA samples (see Methods for details). The mean values ± SD of 3 independent experiments are shown. * P
    Figure Legend Snippet: Efficiency of RNA extraction methods for miRNA detection by RT-qPCR in different cell density conditions, using fixed RNA volumes. RNA samples from ( a,b,c,f ) 25 × 10 3 , 200 × 10 3 and 800 × 10 3 A549 cells (n = 3) and ( d,e,g ) 100, 1000 and 10 × 10 3 A549 cells (n = 3) were obtained by extraction with either Trizol ® LS, miRNeasy ® , or miRCURY™, in the presence or absence of MS2 carrier. The results represent average Cq values obtained for ( a,d ) mir-106a, ( b,e ) mir-222, ( c ) mir-141 and ( f,g ) U6 snRNA. The detection of miRNA was performed by RT-qPCR using a fixed volume of RNA samples (see Methods for details). The mean values ± SD of 3 independent experiments are shown. * P

    Techniques Used: RNA Extraction, Quantitative RT-PCR

    Detection of microRNAs in bodily fluids by RT-qPCR, using different RNA extraction protocols and fixed RNA volumes. ( a ) RNA was extracted from 200 μL of plasma (n = 6) using either miRCURY™, miRCURY™ biofluids or miRNeasy ® protocol. Exosomes were isolated from 2 × 2 mL of plasma (n = 3), then subjected to RNA isolation by either miRNeasy ® or miRCURY™ kit. The results represent mean Cq values ± SD obtained for mir-106a, mir-222, mir-16 and mir-223, using 2.5 μL of RNA/RT reaction. Expression levels of plasma mir-106a, mir-222 and mir-223 were normalized to mir-16 levels and expressed as fold change relative to miRNeasy ® condition under the histograms. ( b ) RNA was isolated from 200 μL of plasma (n = 3) containing 25 fmol of cel-mir-39-3p as a spike-in control directly added into the lysis solution before mixing it with the plasma sample. RNA was isolated with either miRCURY™, miRCURY™ biofluids or miRNeasy ® protocols. The results represent mean Cq values ± SD obtained for the exogenous cel-mir-39, using 2.5 μL of RNA/RT reaction. ( c ) 50 to 100 mL of urine were used for urinary exosome isolation in two equal fractions. RNA was then extracted by either miRNeasy ® or miRCURY™ kit. The results represent the Cq values obtained for mir-30c-2-3p, mir-106a, mir-204, mir-222 and mir-141, generated from 3 different urinary exosome samples, using 2.5 μL of RNA/RT reaction. ** P
    Figure Legend Snippet: Detection of microRNAs in bodily fluids by RT-qPCR, using different RNA extraction protocols and fixed RNA volumes. ( a ) RNA was extracted from 200 μL of plasma (n = 6) using either miRCURY™, miRCURY™ biofluids or miRNeasy ® protocol. Exosomes were isolated from 2 × 2 mL of plasma (n = 3), then subjected to RNA isolation by either miRNeasy ® or miRCURY™ kit. The results represent mean Cq values ± SD obtained for mir-106a, mir-222, mir-16 and mir-223, using 2.5 μL of RNA/RT reaction. Expression levels of plasma mir-106a, mir-222 and mir-223 were normalized to mir-16 levels and expressed as fold change relative to miRNeasy ® condition under the histograms. ( b ) RNA was isolated from 200 μL of plasma (n = 3) containing 25 fmol of cel-mir-39-3p as a spike-in control directly added into the lysis solution before mixing it with the plasma sample. RNA was isolated with either miRCURY™, miRCURY™ biofluids or miRNeasy ® protocols. The results represent mean Cq values ± SD obtained for the exogenous cel-mir-39, using 2.5 μL of RNA/RT reaction. ( c ) 50 to 100 mL of urine were used for urinary exosome isolation in two equal fractions. RNA was then extracted by either miRNeasy ® or miRCURY™ kit. The results represent the Cq values obtained for mir-30c-2-3p, mir-106a, mir-204, mir-222 and mir-141, generated from 3 different urinary exosome samples, using 2.5 μL of RNA/RT reaction. ** P

    Techniques Used: Quantitative RT-PCR, RNA Extraction, Isolation, Expressing, Lysis, Generated

    Impact of the RNA extraction method on miRNA profiling in plasma and bodily fluid-derived exosomes, using TLDA. The Venn diagrams compare the numbers of unique and overlapping miRNAs, detected by TLDA, in RNA samples extracted with either miRNeasy ® or miRCURY™ kit. The comparison miRNeasy ® versus miRCURY™ was performed in ( a ) plasma, ( b ) plasma exosomes and ( c ) urinary exosomes. RNA extraction was done using ( a ) 200 μL of plasma, ( b ) exosomes originating from 2 mL of plasma and ( c ) exosomes isolated from 25 to 50 mL of urine. For each biological source (each panel represents data from one biological source, i.e., from plasma, plasma exosomes or urinary exosomes), two histograms display the number of miRNAs detected at high (Cq
    Figure Legend Snippet: Impact of the RNA extraction method on miRNA profiling in plasma and bodily fluid-derived exosomes, using TLDA. The Venn diagrams compare the numbers of unique and overlapping miRNAs, detected by TLDA, in RNA samples extracted with either miRNeasy ® or miRCURY™ kit. The comparison miRNeasy ® versus miRCURY™ was performed in ( a ) plasma, ( b ) plasma exosomes and ( c ) urinary exosomes. RNA extraction was done using ( a ) 200 μL of plasma, ( b ) exosomes originating from 2 mL of plasma and ( c ) exosomes isolated from 25 to 50 mL of urine. For each biological source (each panel represents data from one biological source, i.e., from plasma, plasma exosomes or urinary exosomes), two histograms display the number of miRNAs detected at high (Cq

    Techniques Used: RNA Extraction, Derivative Assay, TLDA Assay, Isolation

    5) Product Images from "Optimized microRNA purification from TRIzol-treated plasma"

    Article Title: Optimized microRNA purification from TRIzol-treated plasma

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-1299-5

    MiRNA recovery from decreasing amounts of plasma input. The impact of plasma volume on the recovery of (A) exogenous RNA sequences and (B) endogenous miRNAs was evaluated using real-time RT-PCR. Plasma samples were diluted in water to 50 μL and processed with the QIAGEN miRNeasy Mini Kit. In (A) , three synthetic sequences of different amounts were spiked into the samples and measured in six technical replicates. Significance compared to the water-only control was determined using a linear mixed effects model, **** = p
    Figure Legend Snippet: MiRNA recovery from decreasing amounts of plasma input. The impact of plasma volume on the recovery of (A) exogenous RNA sequences and (B) endogenous miRNAs was evaluated using real-time RT-PCR. Plasma samples were diluted in water to 50 μL and processed with the QIAGEN miRNeasy Mini Kit. In (A) , three synthetic sequences of different amounts were spiked into the samples and measured in six technical replicates. Significance compared to the water-only control was determined using a linear mixed effects model, **** = p

    Techniques Used: Quantitative RT-PCR

    MiRNA recovery with 5 μg glycogen or linear acrylamide as a co-precipitant during RNA extraction. A . The effect of glycogen or linear acrylamide (LA) on miRNA recovery was determined for the RNeasy and miRNeasy kits. Boxplot whiskers indicate minimum and maximum values, with the line drawn at the median. Individual datapoints show the spread (n = 6 for each sequence; total n = 18). Extraction efficiencies were compared to the no carrier control sample, and significance was calculated using a linear mixed effects model. **** indicates p
    Figure Legend Snippet: MiRNA recovery with 5 μg glycogen or linear acrylamide as a co-precipitant during RNA extraction. A . The effect of glycogen or linear acrylamide (LA) on miRNA recovery was determined for the RNeasy and miRNeasy kits. Boxplot whiskers indicate minimum and maximum values, with the line drawn at the median. Individual datapoints show the spread (n = 6 for each sequence; total n = 18). Extraction efficiencies were compared to the no carrier control sample, and significance was calculated using a linear mixed effects model. **** indicates p

    Techniques Used: RNA Extraction, Sequencing

    6) Product Images from "Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients"

    Article Title: Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients

    Journal:

    doi: 10.5582/irdr.2017.01091

    Extraction and identification methods of exosome miRNA in the study of ALS patients. A diagram showing the conditions and methods for extraction and detection and their applications. Exosome were isolated from ALS patients and healthy subject's serum by Exoquick reagent or exoEasy Maxi Kit, then using Qiagen miRNeasy Mini Kit to isolate RNA from serum exosomes, finally using stem loop method to detect the expression of miR-27a-3p in two groups of RNA samples. The results of the different expressions can be used for the clinical diagnosis of ALS patients.
    Figure Legend Snippet: Extraction and identification methods of exosome miRNA in the study of ALS patients. A diagram showing the conditions and methods for extraction and detection and their applications. Exosome were isolated from ALS patients and healthy subject's serum by Exoquick reagent or exoEasy Maxi Kit, then using Qiagen miRNeasy Mini Kit to isolate RNA from serum exosomes, finally using stem loop method to detect the expression of miR-27a-3p in two groups of RNA samples. The results of the different expressions can be used for the clinical diagnosis of ALS patients.

    Techniques Used: Isolation, Expressing

    7) Product Images from "miR-19a contributes to gefitinib resistance and epithelial mesenchymal transition in non-small cell lung cancer cells by targeting c-Met"

    Article Title: miR-19a contributes to gefitinib resistance and epithelial mesenchymal transition in non-small cell lung cancer cells by targeting c-Met

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-01153-0

    miR-19a expression in NSCLC patient serum samples and cell lines ( A ). Patients were treated with gefitinib and examined monthly with Computerized Tomographic Scanning (CT). Patients were sensitive to gefitinib at the initial stage and became resistant to gefitinib, which was detected by CT; ( B ) The expression of miR-19a was detected in patient serum samples. Serum was obtained from fifteen patients prior to oral gefitinib treatment (pre-resistance) and after they had developed gefitinib resistance (post-resistance). Total RNA was extracted from the serum using the miRNeasy mini kit (QIAGEN), and the miR-19a level was measured by real-time PCR (**p
    Figure Legend Snippet: miR-19a expression in NSCLC patient serum samples and cell lines ( A ). Patients were treated with gefitinib and examined monthly with Computerized Tomographic Scanning (CT). Patients were sensitive to gefitinib at the initial stage and became resistant to gefitinib, which was detected by CT; ( B ) The expression of miR-19a was detected in patient serum samples. Serum was obtained from fifteen patients prior to oral gefitinib treatment (pre-resistance) and after they had developed gefitinib resistance (post-resistance). Total RNA was extracted from the serum using the miRNeasy mini kit (QIAGEN), and the miR-19a level was measured by real-time PCR (**p

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction

    8) Product Images from "MicroRNA-205 Directly Regulates the Tumor Suppressor, Interleukin-24, in Human KB Oral Cancer Cells"

    Article Title: MicroRNA-205 Directly Regulates the Tumor Suppressor, Interleukin-24, in Human KB Oral Cancer Cells

    Journal:

    doi: 10.1007/s10059-013-2154-7

    MicroRNA array in KB cells compared with NHOK cells. Total RNA from both KB cells and NHOK were isolated with miRNeasy mini kit following the manufacturer’s instructions. The concentration, purity, and amount of total RNA were quantified using
    Figure Legend Snippet: MicroRNA array in KB cells compared with NHOK cells. Total RNA from both KB cells and NHOK were isolated with miRNeasy mini kit following the manufacturer’s instructions. The concentration, purity, and amount of total RNA were quantified using

    Techniques Used: Isolation, Concentration Assay

    9) Product Images from "Optimized microRNA purification from TRIzol-treated plasma"

    Article Title: Optimized microRNA purification from TRIzol-treated plasma

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-1299-5

    MiRNA recovery from decreasing amounts of plasma input. The impact of plasma volume on the recovery of (A) exogenous RNA sequences and (B) endogenous miRNAs was evaluated using real-time RT-PCR. Plasma samples were diluted in water to 50 μL and processed with the QIAGEN miRNeasy Mini Kit. In (A) , three synthetic sequences of different amounts were spiked into the samples and measured in six technical replicates. Significance compared to the water-only control was determined using a linear mixed effects model, **** = p
    Figure Legend Snippet: MiRNA recovery from decreasing amounts of plasma input. The impact of plasma volume on the recovery of (A) exogenous RNA sequences and (B) endogenous miRNAs was evaluated using real-time RT-PCR. Plasma samples were diluted in water to 50 μL and processed with the QIAGEN miRNeasy Mini Kit. In (A) , three synthetic sequences of different amounts were spiked into the samples and measured in six technical replicates. Significance compared to the water-only control was determined using a linear mixed effects model, **** = p

    Techniques Used: Quantitative RT-PCR

    MiRNA recovery with 5 μg glycogen or linear acrylamide as a co-precipitant during RNA extraction. A . The effect of glycogen or linear acrylamide (LA) on miRNA recovery was determined for the RNeasy and miRNeasy kits. Boxplot whiskers indicate minimum and maximum values, with the line drawn at the median. Individual datapoints show the spread (n = 6 for each sequence; total n = 18). Extraction efficiencies were compared to the no carrier control sample, and significance was calculated using a linear mixed effects model. **** indicates p
    Figure Legend Snippet: MiRNA recovery with 5 μg glycogen or linear acrylamide as a co-precipitant during RNA extraction. A . The effect of glycogen or linear acrylamide (LA) on miRNA recovery was determined for the RNeasy and miRNeasy kits. Boxplot whiskers indicate minimum and maximum values, with the line drawn at the median. Individual datapoints show the spread (n = 6 for each sequence; total n = 18). Extraction efficiencies were compared to the no carrier control sample, and significance was calculated using a linear mixed effects model. **** indicates p

    Techniques Used: RNA Extraction, Sequencing

    10) Product Images from "Bias in recent miRBase annotations potentially associated with RNA quality issues"

    Article Title: Bias in recent miRBase annotations potentially associated with RNA quality issues

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-05070-0

    Experimental design. ( a ) Liver, heart and brain of male mice were harvested immediately after death, divided into 8 parts of about equal size, and stored at either 4 °C or at room temperature (RT) for the indicated time periods before RNA isolation. Experiments were performed in biological triplicates. RNA integrity was measured with Bioanalyzer. Gel-like image of brain tissue is given as example. MiRNA expression profiles of one replicate were measured using microarrays. ( b ) Liver tissue of 3 male mice was harvested immediately after death and divided into 5 parts of about equal size. Three parts were immediately transferred into RNAlater (0 h), two parts were stored for 96 h at room temperature (96 h). Two samples (0 h and 96 h) were isolated using standard procedure with miRNeasy Kit without DNase digestion. Two samples (0 h and 96 h) were isolated with optional DNase digestion to exclude DNA background. From the remaining undegraded sample (0 h), total RNA without small RNAs was isolated using RNeasy Kit with optional DNase digestion. Isolated RNA was further treated with 0 U, 0.026 U and 0.67 U RNase for 30 min to generate artificial RNA degradation. RNA integrity was measured with Bioanalyzer. MiRNA expression profiles of all replicates were measured using microarrays. The schematic drawings were prepared using the Biomedical-PPT-Toolkit-Suite from Motifolio Inc., USA.
    Figure Legend Snippet: Experimental design. ( a ) Liver, heart and brain of male mice were harvested immediately after death, divided into 8 parts of about equal size, and stored at either 4 °C or at room temperature (RT) for the indicated time periods before RNA isolation. Experiments were performed in biological triplicates. RNA integrity was measured with Bioanalyzer. Gel-like image of brain tissue is given as example. MiRNA expression profiles of one replicate were measured using microarrays. ( b ) Liver tissue of 3 male mice was harvested immediately after death and divided into 5 parts of about equal size. Three parts were immediately transferred into RNAlater (0 h), two parts were stored for 96 h at room temperature (96 h). Two samples (0 h and 96 h) were isolated using standard procedure with miRNeasy Kit without DNase digestion. Two samples (0 h and 96 h) were isolated with optional DNase digestion to exclude DNA background. From the remaining undegraded sample (0 h), total RNA without small RNAs was isolated using RNeasy Kit with optional DNase digestion. Isolated RNA was further treated with 0 U, 0.026 U and 0.67 U RNase for 30 min to generate artificial RNA degradation. RNA integrity was measured with Bioanalyzer. MiRNA expression profiles of all replicates were measured using microarrays. The schematic drawings were prepared using the Biomedical-PPT-Toolkit-Suite from Motifolio Inc., USA.

    Techniques Used: Mouse Assay, Isolation, Expressing

    11) Product Images from "Optimizing Preservation of Extracellular Vesicular miRNAs Derived from Clinical Cerebrospinal Fluid"

    Article Title: Optimizing Preservation of Extracellular Vesicular miRNAs Derived from Clinical Cerebrospinal Fluid

    Journal:

    doi: 10.3233/CBM-160609

    Clinical CSF EVs stored under Room Temperature (RT) and −80°C EVs isolated from CSF that were stored at room temperature for 1 and 7 days were comparable to EVs isolated from CSF stored at −80°C. (A) Total number of EVs recovered as determined by Nanoparticle tracking analysis (NTA). (B) Representative TEM images of EVs isolated from CSF stored under different conditions. Scale bar represents 500nm in 5000× magnification images, and 200nm in 25000× magnification images. (C) EV size profile as determined by NTA. (D) Comparison of total EV RNA yield extracted using Qiagen miRNeasy mini kit. (E) Detection of miR-21, miR-24, miR-103 and miR-125 transcripts in EVs by qRT-PCR. EV miRNAs appeared to be stable in CSF at room temperature for up to 7 days. Experiments were performed in triplicate and data are expressed as mean ± SEM.
    Figure Legend Snippet: Clinical CSF EVs stored under Room Temperature (RT) and −80°C EVs isolated from CSF that were stored at room temperature for 1 and 7 days were comparable to EVs isolated from CSF stored at −80°C. (A) Total number of EVs recovered as determined by Nanoparticle tracking analysis (NTA). (B) Representative TEM images of EVs isolated from CSF stored under different conditions. Scale bar represents 500nm in 5000× magnification images, and 200nm in 25000× magnification images. (C) EV size profile as determined by NTA. (D) Comparison of total EV RNA yield extracted using Qiagen miRNeasy mini kit. (E) Detection of miR-21, miR-24, miR-103 and miR-125 transcripts in EVs by qRT-PCR. EV miRNAs appeared to be stable in CSF at room temperature for up to 7 days. Experiments were performed in triplicate and data are expressed as mean ± SEM.

    Techniques Used: Isolation, Transmission Electron Microscopy, Quantitative RT-PCR

    12) Product Images from "Bias in recent miRBase annotations potentially associated with RNA quality issues"

    Article Title: Bias in recent miRBase annotations potentially associated with RNA quality issues

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-05070-0

    Experimental design. ( a ) Liver, heart and brain of male mice were harvested immediately after death, divided into 8 parts of about equal size, and stored at either 4 °C or at room temperature (RT) for the indicated time periods before RNA isolation. Experiments were performed in biological triplicates. RNA integrity was measured with Bioanalyzer. Gel-like image of brain tissue is given as example. MiRNA expression profiles of one replicate were measured using microarrays. ( b ) Liver tissue of 3 male mice was harvested immediately after death and divided into 5 parts of about equal size. Three parts were immediately transferred into RNAlater (0 h), two parts were stored for 96 h at room temperature (96 h). Two samples (0 h and 96 h) were isolated using standard procedure with miRNeasy Kit without DNase digestion. Two samples (0 h and 96 h) were isolated with optional DNase digestion to exclude DNA background. From the remaining undegraded sample (0 h), total RNA without small RNAs was isolated using RNeasy Kit with optional DNase digestion. Isolated RNA was further treated with 0 U, 0.026 U and 0.67 U RNase for 30 min to generate artificial RNA degradation. RNA integrity was measured with Bioanalyzer. MiRNA expression profiles of all replicates were measured using microarrays. The schematic drawings were prepared using the Biomedical-PPT-Toolkit-Suite from Motifolio Inc., USA.
    Figure Legend Snippet: Experimental design. ( a ) Liver, heart and brain of male mice were harvested immediately after death, divided into 8 parts of about equal size, and stored at either 4 °C or at room temperature (RT) for the indicated time periods before RNA isolation. Experiments were performed in biological triplicates. RNA integrity was measured with Bioanalyzer. Gel-like image of brain tissue is given as example. MiRNA expression profiles of one replicate were measured using microarrays. ( b ) Liver tissue of 3 male mice was harvested immediately after death and divided into 5 parts of about equal size. Three parts were immediately transferred into RNAlater (0 h), two parts were stored for 96 h at room temperature (96 h). Two samples (0 h and 96 h) were isolated using standard procedure with miRNeasy Kit without DNase digestion. Two samples (0 h and 96 h) were isolated with optional DNase digestion to exclude DNA background. From the remaining undegraded sample (0 h), total RNA without small RNAs was isolated using RNeasy Kit with optional DNase digestion. Isolated RNA was further treated with 0 U, 0.026 U and 0.67 U RNase for 30 min to generate artificial RNA degradation. RNA integrity was measured with Bioanalyzer. MiRNA expression profiles of all replicates were measured using microarrays. The schematic drawings were prepared using the Biomedical-PPT-Toolkit-Suite from Motifolio Inc., USA.

    Techniques Used: Mouse Assay, Isolation, Expressing

    13) Product Images from "Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients"

    Article Title: Comparison of the extraction and determination of serum exosome and miRNA in serum and the detection of miR-27a-3p in serum exosome of ALS patients

    Journal:

    doi: 10.5582/irdr.2017.01091

    Extraction and identification methods of exosome miRNA in the study of ALS patients. A diagram showing the conditions and methods for extraction and detection and their applications. Exosome were isolated from ALS patients and healthy subject's serum by Exoquick reagent or exoEasy Maxi Kit, then using Qiagen miRNeasy Mini Kit to isolate RNA from serum exosomes, finally using stem loop method to detect the expression of miR-27a-3p in two groups of RNA samples. The results of the different expressions can be used for the clinical diagnosis of ALS patients.
    Figure Legend Snippet: Extraction and identification methods of exosome miRNA in the study of ALS patients. A diagram showing the conditions and methods for extraction and detection and their applications. Exosome were isolated from ALS patients and healthy subject's serum by Exoquick reagent or exoEasy Maxi Kit, then using Qiagen miRNeasy Mini Kit to isolate RNA from serum exosomes, finally using stem loop method to detect the expression of miR-27a-3p in two groups of RNA samples. The results of the different expressions can be used for the clinical diagnosis of ALS patients.

    Techniques Used: Isolation, Expressing

    14) Product Images from "Controlled ovarian hyperstimulation induced changes in the expression of circulatory miRNA in bovine follicular fluid and blood plasma"

    Article Title: Controlled ovarian hyperstimulation induced changes in the expression of circulatory miRNA in bovine follicular fluid and blood plasma

    Journal: Journal of Ovarian Research

    doi: 10.1186/s13048-015-0208-5

    Specificity of isolation of exosomes and Ago2 protein complex from follicular fluid and blood plasma. Exosome and Ago2 proteins were isolated from organic-phenol fraction during total RNA isolation using miRNeasy kit and resolved in 8M urea. Protein concentrations were quantified using Bradford assay and total of twenty microgram protein from each group were separated in 12 % SDS-PAGE, transferred nitrocellulose membrane and incubated with specific antibody (CD63 and Ago2). Followed by HRP-conjugated secondary antibody and detected using chemiluminescent substrate. Western-blot results indicate the specificity of exosome and Ago2 protein isolation from follicular fluid (FF) and blood plasma (BP) as indicated in the corresponding figures
    Figure Legend Snippet: Specificity of isolation of exosomes and Ago2 protein complex from follicular fluid and blood plasma. Exosome and Ago2 proteins were isolated from organic-phenol fraction during total RNA isolation using miRNeasy kit and resolved in 8M urea. Protein concentrations were quantified using Bradford assay and total of twenty microgram protein from each group were separated in 12 % SDS-PAGE, transferred nitrocellulose membrane and incubated with specific antibody (CD63 and Ago2). Followed by HRP-conjugated secondary antibody and detected using chemiluminescent substrate. Western-blot results indicate the specificity of exosome and Ago2 protein isolation from follicular fluid (FF) and blood plasma (BP) as indicated in the corresponding figures

    Techniques Used: Isolation, Bradford Assay, SDS Page, Incubation, Western Blot

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    Amplification:

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    Quantitative RT-PCR:

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    SYBR Green Assay:

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    Microarray:

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    Incubation:

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    Expressing:

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    Cell Fractionation:

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    Generated:

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    Polymerase Chain Reaction:

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    MTT Assay:

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    RNA Sequencing Assay:

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    Isolation:

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    Labeling:

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    Purification:

    Article Title: Profiling of long non-coding RNAs identifies LINC00958 and LINC01296 as candidate oncogenes in bladder cancer
    Article Snippet: The P rotein A nd R NA I solation S ystem (PARIS) (Ambion, Life Technologies) was used to partition the bladder cell lines into cytoplasmic and nuclear fractions followed by isolation of RNA from each fraction according to the manufacturer’s instructions. .. In parallel RNA was isolated from unfractionated cells (harvested with Qiazol) (Qiagen, Hilden, Germany) and purified using miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions. .. Cell viability and death were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction (Sigma-Aldrich, St. Louis, MO, USA) and Cytotoxicity Detection Kit (LDH-assay)(Roche, Basel, Switzerland) assays, essentially as described in ref. .

    Sequencing:

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    Article Title: Prenatal exposure to valproic acid increases miR-132 levels in the mouse embryonic brain
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    Article Title: Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
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    IA:

    Article Title: Loss of TNFAIP3 enhances MYD88L265P-driven signaling in non-Hodgkin lymphoma
    Article Snippet: Quantitative reverse transcriptase-PCR was performed using either TaqMan probes (Applied Biosystems, Invitrogen, Carlsbad, CA) or probe-based predesigned qPCR primers (IDT, Coralville, IA, USA). .. For RNAseq, total RNA was extracted using the miRNeasy Mini Plus Kit (Qiagen GmbH, Hilden, Germany).

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
    Article Snippet: Samples were then centrifuged for 10 min at 12,000×g and 4 °C, and the supernatant was transferred to a separate tube and mixed with Chloroform (cat#C298, Fisher Chemical) (0.24 mL). .. After centrifugation for 15 min at 12,000×g and 4 °C, the aqueous phase was transferred to a new tube, mixed with 100% Ethanol (cat2701, Decon Labs; 0.90 mL), and total RNA was cleaned using miRNeasy mini kit columns (cat# 217004, Qiagen) following manufacturer’s protocols. .. During purification, genomic DNA was removed using the RNase-Free DNase Set (cat#79254, Qiagen).

    Software:

    Article Title: MicroRNA-30a Regulation of Epithelial-Mesenchymal Transition in Diabetic Cataracts Through Targeting SNAI1
    Article Snippet: Total RNA was isolated using a miRNeasy mini kit (QIAGEN), and RNA quality and quantity was measured by using a nanodrop spectrophotometer (ND-1000, Nanodrop Technologies). .. The miRNA labeling was prepared using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon), and miRCURYTM LNA array was performed according to the array manual.

    Article Title: MiR-590-3p suppresses epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma by inhibiting SIP1 expression
    Article Snippet: Total RNA was extracted from tissues using TRIzol regent (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. miRNA were isolated using miRNeasy mini Kit (Qiagen, Valencia, CA, USA). mRNA and miRNA were reversely transcribed to cDNA with the stem-loop reverse transcription primer for mRNA and miRNA detection. .. Then, mRNA and miRNA expression levels were quantitated using TaqMan miRNA real-time RT-PCR kit (Applied Biosystems) according to the manufacturer's protocol.

    Real-time Polymerase Chain Reaction:

    Article Title: Predictive value of microRNA let-7a expression for efficacy and prognosis of radiotherapy in patients with lung cancer brain metastasis
    Article Snippet: Paragraph title: 2.5. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) ... Total RNAs of tissues and cells was extracted from 200 μL of serum preserved in the ultralow temperature refrigerator using a miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany).

    Article Title: Molecular subtyping of nasopharyngeal carcinoma (NPC) and a microRNA-based prognostic model for distant metastasis
    Article Snippet: Total RNA containing miRNA were extracted from cell lines using miRNeasy Mini Kit (QIAGEN, USA), and DNase I digestion were performed according to the manufacturer’s instructions. .. Total RNA containing miRNA were extracted from cell lines using miRNeasy Mini Kit (QIAGEN, USA), and DNase I digestion were performed according to the manufacturer’s instructions.

    Article Title: miR-142-5p Disrupts Neuronal Morphogenesis Underlying Porcine Hemagglutinating Encephalomyelitis Virus Infection by Targeting Ulk1
    Article Snippet: For quantitative RT-PCR, total RNA was extracted using Trizol and miRNA was purificated by the miRNeasy Mini Kit (Qiagen, Germany), and all was quantified using a SmartSpec™ plus Spectrophotometer (BIO-RAD, USA). .. For quantitative RT-PCR, total RNA was extracted using Trizol and miRNA was purificated by the miRNeasy Mini Kit (Qiagen, Germany), and all was quantified using a SmartSpec™ plus Spectrophotometer (BIO-RAD, USA).

    Article Title: MicroRNA-101a regulates microglial morphology and inflammation
    Article Snippet: Paragraph title: Real-time PCR analysis ... We isolated mRNA from MG6 and brain cells using the RNeasy Mini Kit (Qiagen), and we isolated miRNA using the miRNeasy Mini Kit (Qiagen).

    Article Title: MiR-590-3p suppresses epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma by inhibiting SIP1 expression
    Article Snippet: Paragraph title: RNA extraction and real-time quantitative polymerase chain reaction (RT-qPCR) ... Total RNA was extracted from tissues using TRIzol regent (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. miRNA were isolated using miRNeasy mini Kit (Qiagen, Valencia, CA, USA). mRNA and miRNA were reversely transcribed to cDNA with the stem-loop reverse transcription primer for mRNA and miRNA detection.

    Article Title: Correlation between miR-148 Expression in Vitreous and Severity of Rhegmatogenous Retinal Detachment
    Article Snippet: Paragraph title: 2.3. Isolation and Real-Time Quantitative PCR for microRNA ... Total RNA was extracted from supernatants using Qiagen miRNeasy® Mini Kits (Qiagen, GmbH, Hilden, Germany), according to the manufacturer's recommendations.

    Article Title: Loss of TNFAIP3 enhances MYD88L265P-driven signaling in non-Hodgkin lymphoma
    Article Snippet: Paragraph title: Quantitative real-time PCR and RNA-Seq ... For RNAseq, total RNA was extracted using the miRNeasy Mini Plus Kit (Qiagen GmbH, Hilden, Germany).

    Article Title: Aberrant plasticity of peripheral sensory axons in a painful neuropathy
    Article Snippet: Paragraph title: RNA isolation and quantitative Real Time PCR ... Total RNA from DRG cultures was isolated and treated using miRNeasy mini and micro kits (QIAGEN) with DNase I (Ambion, Austin, TX).

    RNA Extraction:

    Article Title: MiR-590-3p suppresses epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma by inhibiting SIP1 expression
    Article Snippet: Paragraph title: RNA extraction and real-time quantitative polymerase chain reaction (RT-qPCR) ... Total RNA was extracted from tissues using TRIzol regent (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol. miRNA were isolated using miRNeasy mini Kit (Qiagen, Valencia, CA, USA). mRNA and miRNA were reversely transcribed to cDNA with the stem-loop reverse transcription primer for mRNA and miRNA detection.

    Article Title: Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
    Article Snippet: Paragraph title: RNA extraction, library construction, and sequencing ... After centrifugation for 15 min at 12,000×g and 4 °C, the aqueous phase was transferred to a new tube, mixed with 100% Ethanol (cat#2701, Decon Labs; 0.90 mL), and total RNA was cleaned using miRNeasy mini kit columns (cat# 217004, Qiagen) following manufacturer’s protocols.

    Sample Prep:

    Article Title: Expression of miR-26a exhibits a negative correlation with HMGA1 and regulates cancer progression by targeting HMGA1 in lung adenocarcinoma cells
    Article Snippet: Total RNA was extracted from the lung cancer cells using the miRNeasy Mini kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's protocol. .. An mRNA library was prepared using the TruSeq RNA Sample Prep kit v2 (Illumina, Inc., San Diego, CA, USA).

    Spectrophotometry:

    Article Title: Predictive value of microRNA let-7a expression for efficacy and prognosis of radiotherapy in patients with lung cancer brain metastasis
    Article Snippet: Total RNAs of tissues and cells was extracted from 200 μL of serum preserved in the ultralow temperature refrigerator using a miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). .. Total RNAs of tissues and cells was extracted from 200 μL of serum preserved in the ultralow temperature refrigerator using a miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany).

    Article Title: Molecular subtyping of nasopharyngeal carcinoma (NPC) and a microRNA-based prognostic model for distant metastasis
    Article Snippet: Total RNA containing miRNA were extracted from cell lines using miRNeasy Mini Kit (QIAGEN, USA), and DNase I digestion were performed according to the manufacturer’s instructions. .. Total RNA containing miRNA were extracted from cell lines using miRNeasy Mini Kit (QIAGEN, USA), and DNase I digestion were performed according to the manufacturer’s instructions.

    Article Title: MicroRNA-30a Regulation of Epithelial-Mesenchymal Transition in Diabetic Cataracts Through Targeting SNAI1
    Article Snippet: The miRCURYTM LNA array (v.18.0) (Exiqon, Vedbaek, Denmark) was used in this miRNA microarray study (KangChen Bio-tech, Shanghai, China). .. Total RNA was isolated using a miRNeasy mini kit (QIAGEN), and RNA quality and quantity was measured by using a nanodrop spectrophotometer (ND-1000, Nanodrop Technologies). .. The miRNA labeling was prepared using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon), and miRCURYTM LNA array was performed according to the array manual.

    Article Title: Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors
    Article Snippet: Total RNA was extracted from approximately 10 mg of minced tissue samples using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. .. Total RNA was extracted from approximately 10 mg of minced tissue samples using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

    Article Title: Co-Inflammatory Roles of TGFβ1 in the Presence of TNFα Drive a Pro-inflammatory Fate in Mesenchymal Stem Cells
    Article Snippet: Following MSC stimulation by the cytokines (as described above), total-RNA of frozen cell pellets was isolated using miRNeasy Mini kit (Cat# 217004; Qiagen, Hilden, Germany) according to manufacturer’s protocols. .. The quality of total RNA was checked by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany).

    Concentration Assay:

    Article Title: MicroRNA-34a inhibits metastasis in liver cancer cells
    Article Snippet: The miRNeasy Mini kit was purchased from Qiagen GmbH (Hilden, Germany). .. 5-fluorouracil (5-FU) and MTT were from Sigma-Aldrich (Merck KGaA, Darmstadt, Germany).

    Article Title: Predictive value of microRNA let-7a expression for efficacy and prognosis of radiotherapy in patients with lung cancer brain metastasis
    Article Snippet: Total RNAs of tissues and cells was extracted from 200 μL of serum preserved in the ultralow temperature refrigerator using a miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). .. Total RNAs of tissues and cells was extracted from 200 μL of serum preserved in the ultralow temperature refrigerator using a miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany).

    Article Title: Molecular subtyping of nasopharyngeal carcinoma (NPC) and a microRNA-based prognostic model for distant metastasis
    Article Snippet: Total RNA containing miRNA were extracted from cell lines using miRNeasy Mini Kit (QIAGEN, USA), and DNase I digestion were performed according to the manufacturer’s instructions. .. Total RNA containing miRNA were extracted from cell lines using miRNeasy Mini Kit (QIAGEN, USA), and DNase I digestion were performed according to the manufacturer’s instructions.

    Lysis:

    Article Title: Role of the immune system in the peritoneal tumor spread of high grade serous ovarian cancer
    Article Snippet: Cell doublets and dead cells were excluded from analysis and different cell populations were gated according to expression of surface markers. .. RNA was prepared from previously frozen samples stored in QIAZOL lysis buffer with the miRNeasy® Mini Kit (Qiagen, Hilden, Germany) according to manufacturer's instructions for preparation of RNAs longer than 200 nucleotides. .. The quality was assessed by analysis on an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and samples with RNA Integrity Numbers (RIN) > 7 were used for library preparation.

    Article Title: Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
    Article Snippet: Tissue was weighted (PAR, ~ 0.10 g; MFP, ~ 0.20 g), immediately placed in QIAzol Lysis Reagent (cat#79306, Qiagen) (1.20 mL) and homogenized using a Mini-Beadbeater-24 (cat#112011, Biospec Products Inc.) with two 30 s cycles, and 1 min incubation on ice in between the cycles. .. After centrifugation for 15 min at 12,000×g and 4 °C, the aqueous phase was transferred to a new tube, mixed with 100% Ethanol (cat#2701, Decon Labs; 0.90 mL), and total RNA was cleaned using miRNeasy mini kit columns (cat# 217004, Qiagen) following manufacturer’s protocols.

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    Qiagen mirneasy mini kit
    Correlations between mean “fold recovery” (FR) values of miRNAs and base 10 logarithm of miRNA relative abundance in sample (SRA), using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, <t>miRNeasy</t> Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; SRA, the mean relative abundance of each miRNA on samples isolated without carrier.
    Mirneasy Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 253 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Correlations between mean “fold recovery” (FR) values of miRNAs and base 10 logarithm of miRNA relative abundance in sample (SRA), using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; SRA, the mean relative abundance of each miRNA on samples isolated without carrier.

    Journal: PLoS ONE

    Article Title: Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    doi: 10.1371/journal.pone.0187005

    Figure Lengend Snippet: Correlations between mean “fold recovery” (FR) values of miRNAs and base 10 logarithm of miRNA relative abundance in sample (SRA), using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; SRA, the mean relative abundance of each miRNA on samples isolated without carrier.

    Article Snippet: The quality and isolation efficiency of miRNAs were analyzed in four plasma samples using two protocols: phenol and column based isolation procedures (miRNeasy Mini kit, Qiagen, Q protocol) and column based procedures (miRCURY RNA Isolation kit Biofluids, Exiqon, E protocol).

    Techniques: Isolation, Modification

    Raw Cq values. Evaluation of Cq values of UniSp2, miR-103a-3p and miR-451a in four samples using different isolation protocols and RNA carriers. y, yeast RNA carrier; m, MS2 RNA carrier; w, without carrier; Q, miRNeasy Mini kit modified protocol; E, miRCURY RNA isolation kit Biofluids modified protocol. Mean and standard deviation values are indicated under each box plot diagram.

    Journal: PLoS ONE

    Article Title: Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    doi: 10.1371/journal.pone.0187005

    Figure Lengend Snippet: Raw Cq values. Evaluation of Cq values of UniSp2, miR-103a-3p and miR-451a in four samples using different isolation protocols and RNA carriers. y, yeast RNA carrier; m, MS2 RNA carrier; w, without carrier; Q, miRNeasy Mini kit modified protocol; E, miRCURY RNA isolation kit Biofluids modified protocol. Mean and standard deviation values are indicated under each box plot diagram.

    Article Snippet: The quality and isolation efficiency of miRNAs were analyzed in four plasma samples using two protocols: phenol and column based isolation procedures (miRNeasy Mini kit, Qiagen, Q protocol) and column based procedures (miRCURY RNA Isolation kit Biofluids, Exiqon, E protocol).

    Techniques: Isolation, Modification, Standard Deviation

    Correlations between mean “fold recovery” (FR) values of miRNAs and ΔG of each miRNA, using yE protocol (A) and yQ protocol (B). To avoid the influence of GC content in the analysis of ΔG, for these correlations we used only miRNAs with a GC content between 25% and 75% percentile. yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; ΔG, the free energy of the most stable secondary structure of each miRNA.

    Journal: PLoS ONE

    Article Title: Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    doi: 10.1371/journal.pone.0187005

    Figure Lengend Snippet: Correlations between mean “fold recovery” (FR) values of miRNAs and ΔG of each miRNA, using yE protocol (A) and yQ protocol (B). To avoid the influence of GC content in the analysis of ΔG, for these correlations we used only miRNAs with a GC content between 25% and 75% percentile. yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier; ΔG, the free energy of the most stable secondary structure of each miRNA.

    Article Snippet: The quality and isolation efficiency of miRNAs were analyzed in four plasma samples using two protocols: phenol and column based isolation procedures (miRNeasy Mini kit, Qiagen, Q protocol) and column based procedures (miRCURY RNA Isolation kit Biofluids, Exiqon, E protocol).

    Techniques: Gas Chromatography, Isolation, Modification

    Correlations between mean “fold recovery” (FR) values of miRNAs and GC content of each miRNA, using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier.

    Journal: PLoS ONE

    Article Title: Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    doi: 10.1371/journal.pone.0187005

    Figure Lengend Snippet: Correlations between mean “fold recovery” (FR) values of miRNAs and GC content of each miRNA, using yE protocol (A) and yQ protocol (B). yE, miRCURY RNA isolation kit Biofluids modified protocol using yeast RNA carrier; yQ, miRNeasy Mini kit modified protocol using yeast RNA carrier; FR, the fold recovery of each miRNA vs the same protocol without carrier.

    Article Snippet: The quality and isolation efficiency of miRNAs were analyzed in four plasma samples using two protocols: phenol and column based isolation procedures (miRNeasy Mini kit, Qiagen, Q protocol) and column based procedures (miRCURY RNA Isolation kit Biofluids, Exiqon, E protocol).

    Techniques: Gas Chromatography, Isolation, Modification

    miRNA levels normalized by plasma volume and by an endogenous miRNA. Fold abundance of miRNAs normalized by plasma volume (FR of miRNAs, left column) and normalized by hsa-miR-103a-3p (apFC of miRNAs, right column) and referred to control plasma samples isolated with the E protocol without carrier (in gray). Data were determined in plasma RNA-derived samples isolated with Q and E modified protocols with yeast RNA as carrier (y) or without RNA carrier (w). E, miRCURY RNA isolation kit Biofluids modified protocol; Q, miRNeasy Mini kit modified protocol; FR, fold recovery of miRNAs vs wE protocol; apFC, apparent fold change of miRNAs vs wE protocol. P -values were calculated using Wilcoxon Signed Rank Test, Exact Signification two-tailed, with the IBM SPSS Statistics 20 software. ϕ P

    Journal: PLoS ONE

    Article Title: Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

    doi: 10.1371/journal.pone.0187005

    Figure Lengend Snippet: miRNA levels normalized by plasma volume and by an endogenous miRNA. Fold abundance of miRNAs normalized by plasma volume (FR of miRNAs, left column) and normalized by hsa-miR-103a-3p (apFC of miRNAs, right column) and referred to control plasma samples isolated with the E protocol without carrier (in gray). Data were determined in plasma RNA-derived samples isolated with Q and E modified protocols with yeast RNA as carrier (y) or without RNA carrier (w). E, miRCURY RNA isolation kit Biofluids modified protocol; Q, miRNeasy Mini kit modified protocol; FR, fold recovery of miRNAs vs wE protocol; apFC, apparent fold change of miRNAs vs wE protocol. P -values were calculated using Wilcoxon Signed Rank Test, Exact Signification two-tailed, with the IBM SPSS Statistics 20 software. ϕ P

    Article Snippet: The quality and isolation efficiency of miRNAs were analyzed in four plasma samples using two protocols: phenol and column based isolation procedures (miRNeasy Mini kit, Qiagen, Q protocol) and column based procedures (miRCURY RNA Isolation kit Biofluids, Exiqon, E protocol).

    Techniques: Isolation, Derivative Assay, Modification, Two Tailed Test, Software

    Increased serum miR-155, miR-125b and miR-146a levels in chronic HCV-infected patients. A - C . 100ul of serum was used for total RNA isolation from both healthy controls (n = 12-18) and chronic HCV patients (n = 30-36) with miRNeasy kit (Qiagen). TaqMan miRNA assays (Applied Biosystems) were used to detect miRNA levels and C.elegans (Cel)-miR-39 was used to normalize the ct values. The non-parametric Mann–Whitney test was used for statistical analysis.

    Journal: Journal of Translational Medicine

    Article Title: Increased microRNA-155 expression in the serum and peripheral monocytes in chronic HCV infection

    doi: 10.1186/1479-5876-10-151

    Figure Lengend Snippet: Increased serum miR-155, miR-125b and miR-146a levels in chronic HCV-infected patients. A - C . 100ul of serum was used for total RNA isolation from both healthy controls (n = 12-18) and chronic HCV patients (n = 30-36) with miRNeasy kit (Qiagen). TaqMan miRNA assays (Applied Biosystems) were used to detect miRNA levels and C.elegans (Cel)-miR-39 was used to normalize the ct values. The non-parametric Mann–Whitney test was used for statistical analysis.

    Article Snippet: 100ul of serum from healthy controls and patient samples was used for total RNA isolation with miRNeasy kit (Qiagen).

    Techniques: Infection, Isolation, MANN-WHITNEY

    Decreased miR-125b expression in peripheral monocytes of chronic HCV treatment naïve patients. A - B . Total RNA was isolated from monocytes of healthy volunteers (n = 6), chronic HCV treatment naïve patients (n = 12) and sustained responders (n = 5) with miRNeasy kit (Qiagen). MiR-125b and miR-146a levels were detected by TaqMan miRNA assay (Applied Biosystems), and RNU48 was used as a normalization control. The non-parametric Mann–Whitney test was employed for statistical analysis.

    Journal: Journal of Translational Medicine

    Article Title: Increased microRNA-155 expression in the serum and peripheral monocytes in chronic HCV infection

    doi: 10.1186/1479-5876-10-151

    Figure Lengend Snippet: Decreased miR-125b expression in peripheral monocytes of chronic HCV treatment naïve patients. A - B . Total RNA was isolated from monocytes of healthy volunteers (n = 6), chronic HCV treatment naïve patients (n = 12) and sustained responders (n = 5) with miRNeasy kit (Qiagen). MiR-125b and miR-146a levels were detected by TaqMan miRNA assay (Applied Biosystems), and RNU48 was used as a normalization control. The non-parametric Mann–Whitney test was employed for statistical analysis.

    Article Snippet: 100ul of serum from healthy controls and patient samples was used for total RNA isolation with miRNeasy kit (Qiagen).

    Techniques: Expressing, Isolation, TaqMan microRNA Assay, MANN-WHITNEY

    Increased circulating miR-122 levels correlate with serum ALT, AST and miR-155 levels in chronic HCV-infected patients. A . 100ul of serum was used for total RNA isolation from both healthy controls (n = 12-13) and chronic HCV patients (n = 33) with miRNeasy kit (Qiagen). Serum miR-122 levels were detected with TaqMan miRNA assay as described in the methods. The non-parametric Mann–Whitney test was used for statistical analysis. B . Serum ALT or AST levels of healthy and chronic HCV-infected individuals. C - E . Correlation between serum miR-122 and ALT ( C ) and AST ( D ) and serum miR-155 ( E ) was determined with the Spearman method.

    Journal: Journal of Translational Medicine

    Article Title: Increased microRNA-155 expression in the serum and peripheral monocytes in chronic HCV infection

    doi: 10.1186/1479-5876-10-151

    Figure Lengend Snippet: Increased circulating miR-122 levels correlate with serum ALT, AST and miR-155 levels in chronic HCV-infected patients. A . 100ul of serum was used for total RNA isolation from both healthy controls (n = 12-13) and chronic HCV patients (n = 33) with miRNeasy kit (Qiagen). Serum miR-122 levels were detected with TaqMan miRNA assay as described in the methods. The non-parametric Mann–Whitney test was used for statistical analysis. B . Serum ALT or AST levels of healthy and chronic HCV-infected individuals. C - E . Correlation between serum miR-122 and ALT ( C ) and AST ( D ) and serum miR-155 ( E ) was determined with the Spearman method.

    Article Snippet: 100ul of serum from healthy controls and patient samples was used for total RNA isolation with miRNeasy kit (Qiagen).

    Techniques: AST Assay, Infection, Isolation, TaqMan microRNA Assay, MANN-WHITNEY

    Induction of miR-155 in peripheral monocytes of chronic HCV treatment naïve patients. A . Total RNA was isolated from the monocytes of healthy volunteers (n = 6), chronic HCV treatment naïve patients (n = 12) and sustained responders (n = 5) with miRNeasy kit (Qiagen). B . Monocytes of healthy controls and chronic HCV treatment naïve patients were stimulated with 100 ng/ml LPS for 6-8 h. TaqMan miRNA assay (Applied Biosystems) was used for detection of miR-155. RNU48 was used as a normalization control. The non-parametric Mann–Whitney test was employed for statistical analysis.

    Journal: Journal of Translational Medicine

    Article Title: Increased microRNA-155 expression in the serum and peripheral monocytes in chronic HCV infection

    doi: 10.1186/1479-5876-10-151

    Figure Lengend Snippet: Induction of miR-155 in peripheral monocytes of chronic HCV treatment naïve patients. A . Total RNA was isolated from the monocytes of healthy volunteers (n = 6), chronic HCV treatment naïve patients (n = 12) and sustained responders (n = 5) with miRNeasy kit (Qiagen). B . Monocytes of healthy controls and chronic HCV treatment naïve patients were stimulated with 100 ng/ml LPS for 6-8 h. TaqMan miRNA assay (Applied Biosystems) was used for detection of miR-155. RNU48 was used as a normalization control. The non-parametric Mann–Whitney test was employed for statistical analysis.

    Article Snippet: 100ul of serum from healthy controls and patient samples was used for total RNA isolation with miRNeasy kit (Qiagen).

    Techniques: Isolation, TaqMan microRNA Assay, MANN-WHITNEY