control input dna  (Thermo Fisher)


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    Name:
    Control DNA from CEPH Individual 1347 02
    Description:
    The Control DNA can be used with Linkage Mapping Sets MD10 HD5 and LD20 • Functions as a control template to monitor PCR amplification • Serves as sizing reference for controlling gel to gel or capillary to capillary variation • Aids in the comparison of alleles sizes from different gels allele binning • Enables correlation with allele frequency data from external sources such as others databases and laboratories For Research Use Only Not for use in diagnostics procedures
    Catalog Number:
    403062
    Price:
    None
    Category:
    Standards Ladders Controls
    Applications:
    Genotyping & Genomic Profiling|PCR|PCR & Real-Time PCR|PCR Genotyping|Gene Expression Analysis & Genotyping|Microsatellite Analysis
    Buy from Supplier


    Structured Review

    Thermo Fisher control input dna
    The Control DNA can be used with Linkage Mapping Sets MD10 HD5 and LD20 • Functions as a control template to monitor PCR amplification • Serves as sizing reference for controlling gel to gel or capillary to capillary variation • Aids in the comparison of alleles sizes from different gels allele binning • Enables correlation with allele frequency data from external sources such as others databases and laboratories For Research Use Only Not for use in diagnostics procedures
    https://www.bioz.com/result/control input dna/product/Thermo Fisher
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    control input dna - by Bioz Stars, 2021-07
    94/100 stars

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    Related Articles

    Amplification:

    Article Title: Developmental Validation of the Huaxia Platinum System and application in 3 main ethnic groups of China
    Article Snippet: Primer set and master mix concentration The Huaxia Platinum System was designed to enable fast and robust amplification from single source samples, which has a new improved PCR formulation and optimized PCR cycling conditions. .. To evaluate the performance of primer set and to assess the reliability and robustness of the master mix formulation, 1 ng of Control DNA 007 was amplified in triplicate at the standard primer mix (or master mix) concentration and at increments of ± 25% and ± 50% volume added into the PCR reaction. .. NThermal cycling parameters The thermal cycling parameters were evaluated to establish the optimal performance window of amplification for the Huaxia Platinum System.

    Concentration Assay:

    Article Title: Developmental Validation of the Huaxia Platinum System and application in 3 main ethnic groups of China
    Article Snippet: Primer set and master mix concentration The Huaxia Platinum System was designed to enable fast and robust amplification from single source samples, which has a new improved PCR formulation and optimized PCR cycling conditions. .. To evaluate the performance of primer set and to assess the reliability and robustness of the master mix formulation, 1 ng of Control DNA 007 was amplified in triplicate at the standard primer mix (or master mix) concentration and at increments of ± 25% and ± 50% volume added into the PCR reaction. .. NThermal cycling parameters The thermal cycling parameters were evaluated to establish the optimal performance window of amplification for the Huaxia Platinum System.

    Polymerase Chain Reaction:

    Article Title: Developmental Validation of the Huaxia Platinum System and application in 3 main ethnic groups of China
    Article Snippet: Primer set and master mix concentration The Huaxia Platinum System was designed to enable fast and robust amplification from single source samples, which has a new improved PCR formulation and optimized PCR cycling conditions. .. To evaluate the performance of primer set and to assess the reliability and robustness of the master mix formulation, 1 ng of Control DNA 007 was amplified in triplicate at the standard primer mix (or master mix) concentration and at increments of ± 25% and ± 50% volume added into the PCR reaction. .. NThermal cycling parameters The thermal cycling parameters were evaluated to establish the optimal performance window of amplification for the Huaxia Platinum System.

    Article Title: DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis
    Article Snippet: Dried cleavage product was resuspended (10% ACN, 0.1% formic acid in H2 O, 400 μL) and analyzed using LC-MS (see above) yielding an extracted-ion chromatogram (811 m /z ). .. Control Compound Encoding DNA Quantitation and Sequencing DESPS and DE+ resin samples were aliquoted to separate tubes, washed (BTPWB, 3 × 500 μL) and incubated with rotation (1 h, RT, 8 rpm). qPCR mixture contained Taq (0.05 U/μL), oligonucleotide primers 5′-GCCGCCCAGTCCTGCTCGCTTCGCTAC-3′ and 5′-GTGGCACAACAACTGGCGGGCAAAC-3′ (0.3 μM each), and SYBR Green (0.1×, Life Technologies) in PCR buffer (1×). .. Single resin beads (DESPS or DE+) in BTPWB (1 μL) were added to separate amplification reactions (20 μL, 10 replicates each resin type for each compound).

    Chloramphenicol Acetyltransferase Assay:

    Article Title: Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay
    Article Snippet: .. F a c t o r ] g D N A ( n g ) u s e d i n d d P C R a s s a y × 2 Precision and accuracy determination experiments were carried out with CEPH 1347-02 human female human gDNA reference standard (CAT 403062, Life Technologies, Chicago, USA) and RM gDNA reference standard (CAT# D1534999 G-01, Biochain Institute Inc, USA) containing 15000 RPP30 copies in 50000 pg was used as control gDNA. gDNA extracted from mouse derived SVEC 4-10 LECs served as negative control. .. RPP30 ddPCR assay precision and accuracy determination experiments were performed with human genomic DNA reference standard (Life Technologies, Chicago, USA) and genomic DNA extracted from RMs serially diluted from 100000 to 100 pg used as assay templates to amplify RPP30 genomic sequences.

    Article Title: Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay
    Article Snippet: .. F a c t o r ] g D N A ( n g ) u s e d i n d d P C R a s s a y × 2 Precision and accuracy determination experiments were carried out with CEPH 1347-02 human female human gDNA reference standard (CAT 403062, Life Technologies, Chicago, USA) and RM gDNA reference standard (CAT# D1534999 G-01, Biochain Institute Inc, USA) containing 15000 RPP30 copies in 50000 pg was used as control gDNA. gDNA extracted from mouse derived SVEC 4-10 LECs served as negative control. .. RPP30 ddPCR assay precision and accuracy determination experiments were performed with human genomic DNA reference standard (Life Technologies, Chicago, USA) and genomic DNA extracted from RMs serially diluted from 100000 to 100 pg used as assay templates to amplify RPP30 genomic sequences.

    Derivative Assay:

    Article Title: Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay
    Article Snippet: .. F a c t o r ] g D N A ( n g ) u s e d i n d d P C R a s s a y × 2 Precision and accuracy determination experiments were carried out with CEPH 1347-02 human female human gDNA reference standard (CAT 403062, Life Technologies, Chicago, USA) and RM gDNA reference standard (CAT# D1534999 G-01, Biochain Institute Inc, USA) containing 15000 RPP30 copies in 50000 pg was used as control gDNA. gDNA extracted from mouse derived SVEC 4-10 LECs served as negative control. .. RPP30 ddPCR assay precision and accuracy determination experiments were performed with human genomic DNA reference standard (Life Technologies, Chicago, USA) and genomic DNA extracted from RMs serially diluted from 100000 to 100 pg used as assay templates to amplify RPP30 genomic sequences.

    Article Title: Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay
    Article Snippet: .. F a c t o r ] g D N A ( n g ) u s e d i n d d P C R a s s a y × 2 Precision and accuracy determination experiments were carried out with CEPH 1347-02 human female human gDNA reference standard (CAT 403062, Life Technologies, Chicago, USA) and RM gDNA reference standard (CAT# D1534999 G-01, Biochain Institute Inc, USA) containing 15000 RPP30 copies in 50000 pg was used as control gDNA. gDNA extracted from mouse derived SVEC 4-10 LECs served as negative control. .. RPP30 ddPCR assay precision and accuracy determination experiments were performed with human genomic DNA reference standard (Life Technologies, Chicago, USA) and genomic DNA extracted from RMs serially diluted from 100000 to 100 pg used as assay templates to amplify RPP30 genomic sequences.

    Negative Control:

    Article Title: Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay
    Article Snippet: .. F a c t o r ] g D N A ( n g ) u s e d i n d d P C R a s s a y × 2 Precision and accuracy determination experiments were carried out with CEPH 1347-02 human female human gDNA reference standard (CAT 403062, Life Technologies, Chicago, USA) and RM gDNA reference standard (CAT# D1534999 G-01, Biochain Institute Inc, USA) containing 15000 RPP30 copies in 50000 pg was used as control gDNA. gDNA extracted from mouse derived SVEC 4-10 LECs served as negative control. .. RPP30 ddPCR assay precision and accuracy determination experiments were performed with human genomic DNA reference standard (Life Technologies, Chicago, USA) and genomic DNA extracted from RMs serially diluted from 100000 to 100 pg used as assay templates to amplify RPP30 genomic sequences.

    Article Title: Normalization of cell associated antiretroviral drug concentrations with a novel RPP30 droplet digital PCR assay
    Article Snippet: .. F a c t o r ] g D N A ( n g ) u s e d i n d d P C R a s s a y × 2 Precision and accuracy determination experiments were carried out with CEPH 1347-02 human female human gDNA reference standard (CAT 403062, Life Technologies, Chicago, USA) and RM gDNA reference standard (CAT# D1534999 G-01, Biochain Institute Inc, USA) containing 15000 RPP30 copies in 50000 pg was used as control gDNA. gDNA extracted from mouse derived SVEC 4-10 LECs served as negative control. .. RPP30 ddPCR assay precision and accuracy determination experiments were performed with human genomic DNA reference standard (Life Technologies, Chicago, USA) and genomic DNA extracted from RMs serially diluted from 100000 to 100 pg used as assay templates to amplify RPP30 genomic sequences.

    other:

    Article Title: Developmental Validation of the Huaxia Platinum System and application in 3 main ethnic groups of China
    Article Snippet: The genotypes of the Control DNA 007 (male, M) and 9947A (female, F) are shown in .

    Quantitation Assay:

    Article Title: DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis
    Article Snippet: Dried cleavage product was resuspended (10% ACN, 0.1% formic acid in H2 O, 400 μL) and analyzed using LC-MS (see above) yielding an extracted-ion chromatogram (811 m /z ). .. Control Compound Encoding DNA Quantitation and Sequencing DESPS and DE+ resin samples were aliquoted to separate tubes, washed (BTPWB, 3 × 500 μL) and incubated with rotation (1 h, RT, 8 rpm). qPCR mixture contained Taq (0.05 U/μL), oligonucleotide primers 5′-GCCGCCCAGTCCTGCTCGCTTCGCTAC-3′ and 5′-GTGGCACAACAACTGGCGGGCAAAC-3′ (0.3 μM each), and SYBR Green (0.1×, Life Technologies) in PCR buffer (1×). .. Single resin beads (DESPS or DE+) in BTPWB (1 μL) were added to separate amplification reactions (20 μL, 10 replicates each resin type for each compound).

    Sequencing:

    Article Title: DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis
    Article Snippet: Dried cleavage product was resuspended (10% ACN, 0.1% formic acid in H2 O, 400 μL) and analyzed using LC-MS (see above) yielding an extracted-ion chromatogram (811 m /z ). .. Control Compound Encoding DNA Quantitation and Sequencing DESPS and DE+ resin samples were aliquoted to separate tubes, washed (BTPWB, 3 × 500 μL) and incubated with rotation (1 h, RT, 8 rpm). qPCR mixture contained Taq (0.05 U/μL), oligonucleotide primers 5′-GCCGCCCAGTCCTGCTCGCTTCGCTAC-3′ and 5′-GTGGCACAACAACTGGCGGGCAAAC-3′ (0.3 μM each), and SYBR Green (0.1×, Life Technologies) in PCR buffer (1×). .. Single resin beads (DESPS or DE+) in BTPWB (1 μL) were added to separate amplification reactions (20 μL, 10 replicates each resin type for each compound).

    Incubation:

    Article Title: DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis
    Article Snippet: Dried cleavage product was resuspended (10% ACN, 0.1% formic acid in H2 O, 400 μL) and analyzed using LC-MS (see above) yielding an extracted-ion chromatogram (811 m /z ). .. Control Compound Encoding DNA Quantitation and Sequencing DESPS and DE+ resin samples were aliquoted to separate tubes, washed (BTPWB, 3 × 500 μL) and incubated with rotation (1 h, RT, 8 rpm). qPCR mixture contained Taq (0.05 U/μL), oligonucleotide primers 5′-GCCGCCCAGTCCTGCTCGCTTCGCTAC-3′ and 5′-GTGGCACAACAACTGGCGGGCAAAC-3′ (0.3 μM each), and SYBR Green (0.1×, Life Technologies) in PCR buffer (1×). .. Single resin beads (DESPS or DE+) in BTPWB (1 μL) were added to separate amplification reactions (20 μL, 10 replicates each resin type for each compound).

    Real-time Polymerase Chain Reaction:

    Article Title: DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis
    Article Snippet: Dried cleavage product was resuspended (10% ACN, 0.1% formic acid in H2 O, 400 μL) and analyzed using LC-MS (see above) yielding an extracted-ion chromatogram (811 m /z ). .. Control Compound Encoding DNA Quantitation and Sequencing DESPS and DE+ resin samples were aliquoted to separate tubes, washed (BTPWB, 3 × 500 μL) and incubated with rotation (1 h, RT, 8 rpm). qPCR mixture contained Taq (0.05 U/μL), oligonucleotide primers 5′-GCCGCCCAGTCCTGCTCGCTTCGCTAC-3′ and 5′-GTGGCACAACAACTGGCGGGCAAAC-3′ (0.3 μM each), and SYBR Green (0.1×, Life Technologies) in PCR buffer (1×). .. Single resin beads (DESPS or DE+) in BTPWB (1 μL) were added to separate amplification reactions (20 μL, 10 replicates each resin type for each compound).

    SYBR Green Assay:

    Article Title: DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis
    Article Snippet: Dried cleavage product was resuspended (10% ACN, 0.1% formic acid in H2 O, 400 μL) and analyzed using LC-MS (see above) yielding an extracted-ion chromatogram (811 m /z ). .. Control Compound Encoding DNA Quantitation and Sequencing DESPS and DE+ resin samples were aliquoted to separate tubes, washed (BTPWB, 3 × 500 μL) and incubated with rotation (1 h, RT, 8 rpm). qPCR mixture contained Taq (0.05 U/μL), oligonucleotide primers 5′-GCCGCCCAGTCCTGCTCGCTTCGCTAC-3′ and 5′-GTGGCACAACAACTGGCGGGCAAAC-3′ (0.3 μM each), and SYBR Green (0.1×, Life Technologies) in PCR buffer (1×). .. Single resin beads (DESPS or DE+) in BTPWB (1 μL) were added to separate amplification reactions (20 μL, 10 replicates each resin type for each compound).

    Microarray:

    Article Title: Heat shock drives genomic instability and phenotypic variations in yeast
    Article Snippet: .. In the SNP microarray experiment, the control DNA (200 ng) extracted from the JSC24-2 cells and experimental DNA (400 ng) were labeled dUTP-Cy3 and dUTP-Cy5, respectively, using the Invitrogen BioPrime array CGH labeling system (Thermo Scientific, Waltham, MA, USA). .. The labeled DNAs were purified using a GeneJET PCR purification kit (Thermo Scientific, Waltham, MA, USA) and then cohybridized onto microarray slides at 62 °C for 18 h. A GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) was used to scan the slides, and GenePix 6.0 software (Molecular Devices, Sunnyvale, CA, USA) quantified the hybridization signals.

    Labeling:

    Article Title: Heat shock drives genomic instability and phenotypic variations in yeast
    Article Snippet: .. In the SNP microarray experiment, the control DNA (200 ng) extracted from the JSC24-2 cells and experimental DNA (400 ng) were labeled dUTP-Cy3 and dUTP-Cy5, respectively, using the Invitrogen BioPrime array CGH labeling system (Thermo Scientific, Waltham, MA, USA). .. The labeled DNAs were purified using a GeneJET PCR purification kit (Thermo Scientific, Waltham, MA, USA) and then cohybridized onto microarray slides at 62 °C for 18 h. A GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) was used to scan the slides, and GenePix 6.0 software (Molecular Devices, Sunnyvale, CA, USA) quantified the hybridization signals.

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  • 97
    Thermo Fisher rna input
    Reduction of viral mRNA levels by MβCD treatment. Vero E6 cells were left untreated (Treat:N) or were pretreated with 10 mM MβCD for 30 min at 37 °C (Treat:−0.5), and then infected with SARS-CoV at an MOI of 10. Alternatively, cells were first infected with SARS-CoV, as described above, and then treated with MβCD for 30 min at 37 °C at 3 hpi (Treat:+3). After culturing for 3 and 6 h, respectively, total RNAs were extracted and subjected to Northern blot analysis with a DNA probe for the SARS-CoV N gene. As a control for <t>RNA</t> input, the same amounts of the RNA samples were subjected to Northern blot analysis for <t>GAPDH</t> gene expression.
    Rna Input, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna input/product/Thermo Fisher
    Average 97 stars, based on 1 article reviews
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    97
    Thermo Fisher total rna input
    Armored <t>RNA</t> Quant as a process control. RNA isolation was performed using 16 20-μm slices from 15 pairs of matched FFPE lung tumor and NAT specimens with 10 10 copies of ARQ spiked at the proteinase K digestion step. <t>qRT-PCR</t> were performed in duplicate
    Total Rna Input, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    99
    Thermo Fisher mirnas
    Representation of TFBSs in promoter regions of <t>miRNAs</t> up-regulated in DCs . Depicted are the TFBSs at a motif instance score threshold of at least 6 in the <t>miRNA</t> promoter regions. The scale of the y-axis ranges from 5 to 15 for each subgraph. The legend shows only those TFBSs that are present in all promoter sequences.
    Mirnas, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Reduction of viral mRNA levels by MβCD treatment. Vero E6 cells were left untreated (Treat:N) or were pretreated with 10 mM MβCD for 30 min at 37 °C (Treat:−0.5), and then infected with SARS-CoV at an MOI of 10. Alternatively, cells were first infected with SARS-CoV, as described above, and then treated with MβCD for 30 min at 37 °C at 3 hpi (Treat:+3). After culturing for 3 and 6 h, respectively, total RNAs were extracted and subjected to Northern blot analysis with a DNA probe for the SARS-CoV N gene. As a control for RNA input, the same amounts of the RNA samples were subjected to Northern blot analysis for GAPDH gene expression.

    Journal: Microbes and Infection

    Article Title: Lipid rafts play an important role in the early stage of severe acute respiratory syndrome-coronavirus life cycle

    doi: 10.1016/j.micinf.2006.10.015

    Figure Lengend Snippet: Reduction of viral mRNA levels by MβCD treatment. Vero E6 cells were left untreated (Treat:N) or were pretreated with 10 mM MβCD for 30 min at 37 °C (Treat:−0.5), and then infected with SARS-CoV at an MOI of 10. Alternatively, cells were first infected with SARS-CoV, as described above, and then treated with MβCD for 30 min at 37 °C at 3 hpi (Treat:+3). After culturing for 3 and 6 h, respectively, total RNAs were extracted and subjected to Northern blot analysis with a DNA probe for the SARS-CoV N gene. As a control for RNA input, the same amounts of the RNA samples were subjected to Northern blot analysis for GAPDH gene expression.

    Article Snippet: As a control for RNA input, a probe for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was also prepared by reverse transcriptase-PCR using SuperScript III Reverse Transcriptase (Invitrogen) with the RNAs isolated from uninfected Vero E6 cells.

    Techniques: Infection, Northern Blot, Expressing

    Statistical analysis of expression level measurements for assessing reproducibility and comparability of amplification chemistries . A , we calculated the Pearson's correlation coefficients between technical replicates (same chemistry, same amount of input RNA, but different laboratories). The correlation values were then averaged for each chemistry (grey bars). We also calculated correlation coefficients between results obtained from 250 pg and from 500 pg of RNA input (same chemistry, but different amount of RNA input) and averaged them for each chemistry in order to evaluate the robustness across quantitative variability of RNA input (black bars). Most Epicentre amplifications did not yield sufficient aRNA to carry out hybridisations, and Pearson's correlation coefficients could therefore not be calculated (*). B , Graphic representation of Pearson's correlation coefficients calculated for each pairwise comparison of all assays.

    Journal: BMC Genomics

    Article Title: Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

    doi: 10.1186/1471-2164-10-246

    Figure Lengend Snippet: Statistical analysis of expression level measurements for assessing reproducibility and comparability of amplification chemistries . A , we calculated the Pearson's correlation coefficients between technical replicates (same chemistry, same amount of input RNA, but different laboratories). The correlation values were then averaged for each chemistry (grey bars). We also calculated correlation coefficients between results obtained from 250 pg and from 500 pg of RNA input (same chemistry, but different amount of RNA input) and averaged them for each chemistry in order to evaluate the robustness across quantitative variability of RNA input (black bars). Most Epicentre amplifications did not yield sufficient aRNA to carry out hybridisations, and Pearson's correlation coefficients could therefore not be calculated (*). B , Graphic representation of Pearson's correlation coefficients calculated for each pairwise comparison of all assays.

    Article Snippet: The quality of each amplified product (cRNA or cDNA) was assessed using microfluidic electrophoresis (Figure ) and compared to the amplified aRNA obtained from 2 μg and 100 ng RNA inputs following the standard protocol proposed by Affymetrix (Figure ).

    Techniques: Expressing, Amplification

    Quality of input RNA and targets synthesised from different amounts of input RNA . A , Bioanalyzer electrophoretic profile of the diluted Universal Human Reference RNA used as input for all amplifications. This profile corresponds to a classical and non-degraded human RNA with two fine characteristic peaks corresponding to 18S and 28S RNAs. 8.4 corresponds to the RNA Integrity Number (RIN) and reflects the high quality of this RNA B , electrophoretic profiles of cRNA obtained after one- and two-round Affymetrix amplification using 2 μg, and 100 ng of input RNA respectively or water as negative control. C , D , E , F , electrophoretic profiles of cRNA or cDNA obtained using Ambion ( C ), Arcturus ( D ), Epicentre ( E ) and Nugen ( F ) amplification systems from 250 pg and 500 pg of input RNA, or water as negative control.

    Journal: BMC Genomics

    Article Title: Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

    doi: 10.1186/1471-2164-10-246

    Figure Lengend Snippet: Quality of input RNA and targets synthesised from different amounts of input RNA . A , Bioanalyzer electrophoretic profile of the diluted Universal Human Reference RNA used as input for all amplifications. This profile corresponds to a classical and non-degraded human RNA with two fine characteristic peaks corresponding to 18S and 28S RNAs. 8.4 corresponds to the RNA Integrity Number (RIN) and reflects the high quality of this RNA B , electrophoretic profiles of cRNA obtained after one- and two-round Affymetrix amplification using 2 μg, and 100 ng of input RNA respectively or water as negative control. C , D , E , F , electrophoretic profiles of cRNA or cDNA obtained using Ambion ( C ), Arcturus ( D ), Epicentre ( E ) and Nugen ( F ) amplification systems from 250 pg and 500 pg of input RNA, or water as negative control.

    Article Snippet: The quality of each amplified product (cRNA or cDNA) was assessed using microfluidic electrophoresis (Figure ) and compared to the amplified aRNA obtained from 2 μg and 100 ng RNA inputs following the standard protocol proposed by Affymetrix (Figure ).

    Techniques: Amplification, Negative Control

    Armored RNA Quant as a process control. RNA isolation was performed using 16 20-μm slices from 15 pairs of matched FFPE lung tumor and NAT specimens with 10 10 copies of ARQ spiked at the proteinase K digestion step. qRT-PCR were performed in duplicate

    Journal:

    Article Title: Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues

    doi: 10.2353/jmoldx.2008.070153

    Figure Lengend Snippet: Armored RNA Quant as a process control. RNA isolation was performed using 16 20-μm slices from 15 pairs of matched FFPE lung tumor and NAT specimens with 10 10 copies of ARQ spiked at the proteinase K digestion step. qRT-PCR were performed in duplicate

    Article Snippet: The recovery of miRNA and mRNA species was estimated via quantification of relative expression levels of miR-24, miR-103, miR-191, 18S, and hGUSB. qRT-PCR experiments were performed using 10 ng total RNA input and TaqMan primer/probe sets (TaqMan Gene Expression Assays, Applied Biosystems, Foster City, CA).

    Techniques: Isolation, Formalin-fixed Paraffin-Embedded, Quantitative RT-PCR

    Comparison between FFPE and matching frozen samples. A: Average expression levels for miR-24, -103, and -191 in RNA samples isolated from FFPE and matched frozen breast (three specimens), cervix (three specimens), and gall bladder (two specimens) tissues.

    Journal:

    Article Title: Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues

    doi: 10.2353/jmoldx.2008.070153

    Figure Lengend Snippet: Comparison between FFPE and matching frozen samples. A: Average expression levels for miR-24, -103, and -191 in RNA samples isolated from FFPE and matched frozen breast (three specimens), cervix (three specimens), and gall bladder (two specimens) tissues.

    Article Snippet: The recovery of miRNA and mRNA species was estimated via quantification of relative expression levels of miR-24, miR-103, miR-191, 18S, and hGUSB. qRT-PCR experiments were performed using 10 ng total RNA input and TaqMan primer/probe sets (TaqMan Gene Expression Assays, Applied Biosystems, Foster City, CA).

    Techniques: Formalin-fixed Paraffin-Embedded, Expressing, Isolation

    qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific

    Journal:

    Article Title: Evaluation and Validation of Total RNA Extraction Methods for MicroRNA Expression Analyses in Formalin-Fixed, Paraffin-Embedded Tissues

    doi: 10.2353/jmoldx.2008.070153

    Figure Lengend Snippet: qRT-PCR analysis of RNA samples isolated with the RecoverAll or RNeasy kit. Total RNA was extracted in triplicate from five different FFPE tissue blocks using the indicated method. Each RNA sample was analyzed in duplicate using qRT-PCR assays specific

    Article Snippet: The recovery of miRNA and mRNA species was estimated via quantification of relative expression levels of miR-24, miR-103, miR-191, 18S, and hGUSB. qRT-PCR experiments were performed using 10 ng total RNA input and TaqMan primer/probe sets (TaqMan Gene Expression Assays, Applied Biosystems, Foster City, CA).

    Techniques: Quantitative RT-PCR, Isolation, Formalin-fixed Paraffin-Embedded

    Representation of TFBSs in promoter regions of miRNAs up-regulated in DCs . Depicted are the TFBSs at a motif instance score threshold of at least 6 in the miRNA promoter regions. The scale of the y-axis ranges from 5 to 15 for each subgraph. The legend shows only those TFBSs that are present in all promoter sequences.

    Journal: BMC Genomics

    Article Title: MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    doi: 10.1186/1471-2164-12-330

    Figure Lengend Snippet: Representation of TFBSs in promoter regions of miRNAs up-regulated in DCs . Depicted are the TFBSs at a motif instance score threshold of at least 6 in the miRNA promoter regions. The scale of the y-axis ranges from 5 to 15 for each subgraph. The legend shows only those TFBSs that are present in all promoter sequences.

    Article Snippet: For each miRNA, 4 ng of total RNA was used as input and miRNAs were converted to cDNA using the TaqMan miRNA Reverse Transcription cDNA Synthesis kit and miRNA-specific looped primers from the Early Access miRNA Profiling Kit (both from Applied Biosystems, Foster City, CA) following the manufacturer's recommendations.

    Techniques:

    (A) Degree to which conserved TFBSs in promoter regions of miRNAs up-regulated in DCs are shared among their promoters . (B) The distribution of the number of common TFBS hits per number of common miRNA promoters as in A, for test and random sets of miRNA promoters. (A) Degree to which conserved TFBSs in promoter regions of miRNAs up-regulated in DCs are shared among their promoters. Shown on the x-axis are high-scoring TFBSs filtered at a motif instance score threshold of at least 6 and at a 10 th percentile evolutionary conservation score that occur at least once in the promoters of miRNAs up-regulated in DCs. The y-axis shows the number of promoters that have the TFBS at least once at these thresholds. (B) The distribution of the number of common TFBS hits per number of common miRNA promoters as in A, for test and random sets of miRNA promoters. The values for random are the median values from 1000 random sets of miRNA promoters of the same size and length as those in the DC set. The score is the ratio of the sum of all occurrences of conserved TFBS for the DC set relative to that of the random sets. The p-value is estimated from the number of instances wherein this sum for 1000 random sets of miRNA promoters is greater than or equal to that of the DC set.

    Journal: BMC Genomics

    Article Title: MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    doi: 10.1186/1471-2164-12-330

    Figure Lengend Snippet: (A) Degree to which conserved TFBSs in promoter regions of miRNAs up-regulated in DCs are shared among their promoters . (B) The distribution of the number of common TFBS hits per number of common miRNA promoters as in A, for test and random sets of miRNA promoters. (A) Degree to which conserved TFBSs in promoter regions of miRNAs up-regulated in DCs are shared among their promoters. Shown on the x-axis are high-scoring TFBSs filtered at a motif instance score threshold of at least 6 and at a 10 th percentile evolutionary conservation score that occur at least once in the promoters of miRNAs up-regulated in DCs. The y-axis shows the number of promoters that have the TFBS at least once at these thresholds. (B) The distribution of the number of common TFBS hits per number of common miRNA promoters as in A, for test and random sets of miRNA promoters. The values for random are the median values from 1000 random sets of miRNA promoters of the same size and length as those in the DC set. The score is the ratio of the sum of all occurrences of conserved TFBS for the DC set relative to that of the random sets. The p-value is estimated from the number of instances wherein this sum for 1000 random sets of miRNA promoters is greater than or equal to that of the DC set.

    Article Snippet: For each miRNA, 4 ng of total RNA was used as input and miRNAs were converted to cDNA using the TaqMan miRNA Reverse Transcription cDNA Synthesis kit and miRNA-specific looped primers from the Early Access miRNA Profiling Kit (both from Applied Biosystems, Foster City, CA) following the manufacturer's recommendations.

    Techniques:

    Expression profiles of various miRNAs that are differentially expressed in monocytes and DCs . The upper two charts represent miRNAs over-expressed in monocytes, the middle row of charts represent 3 of the miRNAs over-expressed in DCs, and the lower row of charts represent the 3 miRNAs that are differentially expressed among subsets of DCs. On the Y-axis relative expression is depicted, which is normalized to the expression of hsa -let-7a.

    Journal: BMC Genomics

    Article Title: MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    doi: 10.1186/1471-2164-12-330

    Figure Lengend Snippet: Expression profiles of various miRNAs that are differentially expressed in monocytes and DCs . The upper two charts represent miRNAs over-expressed in monocytes, the middle row of charts represent 3 of the miRNAs over-expressed in DCs, and the lower row of charts represent the 3 miRNAs that are differentially expressed among subsets of DCs. On the Y-axis relative expression is depicted, which is normalized to the expression of hsa -let-7a.

    Article Snippet: For each miRNA, 4 ng of total RNA was used as input and miRNAs were converted to cDNA using the TaqMan miRNA Reverse Transcription cDNA Synthesis kit and miRNA-specific looped primers from the Early Access miRNA Profiling Kit (both from Applied Biosystems, Foster City, CA) following the manufacturer's recommendations.

    Techniques: Expressing

    TFBSs shared among the promoter regions of miRNAs up-regulated in DCs . (A) Shown on the x-axis are the high-scoring TFBSs (i.e. of instance score ≥ 6) that occur at least once in the 2 kb promoters of the miRNA up-regulated in DCs. The y-axis shows the number of promoters that have the TFBS at least once at this threshold. (B) The distribution of the number of common TFBS hits per number of common miRNA promoters as in A, for DCs and random sets of miRNA promoters. The values for random are the median values from 1000 randomly chosen sets of 12 miRNA promoters. The score is the ratio of the sum of all TFBS occurrences across all promoters for the DC set relative to that of the random set. The p-value is the fraction of cases wherein this sum for random sets of miRNA promoters is greater than or equal to that of the DC set.

    Journal: BMC Genomics

    Article Title: MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    doi: 10.1186/1471-2164-12-330

    Figure Lengend Snippet: TFBSs shared among the promoter regions of miRNAs up-regulated in DCs . (A) Shown on the x-axis are the high-scoring TFBSs (i.e. of instance score ≥ 6) that occur at least once in the 2 kb promoters of the miRNA up-regulated in DCs. The y-axis shows the number of promoters that have the TFBS at least once at this threshold. (B) The distribution of the number of common TFBS hits per number of common miRNA promoters as in A, for DCs and random sets of miRNA promoters. The values for random are the median values from 1000 randomly chosen sets of 12 miRNA promoters. The score is the ratio of the sum of all TFBS occurrences across all promoters for the DC set relative to that of the random set. The p-value is the fraction of cases wherein this sum for random sets of miRNA promoters is greater than or equal to that of the DC set.

    Article Snippet: For each miRNA, 4 ng of total RNA was used as input and miRNAs were converted to cDNA using the TaqMan miRNA Reverse Transcription cDNA Synthesis kit and miRNA-specific looped primers from the Early Access miRNA Profiling Kit (both from Applied Biosystems, Foster City, CA) following the manufacturer's recommendations.

    Techniques:

    Distribution and evolutionary conservation of TFBSs in promoter regions of DC-expressed miRNAs . (A) The TFBS motif scores (in blue, y-axis range from 0 to 15 per subgraph) as calculated using Clover and the extent of evolutionary conservation as PhastCons score (in grey, y-axis on the right). (B) Distribution pattern of TFBSs, selected based on various motif score and evolutionary score thresholds, in the promoter region of miRNAs up-regulated in DCs. (C) Comparison of the median conservation scores of the bases in the predicted TFBSs in the promoters of miRNAs that are over-expressed in DCs, with those of randomly chosen sequences of the same length from the same promoters. Boxplots represent the median and interquartile range of the median PhastCons conservation scores. The fold shown is the ratio of the median of the DC conservation scores and the median of the conservation scores of the random sets (n = number of TFBS instances concerned).

    Journal: BMC Genomics

    Article Title: MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

    doi: 10.1186/1471-2164-12-330

    Figure Lengend Snippet: Distribution and evolutionary conservation of TFBSs in promoter regions of DC-expressed miRNAs . (A) The TFBS motif scores (in blue, y-axis range from 0 to 15 per subgraph) as calculated using Clover and the extent of evolutionary conservation as PhastCons score (in grey, y-axis on the right). (B) Distribution pattern of TFBSs, selected based on various motif score and evolutionary score thresholds, in the promoter region of miRNAs up-regulated in DCs. (C) Comparison of the median conservation scores of the bases in the predicted TFBSs in the promoters of miRNAs that are over-expressed in DCs, with those of randomly chosen sequences of the same length from the same promoters. Boxplots represent the median and interquartile range of the median PhastCons conservation scores. The fold shown is the ratio of the median of the DC conservation scores and the median of the conservation scores of the random sets (n = number of TFBS instances concerned).

    Article Snippet: For each miRNA, 4 ng of total RNA was used as input and miRNAs were converted to cDNA using the TaqMan miRNA Reverse Transcription cDNA Synthesis kit and miRNA-specific looped primers from the Early Access miRNA Profiling Kit (both from Applied Biosystems, Foster City, CA) following the manufacturer's recommendations.

    Techniques: