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  • 90
    Thermo Fisher quant it hs reagents
    Quant It Hs Reagents, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it ribogreen rna reagent
    Average recovery of total <t>RNA</t> from kits using manufacturer-provided protocols. Total RNA yield was assessed by <t>RiboGreen</t> Quant-it assay (ng) from 200 μL of plasma. Isolations were performed in triplicate and the average displayed. There is variability
    Quant It Ribogreen Rna Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 586 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it rna assay kit
    Cellular <t>RNA</t> and miR-146a mimics stimulate cfB production in vivo via TLRs signaling RNA (50 μg/mouse) or miR-146a (20 μg/mouse) complexed with <t>lipofectamine</t> was injected i.p. into WT, MyD88 −/− or TLR7 −/− mice with lipofectamine or mutant as the respective control. Twenty hours later, the peritoneal lavage was harvested and cfB protein expression was analyzed by Western blot. The cfB expression levels were quantitated by a NIH ImageJ software and expressed as fold change over Lipofectamine control (A) or no injection group (None, B) in WT mice. A. cfB expression in the peritoneal lavage after RNA injection. n=4 per group, * P
    Quant It Rna Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1083 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it ribogreen rna assay kit
    Weak organic acids reduce total <t>RNA</t> and ribosomal RNA in Candida albicans : Total RNA content and relative rRNA abundance in cell pellets used for RNA deep-sequencing experiment. (A) Total RNA extraction yield quantified by <t>RiboGreen</t> assay. (B) rRNA vs. total RNA ratio estimated by areas under the peaks found on Bioanalyzer electropherograms. n = 4; * P
    Quant It Ribogreen Rna Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1555 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it ribogreen rna assay kits
    Weak organic acids reduce total <t>RNA</t> and ribosomal RNA in Candida albicans : Total RNA content and relative rRNA abundance in cell pellets used for RNA deep-sequencing experiment. (A) Total RNA extraction yield quantified by <t>RiboGreen</t> assay. (B) rRNA vs. total RNA ratio estimated by areas under the peaks found on Bioanalyzer electropherograms. n = 4; * P
    Quant It Ribogreen Rna Assay Kits, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 76/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher qubit rna hs assay kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Qubit Rna Hs Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 2241 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher fluorimetric quant it ribogreen rna assay kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Fluorimetric Quant It Ribogreen Rna Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant ittm ribogreen rna assay kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Quant Ittm Ribogreen Rna Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it ribogreen rna reagent assay kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Quant It Ribogreen Rna Reagent Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 77/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rediplate 96 ribogreen rna quantitation kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Rediplate 96 Ribogreen Rna Quantitation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 95 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant ittm rna broad range kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Quant Ittm Rna Broad Range Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quanti ittm ribogreen rna assay kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Quanti Ittm Ribogreen Rna Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 83/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quan ittm ribo green rna assay kit
    Quantitative and qualitative comparison of <t>RNA</t> recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using <t>Qubit</t> fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Quan Ittm Ribo Green Rna Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 77/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it picogreen dsdna assay kit
    (a) Enhancement of hMSC proliferation using US. MSCs were grown on glass coverslips for 4 days in M2 medium with and without US (14 kPa; 3 min; 1, 2, or 4 times/day). Cells were fixed and stained for Ki67 (mitosis marker) and Hoechst (nuclear marker). Five pictures were randomly taken on three coverslips per condition ( n = 15), and Ki67 and Hoechst positive cells were counted using ImageJ ™ . Data were expressed as percent Ki67 positive. (b) hMSC proliferation is increased with US application. hMSC-seeded scaffolds were cultured in CDM for 14 days and in M3 media for another 7 days in the US-assisted bioreactor according to the culture conditions outlined in Table 2 . <t>dsDNA</t> was assayed by <t>Picogreen</t> assay. Data were presented as average ± standard deviation ( n = 5–8 constructs). Statistically significant data were accounted with respect to respective control and shown as * p
    Quant It Picogreen Dsdna Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 10071 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it dsdna hs kit
    RSV triggers the release of NETs coated with NE and MPO. ( A – D ) Neutrophils (1 × 10 5 /300 μL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 in 8-chamber culture slides. Afterwards, cells were fixed with 4% PFA and stained with (A) Hoechst 33342 (1:2000), anti-RSV fusion protein (1:1000) followed by anti-mouse PE antibody (1:500); (B) Hoechst 33342 (1:2000), anti-elastase (NE; 1:1000) followed by anti-rabbit Cy3 antibody (1:500); (C) Hoechst 33342 (1:2000), anti-myeloperoxidase PE (MPO, 1:1000) antibody; (D) Hoechst 33342 (1:2000). Overlay of the fluorescence images are shown in the penultimate panels. Arrowheads indicate the presence of extracellular <t>DNA</t> lattices co-localized with RSV F protein, NE and MPO, respectively. NETs were magnified four times and are numbered (1, 2, 3 and 4) on the right side. Images are representative of 3 independent experiments. Images were taken in a Zeiss LSM 5 Exciter microscope. Scale bars = 5 μm. (E) Neutrophils (1 × 10 6 /mL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 . Afterwards, NETs were quantified in culture supernatants using Quant-iT <t>dsDNA</t> HS kit (Invitrogen). Data are representative of 2 independent experiments performed in triplicates and represent mean ± SEM. Data were analyzed with Mann Whitney test. *p
    Quant It Dsdna Hs Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 269 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it assay kit
    RSV triggers the release of NETs coated with NE and MPO. ( A – D ) Neutrophils (1 × 10 5 /300 μL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 in 8-chamber culture slides. Afterwards, cells were fixed with 4% PFA and stained with (A) Hoechst 33342 (1:2000), anti-RSV fusion protein (1:1000) followed by anti-mouse PE antibody (1:500); (B) Hoechst 33342 (1:2000), anti-elastase (NE; 1:1000) followed by anti-rabbit Cy3 antibody (1:500); (C) Hoechst 33342 (1:2000), anti-myeloperoxidase PE (MPO, 1:1000) antibody; (D) Hoechst 33342 (1:2000). Overlay of the fluorescence images are shown in the penultimate panels. Arrowheads indicate the presence of extracellular <t>DNA</t> lattices co-localized with RSV F protein, NE and MPO, respectively. NETs were magnified four times and are numbered (1, 2, 3 and 4) on the right side. Images are representative of 3 independent experiments. Images were taken in a Zeiss LSM 5 Exciter microscope. Scale bars = 5 μm. (E) Neutrophils (1 × 10 6 /mL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 . Afterwards, NETs were quantified in culture supernatants using Quant-iT <t>dsDNA</t> HS kit (Invitrogen). Data are representative of 2 independent experiments performed in triplicates and represent mean ± SEM. Data were analyzed with Mann Whitney test. *p
    Quant It Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 216 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it picogreen dsdna reagent
    HuR is required for short-term proliferation of PDA cells Relative proliferation of DOX-inducible MIA PaCa-2 cell lines treated with 0 or 2 μg/ml DOX for the indicated time points, as determined by measurement of <t>dsDNA</t> content by <t>PicoGreen</t> staining. Each data point represents the mean of 5 independent experiments ± standard error of the mean (SEM). * = p
    Quant It Picogreen Dsdna Reagent, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1939 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher oligreen single stranded dna ssdna quantitation kit
    Long <t>ssDNA</t> target sequences (black) are digested by S1 nuclease, leaving intact only those regions bound to the PNA probe (red). CPs (blue) added directly to the resulting solutions can only associate with the remaining <t>PNA-FL/DNA</t> duplex. Any PNA/DNA mismatches will result in complete DNA digestion; therefore, energy transfer from the CP occurs only for the perfect PNA-FL/DNA complement.
    Oligreen Single Stranded Dna Ssdna Quantitation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ribogreen quantification
    Long <t>ssDNA</t> target sequences (black) are digested by S1 nuclease, leaving intact only those regions bound to the PNA probe (red). CPs (blue) added directly to the resulting solutions can only associate with the remaining <t>PNA-FL/DNA</t> duplex. Any PNA/DNA mismatches will result in complete DNA digestion; therefore, energy transfer from the CP occurs only for the perfect PNA-FL/DNA complement.
    Ribogreen Quantification, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher quant it hs dsdna assay
    Long <t>ssDNA</t> target sequences (black) are digested by S1 nuclease, leaving intact only those regions bound to the PNA probe (red). CPs (blue) added directly to the resulting solutions can only associate with the remaining <t>PNA-FL/DNA</t> duplex. Any PNA/DNA mismatches will result in complete DNA digestion; therefore, energy transfer from the CP occurs only for the perfect PNA-FL/DNA complement.
    Quant It Hs Dsdna Assay, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher qubit dsdna hs assay kit
    Storage condition of purified ChIP DNA is important. Purified ChIP DNA was adjusted to a concentration of 1 ng/μL ( a ) or 0.1 ng/μL ( b ), aliquoted into 4 different types of microcentrifuge tubes in 15 μL volume, and stored at −20 °C. DNA was quantified using <t>Qubit</t> <t>dsDNA</t> High Sensitivity assay at the indicated time points and expressed as a percentage of the amount measured at day 0. Three independent DNA samples were used in the experiment and DNA concentration from five tubes were measured at each time point. MaxyClear, Axygen® 1.7 mL MaxyClear Snaplock Microcentrifuge Tube; LoBind, Eppendorf DNA LoBind Snap Cap PCR Tube; Siliconized, Fisherbrand™ Siliconized Low-Retention Microcentrifuge Tube; Premium, Fisherbrand™ Premium Microcentrifuge Tube
    Qubit Dsdna Hs Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 10723 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher qubit double stranded dna dsdna br assay kit
    Comparison of <t>DNA</t> extraction methods. (A) Experimental design. Human feces, pig feces, and hospital sewage were extracted using seven different DNA extraction methods ( Table 1 ): InnuPure C16, MagNA Pure LC DNA isolation kit III, Easy-DNA gDNA purification kit, MP FastDNA Spin kit, PowerSoil DNA isolation kit, QIAamp DNA stool minikit, and QIAamp DNA stool minikit plus bead beating (for details, see Materials and Methods). DNA concentration, purity, and stability were examined, and microbial community composition was determined using 16S rRNA gene profiling and metagenomics (selected samples). (B) DNA from each method was dissolved in 100 µl solution, and DNA concentrations were determined using <t>Qubit</t> <t>dsDNA</t> BR assay kit measurements. Values represent averages from duplicate or triplicate DNA extractions (see also Table S1A in the supplemental material). (C) Ecological richness (Chao 1) and diversity (Shannon index) were determined based on contingency tables from 16S rRNA gene profiling and metagenomic sequencing data at OTU and species levels, respectively (see also Table S1B ).
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    Comparison of <t>DNA</t> extraction methods. (A) Experimental design. Human feces, pig feces, and hospital sewage were extracted using seven different DNA extraction methods ( Table 1 ): InnuPure C16, MagNA Pure LC DNA isolation kit III, Easy-DNA gDNA purification kit, MP FastDNA Spin kit, PowerSoil DNA isolation kit, QIAamp DNA stool minikit, and QIAamp DNA stool minikit plus bead beating (for details, see Materials and Methods). DNA concentration, purity, and stability were examined, and microbial community composition was determined using 16S rRNA gene profiling and metagenomics (selected samples). (B) DNA from each method was dissolved in 100 µl solution, and DNA concentrations were determined using <t>Qubit</t> <t>dsDNA</t> BR assay kit measurements. Values represent averages from duplicate or triplicate DNA extractions (see also Table S1A in the supplemental material). (C) Ecological richness (Chao 1) and diversity (Shannon index) were determined based on contingency tables from 16S rRNA gene profiling and metagenomic sequencing data at OTU and species levels, respectively (see also Table S1B ).
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    Comparison of <t>DNA</t> extraction methods. (A) Experimental design. Human feces, pig feces, and hospital sewage were extracted using seven different DNA extraction methods ( Table 1 ): InnuPure C16, MagNA Pure LC DNA isolation kit III, Easy-DNA gDNA purification kit, MP FastDNA Spin kit, PowerSoil DNA isolation kit, QIAamp DNA stool minikit, and QIAamp DNA stool minikit plus bead beating (for details, see Materials and Methods). DNA concentration, purity, and stability were examined, and microbial community composition was determined using 16S rRNA gene profiling and metagenomics (selected samples). (B) DNA from each method was dissolved in 100 µl solution, and DNA concentrations were determined using <t>Qubit</t> <t>dsDNA</t> BR assay kit measurements. Values represent averages from duplicate or triplicate DNA extractions (see also Table S1A in the supplemental material). (C) Ecological richness (Chao 1) and diversity (Shannon index) were determined based on contingency tables from 16S rRNA gene profiling and metagenomic sequencing data at OTU and species levels, respectively (see also Table S1B ).
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    Fig. 2. During in vitro differentiation of monolayers of ES cells, the expression of mesodermal differentiation marker genes is impaired in cells lacking SRF. ( A ) Expression of differentiation markers in monolayer ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal (semi-quantitative RT–PCR analysis). The ES lines used were E14.1 ( Srf +/+ ; lanes 1–5), 226 ( Srf –/+ ; lanes 6–10) and 226-100 ( Srf –/– ; lanes 11–15). <t>RNA</t> expression levels of the genes indicated on the right of the figure were determined by semi-quantitative RT–PCR studies, covering a differentiation period of 14 days, as indicated. Lane 16 is a negative RT–PCR control lane lacking <t>cDNA</t> in the reaction. Lane 17 is a positive control for RT–PCR amplification of each gene. ( B ) Relative expression levels of differentiation markers in monolayers of ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal plus simultaneous addition of DMSO (quantitative RT–PCR analysis). ES lines used were 226-99 ( Srf –/+ ; left panel) and 226-100 ( Srf –/– ; right panel). Expression was followed for the indicated periods of differentiation (days).
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    Fig. 2. During in vitro differentiation of monolayers of ES cells, the expression of mesodermal differentiation marker genes is impaired in cells lacking SRF. ( A ) Expression of differentiation markers in monolayer ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal (semi-quantitative RT–PCR analysis). The ES lines used were E14.1 ( Srf +/+ ; lanes 1–5), 226 ( Srf –/+ ; lanes 6–10) and 226-100 ( Srf –/– ; lanes 11–15). <t>RNA</t> expression levels of the genes indicated on the right of the figure were determined by semi-quantitative RT–PCR studies, covering a differentiation period of 14 days, as indicated. Lane 16 is a negative RT–PCR control lane lacking <t>cDNA</t> in the reaction. Lane 17 is a positive control for RT–PCR amplification of each gene. ( B ) Relative expression levels of differentiation markers in monolayers of ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal plus simultaneous addition of DMSO (quantitative RT–PCR analysis). ES lines used were 226-99 ( Srf –/+ ; left panel) and 226-100 ( Srf –/– ; right panel). Expression was followed for the indicated periods of differentiation (days).
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    MiR-153 Overexpression repressed the p-SMAD2, p-SMAD3, EGFR and IGFBP-3 expression. The MG-63 was treated in serum-free medium in the presence and absence of TGF-β (50 ng/ml), scramble, or <t>miRNA-153</t> mimic for 24 h. (A) Expression of p-SMAD2, t-SMAD2, p-SMAD3 and t-SMAD3 was detected using western blotting. GAPDH was used as a loading control. (B) Expression of EGFR and IGFBP-3 was detected using western blotting. GAPDH was used as a loading control. (C) The mRNA expression of EGFR was detected using <t>qRT-PCR.</t> The expression of MMP9 was normalized to GAPDH. (D) The mRNA Expression of IGFBP-3 was detected using qRT-PCR. The expression of EGFR was normalized to GAPDH.
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    MiR-153 Overexpression repressed the p-SMAD2, p-SMAD3, EGFR and IGFBP-3 expression. The MG-63 was treated in serum-free medium in the presence and absence of TGF-β (50 ng/ml), scramble, or <t>miRNA-153</t> mimic for 24 h. (A) Expression of p-SMAD2, t-SMAD2, p-SMAD3 and t-SMAD3 was detected using western blotting. GAPDH was used as a loading control. (B) Expression of EGFR and IGFBP-3 was detected using western blotting. GAPDH was used as a loading control. (C) The mRNA expression of EGFR was detected using <t>qRT-PCR.</t> The expression of MMP9 was normalized to GAPDH. (D) The mRNA Expression of IGFBP-3 was detected using qRT-PCR. The expression of EGFR was normalized to GAPDH.
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    A . FFPE samples are usually used for hematoxylin and eosin (H E) and/or immunohistochemistry (IHC) stains. To overcome hurdles associated with gene expression analyses of tissue in FFPE samples, we show that the mH can increase the purification of high-quality <t>RNA</t> for downstream applications. B . H E staining of the four xenograft FFPE samples (BxPC3 [B] and FG [F]) or patient (MDA-AC2 [M]) xenografts (S = subcutaneous, O = orthotopic). C . Nucleic acid (RNA) concentrations (ng/uL) for the four FFPE samples of PDAC using either the standard Qiagen FFPE RNA extraction (-mH) or our mH-modified protocol (+mH). Measurements were made using Nanodrop, <t>Qubit</t> and Experion Bioanalyzer assays. D . Average +/- standard error mean (SEM) RNA 260/280 ratios for the same samples described in (A). *, **, *** indicate student t-test p values
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    A . FFPE samples are usually used for hematoxylin and eosin (H E) and/or immunohistochemistry (IHC) stains. To overcome hurdles associated with gene expression analyses of tissue in FFPE samples, we show that the mH can increase the purification of high-quality <t>RNA</t> for downstream applications. B . H E staining of the four xenograft FFPE samples (BxPC3 [B] and FG [F]) or patient (MDA-AC2 [M]) xenografts (S = subcutaneous, O = orthotopic). C . Nucleic acid (RNA) concentrations (ng/uL) for the four FFPE samples of PDAC using either the standard Qiagen FFPE RNA extraction (-mH) or our mH-modified protocol (+mH). Measurements were made using Nanodrop, <t>Qubit</t> and Experion Bioanalyzer assays. D . Average +/- standard error mean (SEM) RNA 260/280 ratios for the same samples described in (A). *, **, *** indicate student t-test p values
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    Image Search Results


    Average recovery of total RNA from kits using manufacturer-provided protocols. Total RNA yield was assessed by RiboGreen Quant-it assay (ng) from 200 μL of plasma. Isolations were performed in triplicate and the average displayed. There is variability

    Journal: RNA

    Article Title: Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

    doi: 10.1261/rna.036863.112

    Figure Lengend Snippet: Average recovery of total RNA from kits using manufacturer-provided protocols. Total RNA yield was assessed by RiboGreen Quant-it assay (ng) from 200 μL of plasma. Isolations were performed in triplicate and the average displayed. There is variability

    Article Snippet: Quantification of the total RNA yield was determined by Quant-iT RiboGreen RNA reagent (Invitrogen).

    Techniques:

    Cellular RNA and miR-146a mimics stimulate cfB production in vivo via TLRs signaling RNA (50 μg/mouse) or miR-146a (20 μg/mouse) complexed with lipofectamine was injected i.p. into WT, MyD88 −/− or TLR7 −/− mice with lipofectamine or mutant as the respective control. Twenty hours later, the peritoneal lavage was harvested and cfB protein expression was analyzed by Western blot. The cfB expression levels were quantitated by a NIH ImageJ software and expressed as fold change over Lipofectamine control (A) or no injection group (None, B) in WT mice. A. cfB expression in the peritoneal lavage after RNA injection. n=4 per group, * P

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: Splenic RNA and microRNA mimics promote complement factor B production and the alternative pathway activation via innate immune signaling

    doi: 10.4049/jimmunol.1502106

    Figure Lengend Snippet: Cellular RNA and miR-146a mimics stimulate cfB production in vivo via TLRs signaling RNA (50 μg/mouse) or miR-146a (20 μg/mouse) complexed with lipofectamine was injected i.p. into WT, MyD88 −/− or TLR7 −/− mice with lipofectamine or mutant as the respective control. Twenty hours later, the peritoneal lavage was harvested and cfB protein expression was analyzed by Western blot. The cfB expression levels were quantitated by a NIH ImageJ software and expressed as fold change over Lipofectamine control (A) or no injection group (None, B) in WT mice. A. cfB expression in the peritoneal lavage after RNA injection. n=4 per group, * P

    Article Snippet: Bovine pancreas RNase A, lipofectamine 3000, TRIzol LS, SYTO RNASelect Green fluorescent cell stain, and Quant-iT™ RNA assay kit were from Invitrogen Life Technology (Carlsbad, CA).

    Techniques: In Vivo, Injection, Mouse Assay, Mutagenesis, Expressing, Western Blot, Software

    Splenic RNA-induced cfB production was mediated via MyD88 signaling in macrophages A. Complement gene expression in macrophages treated with splenic RNA. Mouse macrophages were treated with lipofectamine alone or splenic RNA (10 μg/ml) complexed with lipofectamine. Six hours later, C3, C4, C5, cfB mRNA was analyzed by qRT-PCR. *** P

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: Splenic RNA and microRNA mimics promote complement factor B production and the alternative pathway activation via innate immune signaling

    doi: 10.4049/jimmunol.1502106

    Figure Lengend Snippet: Splenic RNA-induced cfB production was mediated via MyD88 signaling in macrophages A. Complement gene expression in macrophages treated with splenic RNA. Mouse macrophages were treated with lipofectamine alone or splenic RNA (10 μg/ml) complexed with lipofectamine. Six hours later, C3, C4, C5, cfB mRNA was analyzed by qRT-PCR. *** P

    Article Snippet: Bovine pancreas RNase A, lipofectamine 3000, TRIzol LS, SYTO RNASelect Green fluorescent cell stain, and Quant-iT™ RNA assay kit were from Invitrogen Life Technology (Carlsbad, CA).

    Techniques: Expressing, Quantitative RT-PCR

    Weak organic acids reduce total RNA and ribosomal RNA in Candida albicans : Total RNA content and relative rRNA abundance in cell pellets used for RNA deep-sequencing experiment. (A) Total RNA extraction yield quantified by RiboGreen assay. (B) rRNA vs. total RNA ratio estimated by areas under the peaks found on Bioanalyzer electropherograms. n = 4; * P

    Journal: G3: Genes|Genomes|Genetics

    Article Title: The Transcriptional Stress Response of Candida albicans to Weak Organic Acids

    doi: 10.1534/g3.114.015941

    Figure Lengend Snippet: Weak organic acids reduce total RNA and ribosomal RNA in Candida albicans : Total RNA content and relative rRNA abundance in cell pellets used for RNA deep-sequencing experiment. (A) Total RNA extraction yield quantified by RiboGreen assay. (B) rRNA vs. total RNA ratio estimated by areas under the peaks found on Bioanalyzer electropherograms. n = 4; * P

    Article Snippet: Total RNA yield was quantified with the Quant-iT RiboGreen RNA Assay Kit (Invitrogen) and RNA quality assessed on the 2100 Bioanalyzer (Agilent).

    Techniques: Sequencing, RNA Extraction

    Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.

    Journal: Scientific Reports

    Article Title: Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

    doi: 10.1038/srep41114

    Figure Lengend Snippet: Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.

    Article Snippet: RNA and DNA quantity and quality assessment Where indicated, RNA or DNA was quantified using Qubit RNA HS Assay Kit and Qubit dsDNA HS Assay Kit (Life Technologies), respectively, on the Qubit 2.0 Fluorometer (Life Technologies).

    Techniques: Isolation, Quantitation Assay, RNA HS Assay, Software, Fluorescence

    (a) Enhancement of hMSC proliferation using US. MSCs were grown on glass coverslips for 4 days in M2 medium with and without US (14 kPa; 3 min; 1, 2, or 4 times/day). Cells were fixed and stained for Ki67 (mitosis marker) and Hoechst (nuclear marker). Five pictures were randomly taken on three coverslips per condition ( n = 15), and Ki67 and Hoechst positive cells were counted using ImageJ ™ . Data were expressed as percent Ki67 positive. (b) hMSC proliferation is increased with US application. hMSC-seeded scaffolds were cultured in CDM for 14 days and in M3 media for another 7 days in the US-assisted bioreactor according to the culture conditions outlined in Table 2 . dsDNA was assayed by Picogreen assay. Data were presented as average ± standard deviation ( n = 5–8 constructs). Statistically significant data were accounted with respect to respective control and shown as * p

    Journal: Journal of Tissue Engineering

    Article Title: Growth factor and ultrasound-assisted bioreactor synergism for human mesenchymal stem cell chondrogenesis

    doi: 10.1177/2041731414566529

    Figure Lengend Snippet: (a) Enhancement of hMSC proliferation using US. MSCs were grown on glass coverslips for 4 days in M2 medium with and without US (14 kPa; 3 min; 1, 2, or 4 times/day). Cells were fixed and stained for Ki67 (mitosis marker) and Hoechst (nuclear marker). Five pictures were randomly taken on three coverslips per condition ( n = 15), and Ki67 and Hoechst positive cells were counted using ImageJ ™ . Data were expressed as percent Ki67 positive. (b) hMSC proliferation is increased with US application. hMSC-seeded scaffolds were cultured in CDM for 14 days and in M3 media for another 7 days in the US-assisted bioreactor according to the culture conditions outlined in Table 2 . dsDNA was assayed by Picogreen assay. Data were presented as average ± standard deviation ( n = 5–8 constructs). Statistically significant data were accounted with respect to respective control and shown as * p

    Article Snippet: Double-stranded DNA (dsDNA) was measured using Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) according to manufacturer’s instructions.

    Techniques: Staining, Marker, Cell Culture, Picogreen Assay, Standard Deviation, Construct

    RSV triggers the release of NETs coated with NE and MPO. ( A – D ) Neutrophils (1 × 10 5 /300 μL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 in 8-chamber culture slides. Afterwards, cells were fixed with 4% PFA and stained with (A) Hoechst 33342 (1:2000), anti-RSV fusion protein (1:1000) followed by anti-mouse PE antibody (1:500); (B) Hoechst 33342 (1:2000), anti-elastase (NE; 1:1000) followed by anti-rabbit Cy3 antibody (1:500); (C) Hoechst 33342 (1:2000), anti-myeloperoxidase PE (MPO, 1:1000) antibody; (D) Hoechst 33342 (1:2000). Overlay of the fluorescence images are shown in the penultimate panels. Arrowheads indicate the presence of extracellular DNA lattices co-localized with RSV F protein, NE and MPO, respectively. NETs were magnified four times and are numbered (1, 2, 3 and 4) on the right side. Images are representative of 3 independent experiments. Images were taken in a Zeiss LSM 5 Exciter microscope. Scale bars = 5 μm. (E) Neutrophils (1 × 10 6 /mL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 . Afterwards, NETs were quantified in culture supernatants using Quant-iT dsDNA HS kit (Invitrogen). Data are representative of 2 independent experiments performed in triplicates and represent mean ± SEM. Data were analyzed with Mann Whitney test. *p

    Journal: Scientific Reports

    Article Title: Respiratory Syncytial Virus induces the classical ROS-dependent NETosis through PAD-4 and necroptosis pathways activation

    doi: 10.1038/s41598-018-32576-y

    Figure Lengend Snippet: RSV triggers the release of NETs coated with NE and MPO. ( A – D ) Neutrophils (1 × 10 5 /300 μL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 in 8-chamber culture slides. Afterwards, cells were fixed with 4% PFA and stained with (A) Hoechst 33342 (1:2000), anti-RSV fusion protein (1:1000) followed by anti-mouse PE antibody (1:500); (B) Hoechst 33342 (1:2000), anti-elastase (NE; 1:1000) followed by anti-rabbit Cy3 antibody (1:500); (C) Hoechst 33342 (1:2000), anti-myeloperoxidase PE (MPO, 1:1000) antibody; (D) Hoechst 33342 (1:2000). Overlay of the fluorescence images are shown in the penultimate panels. Arrowheads indicate the presence of extracellular DNA lattices co-localized with RSV F protein, NE and MPO, respectively. NETs were magnified four times and are numbered (1, 2, 3 and 4) on the right side. Images are representative of 3 independent experiments. Images were taken in a Zeiss LSM 5 Exciter microscope. Scale bars = 5 μm. (E) Neutrophils (1 × 10 6 /mL) were stimulated with active RSV (10 4 PFU/mL) or UV-inactivated RSV (10 4 PFU/mL) for 180 min at 37 °C with 5% CO 2 . Afterwards, NETs were quantified in culture supernatants using Quant-iT dsDNA HS kit (Invitrogen). Data are representative of 2 independent experiments performed in triplicates and represent mean ± SEM. Data were analyzed with Mann Whitney test. *p

    Article Snippet: After the stimulation period, culture supernatant was collected and extracellular DNA was measured using the dsDNA Picogreen kit or Quant-iT dsDNA HS kit (both from Invitrogen), following manufacturer’s instructions and obtaining similar results.

    Techniques: Staining, Fluorescence, Microscopy, MANN-WHITNEY

    HuR is required for short-term proliferation of PDA cells Relative proliferation of DOX-inducible MIA PaCa-2 cell lines treated with 0 or 2 μg/ml DOX for the indicated time points, as determined by measurement of dsDNA content by PicoGreen staining. Each data point represents the mean of 5 independent experiments ± standard error of the mean (SEM). * = p

    Journal: Oncotarget

    Article Title: Targeting the mRNA-binding protein HuR impairs malignant characteristics of pancreatic ductal adenocarcinoma cells

    doi:

    Figure Lengend Snippet: HuR is required for short-term proliferation of PDA cells Relative proliferation of DOX-inducible MIA PaCa-2 cell lines treated with 0 or 2 μg/ml DOX for the indicated time points, as determined by measurement of dsDNA content by PicoGreen staining. Each data point represents the mean of 5 independent experiments ± standard error of the mean (SEM). * = p

    Article Snippet: Double-stranded DNA (dsDNA) was stained by Quant-iT PicoGreen dsDNA reagent (Life Technologies, cat. #P7581), and fluorescence intensity was measured by a microplate reader (Tecan, part #F129015) using excitation wavelength of 485 nm and emission wavelength of 535 nm.

    Techniques: Staining

    Long ssDNA target sequences (black) are digested by S1 nuclease, leaving intact only those regions bound to the PNA probe (red). CPs (blue) added directly to the resulting solutions can only associate with the remaining PNA-FL/DNA duplex. Any PNA/DNA mismatches will result in complete DNA digestion; therefore, energy transfer from the CP occurs only for the perfect PNA-FL/DNA complement.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: SNP detection using peptide nucleic acid probes and conjugated polymers: Applications in neurodegenerative disease identification

    doi: 10.1073/pnas.0407578101

    Figure Lengend Snippet: Long ssDNA target sequences (black) are digested by S1 nuclease, leaving intact only those regions bound to the PNA probe (red). CPs (blue) added directly to the resulting solutions can only associate with the remaining PNA-FL/DNA duplex. Any PNA/DNA mismatches will result in complete DNA digestion; therefore, energy transfer from the CP occurs only for the perfect PNA-FL/DNA complement.

    Article Snippet: Concentrations of the larger DNA sequences obtained by PCR and gel purification were measured by fluorescence using an OliGreen single stranded DNA (ssDNA) Quantitation kit (Molecular Probes).

    Techniques:

    Cationic CPs (blue) have the ability to associate nonspecifically along any region of a targeted ssDNA sequence (black). ( A ) Association of a short DNA target with the CP. ( B ) The probability of CP association along a longer DNA target. CPs complexed at distances greater than R o from the FL acceptor will be less efficient donors to the PNA-FL probe (red and green).

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: SNP detection using peptide nucleic acid probes and conjugated polymers: Applications in neurodegenerative disease identification

    doi: 10.1073/pnas.0407578101

    Figure Lengend Snippet: Cationic CPs (blue) have the ability to associate nonspecifically along any region of a targeted ssDNA sequence (black). ( A ) Association of a short DNA target with the CP. ( B ) The probability of CP association along a longer DNA target. CPs complexed at distances greater than R o from the FL acceptor will be less efficient donors to the PNA-FL probe (red and green).

    Article Snippet: Concentrations of the larger DNA sequences obtained by PCR and gel purification were measured by fluorescence using an OliGreen single stranded DNA (ssDNA) Quantitation kit (Molecular Probes).

    Techniques: Sequencing

    Fluorescence of PNA-FL annealed to complementary 28 (black, D0) and 249 (red, WT) base ssDNA targets ([PNA/ssDNA] = 1 × 10 -8 M) upon addition and excitation (λ ex = 380 nm) of the CP ([CP] = 2 × 10 -7 M) in 30 mM potassium phosphate buffer, pH 7.4. The noncomplementary (28 base, D3) DNA target is shown in blue for reference. The arrow indicates the drop in the relative FL-to-CP emission peak ratio between the two different DNA target lengths.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: SNP detection using peptide nucleic acid probes and conjugated polymers: Applications in neurodegenerative disease identification

    doi: 10.1073/pnas.0407578101

    Figure Lengend Snippet: Fluorescence of PNA-FL annealed to complementary 28 (black, D0) and 249 (red, WT) base ssDNA targets ([PNA/ssDNA] = 1 × 10 -8 M) upon addition and excitation (λ ex = 380 nm) of the CP ([CP] = 2 × 10 -7 M) in 30 mM potassium phosphate buffer, pH 7.4. The noncomplementary (28 base, D3) DNA target is shown in blue for reference. The arrow indicates the drop in the relative FL-to-CP emission peak ratio between the two different DNA target lengths.

    Article Snippet: Concentrations of the larger DNA sequences obtained by PCR and gel purification were measured by fluorescence using an OliGreen single stranded DNA (ssDNA) Quantitation kit (Molecular Probes).

    Techniques: Fluorescence

    Storage condition of purified ChIP DNA is important. Purified ChIP DNA was adjusted to a concentration of 1 ng/μL ( a ) or 0.1 ng/μL ( b ), aliquoted into 4 different types of microcentrifuge tubes in 15 μL volume, and stored at −20 °C. DNA was quantified using Qubit dsDNA High Sensitivity assay at the indicated time points and expressed as a percentage of the amount measured at day 0. Three independent DNA samples were used in the experiment and DNA concentration from five tubes were measured at each time point. MaxyClear, Axygen® 1.7 mL MaxyClear Snaplock Microcentrifuge Tube; LoBind, Eppendorf DNA LoBind Snap Cap PCR Tube; Siliconized, Fisherbrand™ Siliconized Low-Retention Microcentrifuge Tube; Premium, Fisherbrand™ Premium Microcentrifuge Tube

    Journal: BMC Genomics

    Article Title: Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application

    doi: 10.1186/s12864-017-4371-5

    Figure Lengend Snippet: Storage condition of purified ChIP DNA is important. Purified ChIP DNA was adjusted to a concentration of 1 ng/μL ( a ) or 0.1 ng/μL ( b ), aliquoted into 4 different types of microcentrifuge tubes in 15 μL volume, and stored at −20 °C. DNA was quantified using Qubit dsDNA High Sensitivity assay at the indicated time points and expressed as a percentage of the amount measured at day 0. Three independent DNA samples were used in the experiment and DNA concentration from five tubes were measured at each time point. MaxyClear, Axygen® 1.7 mL MaxyClear Snaplock Microcentrifuge Tube; LoBind, Eppendorf DNA LoBind Snap Cap PCR Tube; Siliconized, Fisherbrand™ Siliconized Low-Retention Microcentrifuge Tube; Premium, Fisherbrand™ Premium Microcentrifuge Tube

    Article Snippet: After treatment with RNase A and proteinase K, DNA was purified by Qiagen MinElute PCR Purification Kit (Cat. # 28006, Valencia, CA) and quantified using Qubit dsDNA High Sensitivity assay (Invitrogen, Q32851).

    Techniques: Purification, Chromatin Immunoprecipitation, Concentration Assay, Sensitive Assay, Polymerase Chain Reaction

    Comparison of DNA extraction methods. (A) Experimental design. Human feces, pig feces, and hospital sewage were extracted using seven different DNA extraction methods ( Table 1 ): InnuPure C16, MagNA Pure LC DNA isolation kit III, Easy-DNA gDNA purification kit, MP FastDNA Spin kit, PowerSoil DNA isolation kit, QIAamp DNA stool minikit, and QIAamp DNA stool minikit plus bead beating (for details, see Materials and Methods). DNA concentration, purity, and stability were examined, and microbial community composition was determined using 16S rRNA gene profiling and metagenomics (selected samples). (B) DNA from each method was dissolved in 100 µl solution, and DNA concentrations were determined using Qubit dsDNA BR assay kit measurements. Values represent averages from duplicate or triplicate DNA extractions (see also Table S1A in the supplemental material). (C) Ecological richness (Chao 1) and diversity (Shannon index) were determined based on contingency tables from 16S rRNA gene profiling and metagenomic sequencing data at OTU and species levels, respectively (see also Table S1B ).

    Journal: mSystems

    Article Title: Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

    doi: 10.1128/mSystems.00095-16

    Figure Lengend Snippet: Comparison of DNA extraction methods. (A) Experimental design. Human feces, pig feces, and hospital sewage were extracted using seven different DNA extraction methods ( Table 1 ): InnuPure C16, MagNA Pure LC DNA isolation kit III, Easy-DNA gDNA purification kit, MP FastDNA Spin kit, PowerSoil DNA isolation kit, QIAamp DNA stool minikit, and QIAamp DNA stool minikit plus bead beating (for details, see Materials and Methods). DNA concentration, purity, and stability were examined, and microbial community composition was determined using 16S rRNA gene profiling and metagenomics (selected samples). (B) DNA from each method was dissolved in 100 µl solution, and DNA concentrations were determined using Qubit dsDNA BR assay kit measurements. Values represent averages from duplicate or triplicate DNA extractions (see also Table S1A in the supplemental material). (C) Ecological richness (Chao 1) and diversity (Shannon index) were determined based on contingency tables from 16S rRNA gene profiling and metagenomic sequencing data at OTU and species levels, respectively (see also Table S1B ).

    Article Snippet: DNA concentrations were measured using the Qubit double-stranded DNA (dsDNA) BR assay kit on a Qubit 2.0 fluorometer (Invitrogen, Carlsbad, CA).

    Techniques: DNA Extraction, Purification, Concentration Assay, Sequencing

    Fig. 2. During in vitro differentiation of monolayers of ES cells, the expression of mesodermal differentiation marker genes is impaired in cells lacking SRF. ( A ) Expression of differentiation markers in monolayer ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal (semi-quantitative RT–PCR analysis). The ES lines used were E14.1 ( Srf +/+ ; lanes 1–5), 226 ( Srf –/+ ; lanes 6–10) and 226-100 ( Srf –/– ; lanes 11–15). RNA expression levels of the genes indicated on the right of the figure were determined by semi-quantitative RT–PCR studies, covering a differentiation period of 14 days, as indicated. Lane 16 is a negative RT–PCR control lane lacking cDNA in the reaction. Lane 17 is a positive control for RT–PCR amplification of each gene. ( B ) Relative expression levels of differentiation markers in monolayers of ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal plus simultaneous addition of DMSO (quantitative RT–PCR analysis). ES lines used were 226-99 ( Srf –/+ ; left panel) and 226-100 ( Srf –/– ; right panel). Expression was followed for the indicated periods of differentiation (days).

    Journal: The EMBO Journal

    Article Title: Srf–/– ES cells display non-cell-autonomous impairment in mesodermal differentiation

    doi: 10.1093/emboj/19.21.5835

    Figure Lengend Snippet: Fig. 2. During in vitro differentiation of monolayers of ES cells, the expression of mesodermal differentiation marker genes is impaired in cells lacking SRF. ( A ) Expression of differentiation markers in monolayer ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal (semi-quantitative RT–PCR analysis). The ES lines used were E14.1 ( Srf +/+ ; lanes 1–5), 226 ( Srf –/+ ; lanes 6–10) and 226-100 ( Srf –/– ; lanes 11–15). RNA expression levels of the genes indicated on the right of the figure were determined by semi-quantitative RT–PCR studies, covering a differentiation period of 14 days, as indicated. Lane 16 is a negative RT–PCR control lane lacking cDNA in the reaction. Lane 17 is a positive control for RT–PCR amplification of each gene. ( B ) Relative expression levels of differentiation markers in monolayers of ES cells of different Srf genotype upon induction of in vitro differentiation by LIF withdrawal plus simultaneous addition of DMSO (quantitative RT–PCR analysis). ES lines used were 226-99 ( Srf –/+ ; left panel) and 226-100 ( Srf –/– ; right panel). Expression was followed for the indicated periods of differentiation (days).

    Article Snippet: Preparation of total RNA [using an RNeasy kit (Qiagen)] and first-strand cDNA synthesis (Superscript II; Gibco) were done according to the manufacturers’ protocols.

    Techniques: In Vitro, Expressing, Marker, Quantitative RT-PCR, RNA Expression, Reverse Transcription Polymerase Chain Reaction, Positive Control, Amplification

    MiR-153 Overexpression repressed the p-SMAD2, p-SMAD3, EGFR and IGFBP-3 expression. The MG-63 was treated in serum-free medium in the presence and absence of TGF-β (50 ng/ml), scramble, or miRNA-153 mimic for 24 h. (A) Expression of p-SMAD2, t-SMAD2, p-SMAD3 and t-SMAD3 was detected using western blotting. GAPDH was used as a loading control. (B) Expression of EGFR and IGFBP-3 was detected using western blotting. GAPDH was used as a loading control. (C) The mRNA expression of EGFR was detected using qRT-PCR. The expression of MMP9 was normalized to GAPDH. (D) The mRNA Expression of IGFBP-3 was detected using qRT-PCR. The expression of EGFR was normalized to GAPDH.

    Journal: PLoS ONE

    Article Title: MicroRNA-153 Inhibits Osteosarcoma Cells Proliferation and Invasion by Targeting TGF-β2

    doi: 10.1371/journal.pone.0119225

    Figure Lengend Snippet: MiR-153 Overexpression repressed the p-SMAD2, p-SMAD3, EGFR and IGFBP-3 expression. The MG-63 was treated in serum-free medium in the presence and absence of TGF-β (50 ng/ml), scramble, or miRNA-153 mimic for 24 h. (A) Expression of p-SMAD2, t-SMAD2, p-SMAD3 and t-SMAD3 was detected using western blotting. GAPDH was used as a loading control. (B) Expression of EGFR and IGFBP-3 was detected using western blotting. GAPDH was used as a loading control. (C) The mRNA expression of EGFR was detected using qRT-PCR. The expression of MMP9 was normalized to GAPDH. (D) The mRNA Expression of IGFBP-3 was detected using qRT-PCR. The expression of EGFR was normalized to GAPDH.

    Article Snippet: RNA extraction and quantitative real-time PCR Total RNAs were extracted from the cells or tissues using the miRNA Isolation Kit (Ambion, TX, USA).

    Techniques: Over Expression, Expressing, Western Blot, Quantitative RT-PCR

    Overexpression of miR-153 inhibited osteosarcoma cell proliferation and invasion. (A) qRT-PCR analysis of miR-153 expression after the transfection of miR-153 mimics or scramble or no treat. (B) The CCK8 assay used to evaluate the proliferation of the MG-63 cells after transferred with the miR-153 mimics or scramble or no treat. (C) Invasion analysis of the MG-63 cells after treatment with miRNA mimics, inhibitors or no treat; the relative ratio of invasive cells per field is shown on the right, ** p

    Journal: PLoS ONE

    Article Title: MicroRNA-153 Inhibits Osteosarcoma Cells Proliferation and Invasion by Targeting TGF-β2

    doi: 10.1371/journal.pone.0119225

    Figure Lengend Snippet: Overexpression of miR-153 inhibited osteosarcoma cell proliferation and invasion. (A) qRT-PCR analysis of miR-153 expression after the transfection of miR-153 mimics or scramble or no treat. (B) The CCK8 assay used to evaluate the proliferation of the MG-63 cells after transferred with the miR-153 mimics or scramble or no treat. (C) Invasion analysis of the MG-63 cells after treatment with miRNA mimics, inhibitors or no treat; the relative ratio of invasive cells per field is shown on the right, ** p

    Article Snippet: RNA extraction and quantitative real-time PCR Total RNAs were extracted from the cells or tissues using the miRNA Isolation Kit (Ambion, TX, USA).

    Techniques: Over Expression, Quantitative RT-PCR, Expressing, Transfection, CCK-8 Assay

    A . FFPE samples are usually used for hematoxylin and eosin (H E) and/or immunohistochemistry (IHC) stains. To overcome hurdles associated with gene expression analyses of tissue in FFPE samples, we show that the mH can increase the purification of high-quality RNA for downstream applications. B . H E staining of the four xenograft FFPE samples (BxPC3 [B] and FG [F]) or patient (MDA-AC2 [M]) xenografts (S = subcutaneous, O = orthotopic). C . Nucleic acid (RNA) concentrations (ng/uL) for the four FFPE samples of PDAC using either the standard Qiagen FFPE RNA extraction (-mH) or our mH-modified protocol (+mH). Measurements were made using Nanodrop, Qubit and Experion Bioanalyzer assays. D . Average +/- standard error mean (SEM) RNA 260/280 ratios for the same samples described in (A). *, **, *** indicate student t-test p values

    Journal: Oncotarget

    Article Title: A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts

    doi: 10.18632/oncotarget.11809

    Figure Lengend Snippet: A . FFPE samples are usually used for hematoxylin and eosin (H E) and/or immunohistochemistry (IHC) stains. To overcome hurdles associated with gene expression analyses of tissue in FFPE samples, we show that the mH can increase the purification of high-quality RNA for downstream applications. B . H E staining of the four xenograft FFPE samples (BxPC3 [B] and FG [F]) or patient (MDA-AC2 [M]) xenografts (S = subcutaneous, O = orthotopic). C . Nucleic acid (RNA) concentrations (ng/uL) for the four FFPE samples of PDAC using either the standard Qiagen FFPE RNA extraction (-mH) or our mH-modified protocol (+mH). Measurements were made using Nanodrop, Qubit and Experion Bioanalyzer assays. D . Average +/- standard error mean (SEM) RNA 260/280 ratios for the same samples described in (A). *, **, *** indicate student t-test p values

    Article Snippet: For Qubit runs, the instrument was calibrated using Qubit® RNA Broad-Range assay kit by Life Technologies.

    Techniques: Formalin-fixed Paraffin-Embedded, Immunohistochemistry, Expressing, Purification, Staining, Multiple Displacement Amplification, RNA Extraction, Modification