liver rna Search Results


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  • 99
    Thermo Fisher mice livers
    MicroRNA (miRNA) and RLuc mRNA analysis of <t>scAAV2-HCV-miR-Cluster</t> 5-injected mice. ( a–e ) Northern blot analyses of miRNA guide strands. Twenty-five µg of total <t>RNA</t> from mice injected with increasing doses of scAAV8-HCV-miR-Cluster 5 (2.5
    Mice Livers, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 130 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher rat livers
    Efficacy and the duration of knockdown after coinjection of chol-siHBVs and NAG-MLP in the <t>pHBV</t> mouse model of chronic hepatitis B virus (HBV) infection. NOD-SCID mice were given a hydrodynamic tail vein injection with ( a , e ) 13.5 µg pHBV1.3 or ( b – d ) 10 µg pHBV1.3. Three or more weeks thereafter, mice were given one 200 µl IV coinjection of 6 mg/kg NAG-MLP and 0.25 mg/kg, 1 mg/kg or 6 mg/kg chol-siHBV-74, -75, -76, or 77 ( n = 3–4). ( a , b ) HBsAg and ( c ) HBeAg in serum were measured by enzyme linked immunosorbent assay at the indicated times relative to injection on day 1; LOD, limit of detection. ( d ) DNA was isolated from serum and the concentration of HBV genomes was quantitated by qPCR. ( e ) <t>RNA</t> was isolated from the liver 14 days after chol-siRNA injection. The relative amount of HBV transcripts was determined by RT-qPCR using a probe that was within the S gene and normalizing to the endogenous β-actin mRNA. At each dose level the chol-siRNA injected mice were compared with isotonic glucose-injected mice with similar initial HBsAg levels (isotonic glucose groups A and B). Standard deviation bars are shown for HBsAg and HBV RNA quantitation. Serum HBV DNA and HBeAg levels for each group were determined by combining equal proportions of serum from each mouse within the group to obtain sufficient pooled sample at each time point ( n = 3–4).
    Rat Livers, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 596 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    TaKaRa mouse livers
    Efficacy and the duration of knockdown after coinjection of chol-siHBVs and NAG-MLP in the <t>pHBV</t> mouse model of chronic hepatitis B virus (HBV) infection. NOD-SCID mice were given a hydrodynamic tail vein injection with ( a , e ) 13.5 µg pHBV1.3 or ( b – d ) 10 µg pHBV1.3. Three or more weeks thereafter, mice were given one 200 µl IV coinjection of 6 mg/kg NAG-MLP and 0.25 mg/kg, 1 mg/kg or 6 mg/kg chol-siHBV-74, -75, -76, or 77 ( n = 3–4). ( a , b ) HBsAg and ( c ) HBeAg in serum were measured by enzyme linked immunosorbent assay at the indicated times relative to injection on day 1; LOD, limit of detection. ( d ) DNA was isolated from serum and the concentration of HBV genomes was quantitated by qPCR. ( e ) <t>RNA</t> was isolated from the liver 14 days after chol-siRNA injection. The relative amount of HBV transcripts was determined by RT-qPCR using a probe that was within the S gene and normalizing to the endogenous β-actin mRNA. At each dose level the chol-siRNA injected mice were compared with isotonic glucose-injected mice with similar initial HBsAg levels (isotonic glucose groups A and B). Standard deviation bars are shown for HBsAg and HBV RNA quantitation. Serum HBV DNA and HBeAg levels for each group were determined by combining equal proportions of serum from each mouse within the group to obtain sufficient pooled sample at each time point ( n = 3–4).
    Mouse Livers, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    98
    Thermo Fisher human liver total rna
    Dynamic range of known concentration of spike-in synthetic has-miR-10a-5p. A set of 10-fold serial dilutions of synthetic hsa-miR-10a-5p <t>miRNA</t> were spiked into the same amount of Universal Human miRNA reference <t>RNA</t> (samples 16–22, miRQC A) to generate cDNA for qPCR analysis. 20 ng of the RNA input was used for the spike-in test. qPCR results illustrated a dynamic range of at least 7 orders of magnitude ranging from 80 to 8 × 10 7 copies per nanowell.
    Human Liver Total Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 3712 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies liver rna
    Dynamic range of known concentration of spike-in synthetic has-miR-10a-5p. A set of 10-fold serial dilutions of synthetic hsa-miR-10a-5p <t>miRNA</t> were spiked into the same amount of Universal Human miRNA reference <t>RNA</t> (samples 16–22, miRQC A) to generate cDNA for qPCR analysis. 20 ng of the RNA input was used for the spike-in test. qPCR results illustrated a dynamic range of at least 7 orders of magnitude ranging from 80 to 8 × 10 7 copies per nanowell.
    Liver Rna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    rna  (TaKaRa)
    94
    TaKaRa rna
    Differential display identification of 25-Dx. ( a ) <t>DD-PCR</t> was performed on total hypothalamic <t>RNA</t> isolated from ovx female rats treated with EB (lanes 1 and 2) and EB + P (lanes 3 and 4) (see Materials and Methods ). The cloning of band P-T into a plasmid vector resulted in two unique gene sequences. ( b ) Reverse Northern blot to elucidate the DD-PCR results. One of the transcripts (pP-T.27; tissue carboxypeptidase inhibitor/latexin) is up-regulated by P, in a pattern similar to that observed in the DD-PCR gel, whereas the other (pP-T.20; 25-Dx) is down-regulated by P. ( c ) Quantitative analysis of the results shown in b . Graphed are the means and standard errors from three separate slot blots hybridized with radiolabeled cDNA probes derived from two independent groups of hormonally treated animals. This precaution ensured replicatability of both the blotting and probe synthesis procedures. ( d ) 25-Dx expression is repressed by P after E priming. Riboprobe synthesized from pP-T.20 was hybridized in situ to the VMH of vehicle, vehicle + EB, and EB + P-treated ovx female rats. The results are expressed as the percentage of silver grains per cell normalized to animals treated with EB + vehicle (100%). ( e ) Alignment of the sequence of pP-T.20 with rat 25-Dx. The numbers correspond to the cDNA sequence according to Selmin et al. ). Vertical lines indicate identity. The bold text indicates the sequence and location of the arbitrary primer, AP10, used in the differential display reaction.
    Rna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 14189 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    TaKaRa human liver total rna
    HCV core sensitized ATRA-induced cell death. (A) Production levels of the core in each clone of MCF-7 cells stably transfected with pLXSH-core (MCF-7-core 6 and -core 21) or the empty vector pLXSH (MCF-7-vec) were analyzed by immunoblot analysis with an anti-core (right, upper panel) and an anti-α-tubulin (right, lower panel) antibody as an internal control. MCF-7-core 6, MCF-7-core 21, and MCF-7-vec cells (5 × 10 4 each) were incubated in the absence (no treatment) or presence (ATRA) of 1 μM ATRA for 96 h. Living and dead cells were quantitated by staining with trypan blue. The average percentage of cell death from three independent experiments is presented. Open (bars 1 and 4), solid (bars 2 and 5), and hatched (bars 3 and 6) bars, MCF-7-vec, -core 6, and -core 21, respectively. (B) MCF-7 cells (5 × 10 4 ) transfected with 2.5 μg of pMACS-K k and each expression plasmid given below were treated with (solid bars) or without (open bars) 1 μM ATRA for 96 h after the concentration of transfected cells by using the MACSelect system (see Materials and Methods). For bars 11 and 12, 50 μM monodansylcadaverine (MDC) was added simultaneously with ATRA. The percentage of cell death was estimated as described for panel A. Bars 1 and 2, empty vector; bars 3, 4, 11, and 12, pCMV-core (3 μg); bars 5 and 6, pCMV-core (6 μg); bars 7 and 8, pCMV-core (3 μg) and pCMV-Sp110b(389-453) (CBR fragment; 4.5 μg); bars 9 and 10, pCMV-core(6162M) (3 μg). (C) Enhancement of ATRA-induced tTGase expression by the core. MCF-7 cells (2 × 10 5 ) transfected with pMACS-K k and each expression plasmid given below were treated for 48 h with (lanes 4 to 6) or without (lanes 1 to 3) 1 μM ATRA after cell concentration as described for panel B. Following the extraction of total <t>RNA</t> from these cells, mRNA levels of tTGase (upper panel) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal control (lower panel) were semiquantified by <t>RT-PCR</t> as described in Materials and Methods. RTase(−), experimental control treated like other samples, but without reverse transcriptase. Lanes: 1 and 4, empty vector; 2 and 5, pCMV-core; 3 and 6, pCMV-core and pCMV-Sp110b(389-453) (CBR fragment).
    Human Liver Total Rna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 95/100, based on 1166 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Stratagene liver rna
    MA plot (log-ratio of the expression intensities versus the mean log-expression of the intensities) for a typical ToxArray™ hybridization containing a mouse liver experimental <t>RNA</t> sample (Cy5-labeled) and <t>Stratagene</t> Universal Reference RNA (Cy3-labeled), each with A. thaliana spike-in control RNA added prior to labelling. The green circles indicate the mouse genes and red circles are the Rpl5 gene which reached scanner saturation in the Cy3 channel at many spots. The EC series covers the full range of signal intensities with no signal gaps. The LOWESS fit shown is through the external controls only, with a span of 0.3.
    Liver Rna, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 145 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc liver rna
    A treatment/control experimental design. Ten mice were treated with <t>IL-1β</t> ( n = 5), or saline ( n = 5; referred to as untreated). Four hours after treatment, the mice were sacrificed, liver samples were collected, and total <t>RNA</t> was extracted from the tissue. At this point, aliquots of the same RNA sample were sequenced on both an Illumina HiSeq 2500 and an Ion Torrent Proton. Next, RNA-Seq reads from each platform were aligned using three alignment algorithms: 1) GSNAP, 2) STAR, and 3) STAR, followed by Bowtie2 to align reads not mapped by STAR (STAR + Bowtie2). Lastly, all aligned data were normalized using the P ipeline O f R NA-Seq T ransformations (PORT)
    Liver Rna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    MicroRNA (miRNA) and RLuc mRNA analysis of scAAV2-HCV-miR-Cluster 5-injected mice. ( a–e ) Northern blot analyses of miRNA guide strands. Twenty-five µg of total RNA from mice injected with increasing doses of scAAV8-HCV-miR-Cluster 5 (2.5

    Journal: Molecular Therapy

    Article Title: Preclinical Evaluation of An Anti-HCV miRNA Cluster for Treatment of HCV Infection

    doi: 10.1038/mt.2012.247

    Figure Lengend Snippet: MicroRNA (miRNA) and RLuc mRNA analysis of scAAV2-HCV-miR-Cluster 5-injected mice. ( a–e ) Northern blot analyses of miRNA guide strands. Twenty-five µg of total RNA from mice injected with increasing doses of scAAV8-HCV-miR-Cluster 5 (2.5

    Article Snippet: Quantitation of the anti-HCV miRNAs in Huh-7.5 cell extracts and mouse liver RNA was performed using custom TaqMan small RNA QRT-PCR assays (Applied Biosystems) according to the manufacturer's instructions, using synthetic oligonucleotides to generate standard curves.

    Techniques: Injection, Mouse Assay, Northern Blot

    Circularization of miRNAs having nonmethylated 3′-ends (2′-OH miRNAs). ( A ) Using T4 RNA ligase 1 (Rnl1) at 37°C. ( B ) Using CircLigase II (CLII) at 60°C. 80 nM synthetic miRNAs (let-7b, let-7g, miR-16, and miR-23a, which

    Journal: RNA

    Article Title: miR-ID: A novel, circularization-based platform for detection of microRNAs

    doi: 10.1261/rna.2490111

    Figure Lengend Snippet: Circularization of miRNAs having nonmethylated 3′-ends (2′-OH miRNAs). ( A ) Using T4 RNA ligase 1 (Rnl1) at 37°C. ( B ) Using CircLigase II (CLII) at 60°C. 80 nM synthetic miRNAs (let-7b, let-7g, miR-16, and miR-23a, which

    Article Snippet: MiRNA profiling of mouse tissue One hundred nanograms of mouse total RNA from brain, heart, liver, thymus, lung, embryo, and ovary (AB Cat. No. AM7800) was subjected to RT and qPCR using individual RT and PCR primer probes specific for let-7a (AB Kit 4373169), miR-16 (AB Kit 4373121), miR-20 (AB Kit 4373286), miR-21 (AB Kit 4373090), miR-22 (AB Kit 4373079), and sno234 (AB Kit 4380915) as described (AB/Life Technologies, Cat. No. 4366596).

    Techniques:

    Circularization of miRNAs having a 2′-oxymethyl modification at their 3′-ends (2′-OMe miRNAs). ( A ) Using T4 RNA ligase 1 (Rnl1) at 37°C. ( B ) Using CircLigase II (CLII) at 60°C. 80 nM synthetic miRNAs (let-7b, let-7g,

    Journal: RNA

    Article Title: miR-ID: A novel, circularization-based platform for detection of microRNAs

    doi: 10.1261/rna.2490111

    Figure Lengend Snippet: Circularization of miRNAs having a 2′-oxymethyl modification at their 3′-ends (2′-OMe miRNAs). ( A ) Using T4 RNA ligase 1 (Rnl1) at 37°C. ( B ) Using CircLigase II (CLII) at 60°C. 80 nM synthetic miRNAs (let-7b, let-7g,

    Article Snippet: MiRNA profiling of mouse tissue One hundred nanograms of mouse total RNA from brain, heart, liver, thymus, lung, embryo, and ovary (AB Cat. No. AM7800) was subjected to RT and qPCR using individual RT and PCR primer probes specific for let-7a (AB Kit 4373169), miR-16 (AB Kit 4373121), miR-20 (AB Kit 4373286), miR-21 (AB Kit 4373090), miR-22 (AB Kit 4373079), and sno234 (AB Kit 4380915) as described (AB/Life Technologies, Cat. No. 4366596).

    Techniques: Modification

    Circularization of miRNAs by T4 RNA ligase and CircLigase

    Journal: RNA

    Article Title: miR-ID: A novel, circularization-based platform for detection of microRNAs

    doi: 10.1261/rna.2490111

    Figure Lengend Snippet: Circularization of miRNAs by T4 RNA ligase and CircLigase

    Article Snippet: MiRNA profiling of mouse tissue One hundred nanograms of mouse total RNA from brain, heart, liver, thymus, lung, embryo, and ovary (AB Cat. No. AM7800) was subjected to RT and qPCR using individual RT and PCR primer probes specific for let-7a (AB Kit 4373169), miR-16 (AB Kit 4373121), miR-20 (AB Kit 4373286), miR-21 (AB Kit 4373090), miR-22 (AB Kit 4373079), and sno234 (AB Kit 4380915) as described (AB/Life Technologies, Cat. No. 4366596).

    Techniques:

    Sensitivity and detection limit of an individual miRNA are not affected by the presence of total cellular RNA. Synthetic miR-127 miRNA having 5′-p and 2′-OH/3′-OH ends was used in this example. Standard curves were generated for

    Journal: RNA

    Article Title: miR-ID: A novel, circularization-based platform for detection of microRNAs

    doi: 10.1261/rna.2490111

    Figure Lengend Snippet: Sensitivity and detection limit of an individual miRNA are not affected by the presence of total cellular RNA. Synthetic miR-127 miRNA having 5′-p and 2′-OH/3′-OH ends was used in this example. Standard curves were generated for

    Article Snippet: MiRNA profiling of mouse tissue One hundred nanograms of mouse total RNA from brain, heart, liver, thymus, lung, embryo, and ovary (AB Cat. No. AM7800) was subjected to RT and qPCR using individual RT and PCR primer probes specific for let-7a (AB Kit 4373169), miR-16 (AB Kit 4373121), miR-20 (AB Kit 4373286), miR-21 (AB Kit 4373090), miR-22 (AB Kit 4373079), and sno234 (AB Kit 4380915) as described (AB/Life Technologies, Cat. No. 4366596).

    Techniques: Generated

    Efficacy and the duration of knockdown after coinjection of chol-siHBVs and NAG-MLP in the pHBV mouse model of chronic hepatitis B virus (HBV) infection. NOD-SCID mice were given a hydrodynamic tail vein injection with ( a , e ) 13.5 µg pHBV1.3 or ( b – d ) 10 µg pHBV1.3. Three or more weeks thereafter, mice were given one 200 µl IV coinjection of 6 mg/kg NAG-MLP and 0.25 mg/kg, 1 mg/kg or 6 mg/kg chol-siHBV-74, -75, -76, or 77 ( n = 3–4). ( a , b ) HBsAg and ( c ) HBeAg in serum were measured by enzyme linked immunosorbent assay at the indicated times relative to injection on day 1; LOD, limit of detection. ( d ) DNA was isolated from serum and the concentration of HBV genomes was quantitated by qPCR. ( e ) RNA was isolated from the liver 14 days after chol-siRNA injection. The relative amount of HBV transcripts was determined by RT-qPCR using a probe that was within the S gene and normalizing to the endogenous β-actin mRNA. At each dose level the chol-siRNA injected mice were compared with isotonic glucose-injected mice with similar initial HBsAg levels (isotonic glucose groups A and B). Standard deviation bars are shown for HBsAg and HBV RNA quantitation. Serum HBV DNA and HBeAg levels for each group were determined by combining equal proportions of serum from each mouse within the group to obtain sufficient pooled sample at each time point ( n = 3–4).

    Journal: Molecular Therapy

    Article Title: Hepatocyte-targeted RNAi Therapeutics for the Treatment of Chronic Hepatitis B Virus Infection

    doi: 10.1038/mt.2013.31

    Figure Lengend Snippet: Efficacy and the duration of knockdown after coinjection of chol-siHBVs and NAG-MLP in the pHBV mouse model of chronic hepatitis B virus (HBV) infection. NOD-SCID mice were given a hydrodynamic tail vein injection with ( a , e ) 13.5 µg pHBV1.3 or ( b – d ) 10 µg pHBV1.3. Three or more weeks thereafter, mice were given one 200 µl IV coinjection of 6 mg/kg NAG-MLP and 0.25 mg/kg, 1 mg/kg or 6 mg/kg chol-siHBV-74, -75, -76, or 77 ( n = 3–4). ( a , b ) HBsAg and ( c ) HBeAg in serum were measured by enzyme linked immunosorbent assay at the indicated times relative to injection on day 1; LOD, limit of detection. ( d ) DNA was isolated from serum and the concentration of HBV genomes was quantitated by qPCR. ( e ) RNA was isolated from the liver 14 days after chol-siRNA injection. The relative amount of HBV transcripts was determined by RT-qPCR using a probe that was within the S gene and normalizing to the endogenous β-actin mRNA. At each dose level the chol-siRNA injected mice were compared with isotonic glucose-injected mice with similar initial HBsAg levels (isotonic glucose groups A and B). Standard deviation bars are shown for HBsAg and HBV RNA quantitation. Serum HBV DNA and HBeAg levels for each group were determined by combining equal proportions of serum from each mouse within the group to obtain sufficient pooled sample at each time point ( n = 3–4).

    Article Snippet: For liver RNA samples from pHBV mice, 50–500 ng of total RNA was reverse transcribed using the High Capacity cDNA Reverse Transcription Kit (Life Technologies).

    Techniques: Infection, Mouse Assay, Injection, Enzyme-linked Immunosorbent Assay, Isolation, Concentration Assay, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Standard Deviation, Quantitation Assay

    Distribution of log2 expression ratios. Labeled mouse liver RNA (Cy5) and Universal Mouse Reference RNA samples (Cy3) were hybridized with MWG mouse 20 K using GlassHyb™ buffer or 5× SSC, 0.1% SDS buffer with different concentrations of formamide: A. GlassHyb™ buffer. B. 27% formamide. C. 35% formamide. D. 40% formamide. The log2 expression ratio (liver/reference) is plotted on the x-axis and the probability is on the y-axis.

    Journal: BMC Bioinformatics

    Article Title: Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions

    doi: 10.1186/1471-2105-7-S2-S17

    Figure Lengend Snippet: Distribution of log2 expression ratios. Labeled mouse liver RNA (Cy5) and Universal Mouse Reference RNA samples (Cy3) were hybridized with MWG mouse 20 K using GlassHyb™ buffer or 5× SSC, 0.1% SDS buffer with different concentrations of formamide: A. GlassHyb™ buffer. B. 27% formamide. C. 35% formamide. D. 40% formamide. The log2 expression ratio (liver/reference) is plotted on the x-axis and the probability is on the y-axis.

    Article Snippet: To further evaluate the reproducibility of microarray experiments with this hybridization buffer, rat liver total RNA (Cy5, Ambion), rat brain total RNA (Cy5, Ambion) and Universal Rat Reference RNA (Cy3, Stratagene) were hybridized with MWG rat 10 k arrays using a reference design, and washed with washing condition 3.

    Techniques: Expressing, Labeling

    Signal-to-background ratios under different hybridization conditions. Labeled mouse liver RNA (Cy5) and Universal Mouse Reference RNA samples (Cy3) were hybridized with MWG mouse 20 K using GlassHyb™ buffer or 5× SSC, 0.1% SDS buffer with different concentrations of formamide: A. GlassHyb™ buffer. B. 27% formamide. C. 35% formamide. D. 40% formamide. Oligo, mouse-specific probe; Control, Arabidopsis-specific probe; Blank, no probe printed.

    Journal: BMC Bioinformatics

    Article Title: Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions

    doi: 10.1186/1471-2105-7-S2-S17

    Figure Lengend Snippet: Signal-to-background ratios under different hybridization conditions. Labeled mouse liver RNA (Cy5) and Universal Mouse Reference RNA samples (Cy3) were hybridized with MWG mouse 20 K using GlassHyb™ buffer or 5× SSC, 0.1% SDS buffer with different concentrations of formamide: A. GlassHyb™ buffer. B. 27% formamide. C. 35% formamide. D. 40% formamide. Oligo, mouse-specific probe; Control, Arabidopsis-specific probe; Blank, no probe printed.

    Article Snippet: To further evaluate the reproducibility of microarray experiments with this hybridization buffer, rat liver total RNA (Cy5, Ambion), rat brain total RNA (Cy5, Ambion) and Universal Rat Reference RNA (Cy3, Stratagene) were hybridized with MWG rat 10 k arrays using a reference design, and washed with washing condition 3.

    Techniques: Hybridization, Labeling

    Scatterplots of log2 spot intensities under optimized hybridization and washing conditions. Ambion rat liver RNA samples (AL) were labeled with Cy3 and Stratagene Universal Rat Reference RNAs (URRR) were labeled with Cy5. The labels for the x and y axes are given on the diagonal.

    Journal: BMC Bioinformatics

    Article Title: Improvement in the Reproducibility and Accuracy of DNA Microarray Quantification by Optimizing Hybridization Conditions

    doi: 10.1186/1471-2105-7-S2-S17

    Figure Lengend Snippet: Scatterplots of log2 spot intensities under optimized hybridization and washing conditions. Ambion rat liver RNA samples (AL) were labeled with Cy3 and Stratagene Universal Rat Reference RNAs (URRR) were labeled with Cy5. The labels for the x and y axes are given on the diagonal.

    Article Snippet: To further evaluate the reproducibility of microarray experiments with this hybridization buffer, rat liver total RNA (Cy5, Ambion), rat brain total RNA (Cy5, Ambion) and Universal Rat Reference RNA (Cy3, Stratagene) were hybridized with MWG rat 10 k arrays using a reference design, and washed with washing condition 3.

    Techniques: Hybridization, Labeling

    Mini gene assay for exon-2 skipping of CYP2C93. Preparation of expression plasmids and in vitro splicing analysis were performed as described in Materials and Methods . ( A ) Schematic illustration of the CYP2C93 gene fragments (exon 1 to exon 3) used to generate mini gene plasmids. ( B ) In vitro splicing analysis. Each expression plasmid was transfected into COS1 cells, from which total RNA was extracted and used for amplification of CYP2C93 cDNA (from exon 1 to exon 3) by RT-PCR. The amplified products were visualized on an agarose gel. Lanes 1 and 2, liver total RNAs of the cynomolgus monkey (mfF1) expressing both SV1 and SV2 and the rhesus monkey (mm35) expressing SV1, respectively; lanes 3 and 4, IVS2-1G and IVS2-1T of cynomolgus monkey CYP2C93, respectively; lanes 5 and 6, IVS2-1G and IVS2-1T of rhesus monkey CYP2C93, respectively; and lane 7, mock. The upper band (360 bp) and lower band (200 bp) correspond to CYP2C93 SV1 and SV2 transcripts, respectively. For cynomolgus monkey and rhesus monkey CYP2C93, only exon-2 lacking SV2 was transcribed in the presence of IVS2-1T, whereas both SV1 and SV2 were transcribed in the presence of IVS2-1G. β-actin was also analyzed as a control.

    Journal: PLoS ONE

    Article Title: Newly Identified CYP2C93 Is a Functional Enzyme in Rhesus Monkey, but Not in Cynomolgus Monkey

    doi: 10.1371/journal.pone.0016923

    Figure Lengend Snippet: Mini gene assay for exon-2 skipping of CYP2C93. Preparation of expression plasmids and in vitro splicing analysis were performed as described in Materials and Methods . ( A ) Schematic illustration of the CYP2C93 gene fragments (exon 1 to exon 3) used to generate mini gene plasmids. ( B ) In vitro splicing analysis. Each expression plasmid was transfected into COS1 cells, from which total RNA was extracted and used for amplification of CYP2C93 cDNA (from exon 1 to exon 3) by RT-PCR. The amplified products were visualized on an agarose gel. Lanes 1 and 2, liver total RNAs of the cynomolgus monkey (mfF1) expressing both SV1 and SV2 and the rhesus monkey (mm35) expressing SV1, respectively; lanes 3 and 4, IVS2-1G and IVS2-1T of cynomolgus monkey CYP2C93, respectively; lanes 5 and 6, IVS2-1G and IVS2-1T of rhesus monkey CYP2C93, respectively; and lane 7, mock. The upper band (360 bp) and lower band (200 bp) correspond to CYP2C93 SV1 and SV2 transcripts, respectively. For cynomolgus monkey and rhesus monkey CYP2C93, only exon-2 lacking SV2 was transcribed in the presence of IVS2-1T, whereas both SV1 and SV2 were transcribed in the presence of IVS2-1G. β-actin was also analyzed as a control.

    Article Snippet: 5′ rapid amplification of cDNA ends To verify the translational initiation codon of the cDNA sequence, 5′ rapid amplification of cDNA ends (RACE) was carried out with liver total RNA of cynomolgus monkey (mfF1) and rhesus monkey (mm35) using 5′ RACE System for Rapid Amplification of cDNA Ends (Invitrogen) according to the manufacturer's protocol.

    Techniques: Mini Gene Assay, Expressing, In Vitro, Plasmid Preparation, Transfection, Amplification, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis

    Dynamic range of known concentration of spike-in synthetic has-miR-10a-5p. A set of 10-fold serial dilutions of synthetic hsa-miR-10a-5p miRNA were spiked into the same amount of Universal Human miRNA reference RNA (samples 16–22, miRQC A) to generate cDNA for qPCR analysis. 20 ng of the RNA input was used for the spike-in test. qPCR results illustrated a dynamic range of at least 7 orders of magnitude ranging from 80 to 8 × 10 7 copies per nanowell.

    Journal: Scientific Reports

    Article Title: A Novel Multi-Gene Detection Platform for the Analysis of miRNA Expression

    doi: 10.1038/s41598-018-29146-7

    Figure Lengend Snippet: Dynamic range of known concentration of spike-in synthetic has-miR-10a-5p. A set of 10-fold serial dilutions of synthetic hsa-miR-10a-5p miRNA were spiked into the same amount of Universal Human miRNA reference RNA (samples 16–22, miRQC A) to generate cDNA for qPCR analysis. 20 ng of the RNA input was used for the spike-in test. qPCR results illustrated a dynamic range of at least 7 orders of magnitude ranging from 80 to 8 × 10 7 copies per nanowell.

    Article Snippet: RNA samples for miRQC analysis Universal Human miRNA reference RNA (miRQC A for samples 1–2; Agilent Technologies, #750700) and human brain total RNA (miRQC B for samples 3–4; Life Technologies, AM7960) were purchased from Agilent and Life Technologies, respectively.

    Techniques: Concentration Assay, Real-time Polymerase Chain Reaction

    PCR efficiency of 9 representative miRNA assays on miRSCan™ PanCancer Chips. Real-time qPCR was carried out for each miRNA cluster using 3-fold serially diluted cDNA template synthesized from Universal Human miRNA Reference RNA (UHmiRR; miRQC A). The resulting Cq values were plotted against the respective miRNA concentrations to derive the PCR efficiency for each assay. All 9 assays fell within acceptable PCR efficiency of 90–110%.

    Journal: Scientific Reports

    Article Title: A Novel Multi-Gene Detection Platform for the Analysis of miRNA Expression

    doi: 10.1038/s41598-018-29146-7

    Figure Lengend Snippet: PCR efficiency of 9 representative miRNA assays on miRSCan™ PanCancer Chips. Real-time qPCR was carried out for each miRNA cluster using 3-fold serially diluted cDNA template synthesized from Universal Human miRNA Reference RNA (UHmiRR; miRQC A). The resulting Cq values were plotted against the respective miRNA concentrations to derive the PCR efficiency for each assay. All 9 assays fell within acceptable PCR efficiency of 90–110%.

    Article Snippet: RNA samples for miRQC analysis Universal Human miRNA reference RNA (miRQC A for samples 1–2; Agilent Technologies, #750700) and human brain total RNA (miRQC B for samples 3–4; Life Technologies, AM7960) were purchased from Agilent and Life Technologies, respectively.

    Techniques: Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Synthesized

    Estrogen regulation of PEMT is transcript-specific. Using RNA isolated from primary hepatocytes cultured in the absence (−) or presence (+) of 100 nmol/liter moxestrol for the lengths of time noted, PEMT transcripts were quantified using transcript-specific

    Journal: The Journal of Biological Chemistry

    Article Title: Aberrant Estrogen Regulation of PEMT Results in Choline Deficiency-associated Liver Dysfunction *

    doi: 10.1074/jbc.M110.106922

    Figure Lengend Snippet: Estrogen regulation of PEMT is transcript-specific. Using RNA isolated from primary hepatocytes cultured in the absence (−) or presence (+) of 100 nmol/liter moxestrol for the lengths of time noted, PEMT transcripts were quantified using transcript-specific

    Article Snippet: To determine the absolute copy number of the target transcripts, we cloned a cDNA fragment unique to each PEMT transcript isolated from human liver RNA into a TOPOII TA (Invitrogen).

    Techniques: Isolation, Cell Culture

    PEMT risk allele is not estrogen-responsive. A , RNA isolated from primary hepatocytes heterozygous for the risk allele was subjected to allele-specific quantitative PCR. Results were normalized to genomic DNA ( black bars ). The estimated relative expression

    Journal: The Journal of Biological Chemistry

    Article Title: Aberrant Estrogen Regulation of PEMT Results in Choline Deficiency-associated Liver Dysfunction *

    doi: 10.1074/jbc.M110.106922

    Figure Lengend Snippet: PEMT risk allele is not estrogen-responsive. A , RNA isolated from primary hepatocytes heterozygous for the risk allele was subjected to allele-specific quantitative PCR. Results were normalized to genomic DNA ( black bars ). The estimated relative expression

    Article Snippet: To determine the absolute copy number of the target transcripts, we cloned a cDNA fragment unique to each PEMT transcript isolated from human liver RNA into a TOPOII TA (Invitrogen).

    Techniques: Isolation, Real-time Polymerase Chain Reaction, Expressing

    Differential display identification of 25-Dx. ( a ) DD-PCR was performed on total hypothalamic RNA isolated from ovx female rats treated with EB (lanes 1 and 2) and EB + P (lanes 3 and 4) (see Materials and Methods ). The cloning of band P-T into a plasmid vector resulted in two unique gene sequences. ( b ) Reverse Northern blot to elucidate the DD-PCR results. One of the transcripts (pP-T.27; tissue carboxypeptidase inhibitor/latexin) is up-regulated by P, in a pattern similar to that observed in the DD-PCR gel, whereas the other (pP-T.20; 25-Dx) is down-regulated by P. ( c ) Quantitative analysis of the results shown in b . Graphed are the means and standard errors from three separate slot blots hybridized with radiolabeled cDNA probes derived from two independent groups of hormonally treated animals. This precaution ensured replicatability of both the blotting and probe synthesis procedures. ( d ) 25-Dx expression is repressed by P after E priming. Riboprobe synthesized from pP-T.20 was hybridized in situ to the VMH of vehicle, vehicle + EB, and EB + P-treated ovx female rats. The results are expressed as the percentage of silver grains per cell normalized to animals treated with EB + vehicle (100%). ( e ) Alignment of the sequence of pP-T.20 with rat 25-Dx. The numbers correspond to the cDNA sequence according to Selmin et al. ). Vertical lines indicate identity. The bold text indicates the sequence and location of the arbitrary primer, AP10, used in the differential display reaction.

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

    Article Title: A membrane-associated progesterone-binding protein, 25-Dx, is regulated by progesterone in brain regions involved in female reproductive behaviors

    doi:

    Figure Lengend Snippet: Differential display identification of 25-Dx. ( a ) DD-PCR was performed on total hypothalamic RNA isolated from ovx female rats treated with EB (lanes 1 and 2) and EB + P (lanes 3 and 4) (see Materials and Methods ). The cloning of band P-T into a plasmid vector resulted in two unique gene sequences. ( b ) Reverse Northern blot to elucidate the DD-PCR results. One of the transcripts (pP-T.27; tissue carboxypeptidase inhibitor/latexin) is up-regulated by P, in a pattern similar to that observed in the DD-PCR gel, whereas the other (pP-T.20; 25-Dx) is down-regulated by P. ( c ) Quantitative analysis of the results shown in b . Graphed are the means and standard errors from three separate slot blots hybridized with radiolabeled cDNA probes derived from two independent groups of hormonally treated animals. This precaution ensured replicatability of both the blotting and probe synthesis procedures. ( d ) 25-Dx expression is repressed by P after E priming. Riboprobe synthesized from pP-T.20 was hybridized in situ to the VMH of vehicle, vehicle + EB, and EB + P-treated ovx female rats. The results are expressed as the percentage of silver grains per cell normalized to animals treated with EB + vehicle (100%). ( e ) Alignment of the sequence of pP-T.20 with rat 25-Dx. The numbers correspond to the cDNA sequence according to Selmin et al. ). Vertical lines indicate identity. The bold text indicates the sequence and location of the arbitrary primer, AP10, used in the differential display reaction.

    Article Snippet: Reverse transcription–PCR was performed on total RNA isolated from rat liver, and the resulting 693-bp fragment was directionally cloned into pEGFP-N1 (CLONTECH) predigested with Eco RI and Bam HI.

    Techniques: Polymerase Chain Reaction, Isolation, Clone Assay, Plasmid Preparation, Northern Blot, Derivative Assay, Expressing, Synthesized, In Situ, Sequencing

    The expression of 25-Dx is sexually dimorphic in the PRKO mouse hypothalamus. Northern blots were used to examine the expression of 25-Dx in the hypothalamus of male and female PRKO mice. ( a ) The expression of 25-Dx in the hypothalamus of female PRKO (ko) mice is higher than in wild-type (wt) littermates. The 25-Dx probe hybridizes to a single 1.9-kb transcript in the mouse hypothalamus ( Top ). The ethidium bromide-stained gels demonstrate the equal loading of RNA across lanes for the Northern blot ( Middle ) and the corresponding genotype of each animal, as determined by PCR ( Bottom ). ( b ) Quantitative analysis of Northern blots. Blots similar to the one shown in a were prepared for male (+/+, n = 3; +/−, n = 12; −/−, n = 14) and female (+/+, n = 12; +/−, n = 13; −/−, n = 14) PRKO mice and quantified by PhosphorImager analysis. *, P

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

    Article Title: A membrane-associated progesterone-binding protein, 25-Dx, is regulated by progesterone in brain regions involved in female reproductive behaviors

    doi:

    Figure Lengend Snippet: The expression of 25-Dx is sexually dimorphic in the PRKO mouse hypothalamus. Northern blots were used to examine the expression of 25-Dx in the hypothalamus of male and female PRKO mice. ( a ) The expression of 25-Dx in the hypothalamus of female PRKO (ko) mice is higher than in wild-type (wt) littermates. The 25-Dx probe hybridizes to a single 1.9-kb transcript in the mouse hypothalamus ( Top ). The ethidium bromide-stained gels demonstrate the equal loading of RNA across lanes for the Northern blot ( Middle ) and the corresponding genotype of each animal, as determined by PCR ( Bottom ). ( b ) Quantitative analysis of Northern blots. Blots similar to the one shown in a were prepared for male (+/+, n = 3; +/−, n = 12; −/−, n = 14) and female (+/+, n = 12; +/−, n = 13; −/−, n = 14) PRKO mice and quantified by PhosphorImager analysis. *, P

    Article Snippet: Reverse transcription–PCR was performed on total RNA isolated from rat liver, and the resulting 693-bp fragment was directionally cloned into pEGFP-N1 (CLONTECH) predigested with Eco RI and Bam HI.

    Techniques: Expressing, Northern Blot, Mouse Assay, Staining, Polymerase Chain Reaction

    HCV core sensitized ATRA-induced cell death. (A) Production levels of the core in each clone of MCF-7 cells stably transfected with pLXSH-core (MCF-7-core 6 and -core 21) or the empty vector pLXSH (MCF-7-vec) were analyzed by immunoblot analysis with an anti-core (right, upper panel) and an anti-α-tubulin (right, lower panel) antibody as an internal control. MCF-7-core 6, MCF-7-core 21, and MCF-7-vec cells (5 × 10 4 each) were incubated in the absence (no treatment) or presence (ATRA) of 1 μM ATRA for 96 h. Living and dead cells were quantitated by staining with trypan blue. The average percentage of cell death from three independent experiments is presented. Open (bars 1 and 4), solid (bars 2 and 5), and hatched (bars 3 and 6) bars, MCF-7-vec, -core 6, and -core 21, respectively. (B) MCF-7 cells (5 × 10 4 ) transfected with 2.5 μg of pMACS-K k and each expression plasmid given below were treated with (solid bars) or without (open bars) 1 μM ATRA for 96 h after the concentration of transfected cells by using the MACSelect system (see Materials and Methods). For bars 11 and 12, 50 μM monodansylcadaverine (MDC) was added simultaneously with ATRA. The percentage of cell death was estimated as described for panel A. Bars 1 and 2, empty vector; bars 3, 4, 11, and 12, pCMV-core (3 μg); bars 5 and 6, pCMV-core (6 μg); bars 7 and 8, pCMV-core (3 μg) and pCMV-Sp110b(389-453) (CBR fragment; 4.5 μg); bars 9 and 10, pCMV-core(6162M) (3 μg). (C) Enhancement of ATRA-induced tTGase expression by the core. MCF-7 cells (2 × 10 5 ) transfected with pMACS-K k and each expression plasmid given below were treated for 48 h with (lanes 4 to 6) or without (lanes 1 to 3) 1 μM ATRA after cell concentration as described for panel B. Following the extraction of total RNA from these cells, mRNA levels of tTGase (upper panel) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal control (lower panel) were semiquantified by RT-PCR as described in Materials and Methods. RTase(−), experimental control treated like other samples, but without reverse transcriptase. Lanes: 1 and 4, empty vector; 2 and 5, pCMV-core; 3 and 6, pCMV-core and pCMV-Sp110b(389-453) (CBR fragment).

    Journal: Molecular and Cellular Biology

    Article Title: Modulation of Retinoid Signaling by a Cytoplasmic Viral Protein via Sequestration of Sp110b, a Potent Transcriptional Corepressor of Retinoic Acid Receptor, from the Nucleus

    doi: 10.1128/MCB.23.21.7498-7509.2003

    Figure Lengend Snippet: HCV core sensitized ATRA-induced cell death. (A) Production levels of the core in each clone of MCF-7 cells stably transfected with pLXSH-core (MCF-7-core 6 and -core 21) or the empty vector pLXSH (MCF-7-vec) were analyzed by immunoblot analysis with an anti-core (right, upper panel) and an anti-α-tubulin (right, lower panel) antibody as an internal control. MCF-7-core 6, MCF-7-core 21, and MCF-7-vec cells (5 × 10 4 each) were incubated in the absence (no treatment) or presence (ATRA) of 1 μM ATRA for 96 h. Living and dead cells were quantitated by staining with trypan blue. The average percentage of cell death from three independent experiments is presented. Open (bars 1 and 4), solid (bars 2 and 5), and hatched (bars 3 and 6) bars, MCF-7-vec, -core 6, and -core 21, respectively. (B) MCF-7 cells (5 × 10 4 ) transfected with 2.5 μg of pMACS-K k and each expression plasmid given below were treated with (solid bars) or without (open bars) 1 μM ATRA for 96 h after the concentration of transfected cells by using the MACSelect system (see Materials and Methods). For bars 11 and 12, 50 μM monodansylcadaverine (MDC) was added simultaneously with ATRA. The percentage of cell death was estimated as described for panel A. Bars 1 and 2, empty vector; bars 3, 4, 11, and 12, pCMV-core (3 μg); bars 5 and 6, pCMV-core (6 μg); bars 7 and 8, pCMV-core (3 μg) and pCMV-Sp110b(389-453) (CBR fragment; 4.5 μg); bars 9 and 10, pCMV-core(6162M) (3 μg). (C) Enhancement of ATRA-induced tTGase expression by the core. MCF-7 cells (2 × 10 5 ) transfected with pMACS-K k and each expression plasmid given below were treated for 48 h with (lanes 4 to 6) or without (lanes 1 to 3) 1 μM ATRA after cell concentration as described for panel B. Following the extraction of total RNA from these cells, mRNA levels of tTGase (upper panel) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal control (lower panel) were semiquantified by RT-PCR as described in Materials and Methods. RTase(−), experimental control treated like other samples, but without reverse transcriptase. Lanes: 1 and 4, empty vector; 2 and 5, pCMV-core; 3 and 6, pCMV-core and pCMV-Sp110b(389-453) (CBR fragment).

    Article Snippet: Sp110 and Sp110b cDNAs covering the entire open reading frame regions were obtained by reverse transcriptase PCR (RT-PCR) from a human liver total-RNA (Clontech) template by using primers 5′-GTTGAATTCATGTTCACCATGACAAGAG-3′ and 5′-GTTCTCGAGTCAAGGAAGAGTCCAG-3′ for Sp110 and primers 5′-GTTGAATTCATGTTCACCATGACAAGAG-3′ and 5′-GTTCTCGAGTTATTCTTGGAGGACAG-3′ for Sp110b.

    Techniques: Stable Transfection, Transfection, Plasmid Preparation, Incubation, Staining, Expressing, Concentration Assay, Reverse Transcription Polymerase Chain Reaction

    Hepatic differentiation of the hPSC line predicted a low differentiation tendency. (A) Phase contrast images of hepatocyte-like cells derived from hPSCs, H9, KhES-4, KhES-4, and 201B7 maintained under conventional KSR-based culture condition with feeder cells were shown. Scale bars = 20 μm. (B) albumin secretion, urea production, and CYP3A4 activity of these cells and primary human hepatocytes (PHH) were examined. The results are presented as the mean of three biological independent experiments, and error bars represent SD. (C) Left: albumin secretion from hepatocyte-like cells derived from hPSCs H9, 253G1B1, and 201B7 cultured under feeder-free culture conditions were examined by ELISA on differentiation day 20. Concentration was calculated using a standard reagent followed by normalization to the total RNA content. The results are presented as the mean of three biological independent experiments, and error bars represent SD. Right: custom polymerase chain reaction array analysis of these hepatocyte-like cells. Each gene expression level is compared among three lines ( red > yellow > green ). The mean of gene expression levels of three independent experiments were used for the analysis. (D) Albumin secretion, urea production, and CYP3A4 activity of 19-9-7T, its aberrant clone (19-9-7T abr) and primary human hepatocytes (PHH) were examined. The results are presented as the mean of three biological independent experiments, and error bars represent SD. KSR, knockout serum replacement.

    Journal: Stem Cells and Development

    Article Title: Prediction of Differentiation Tendency Toward Hepatocytes from Gene Expression in Undifferentiated Human Pluripotent Stem Cells

    doi: 10.1089/scd.2016.0099

    Figure Lengend Snippet: Hepatic differentiation of the hPSC line predicted a low differentiation tendency. (A) Phase contrast images of hepatocyte-like cells derived from hPSCs, H9, KhES-4, KhES-4, and 201B7 maintained under conventional KSR-based culture condition with feeder cells were shown. Scale bars = 20 μm. (B) albumin secretion, urea production, and CYP3A4 activity of these cells and primary human hepatocytes (PHH) were examined. The results are presented as the mean of three biological independent experiments, and error bars represent SD. (C) Left: albumin secretion from hepatocyte-like cells derived from hPSCs H9, 253G1B1, and 201B7 cultured under feeder-free culture conditions were examined by ELISA on differentiation day 20. Concentration was calculated using a standard reagent followed by normalization to the total RNA content. The results are presented as the mean of three biological independent experiments, and error bars represent SD. Right: custom polymerase chain reaction array analysis of these hepatocyte-like cells. Each gene expression level is compared among three lines ( red > yellow > green ). The mean of gene expression levels of three independent experiments were used for the analysis. (D) Albumin secretion, urea production, and CYP3A4 activity of 19-9-7T, its aberrant clone (19-9-7T abr) and primary human hepatocytes (PHH) were examined. The results are presented as the mean of three biological independent experiments, and error bars represent SD. KSR, knockout serum replacement.

    Article Snippet: For PCR array, 500 ng of RNA of the cells and total RNA of human fetal and adult liver (Clontech Laboratories, Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription with RT2 First Strand Kit (Qiagen) or High Capacity RNA-to-cDNA kit (Thermo Fisher Scientific) for RT2 Profiler™ PCR Array or TaqMan Array, respectively.

    Techniques: Derivative Assay, Activity Assay, Cell Culture, Enzyme-linked Immunosorbent Assay, Concentration Assay, Polymerase Chain Reaction, Expressing, Knock-Out

    Quantitative PCR analysis of siRNA-treated HepG2 cells. Quantitative real-time PCR (qPCR) was performed on reverse transcribed total RNA isolated from control HepG2 cells and those pretreated with gene-specific short interfering RNA (siRNA). A : hSVCT1-specific

    Journal:

    Article Title: Mechanisms and regulation of vitamin C uptake: studies of the hSVCT systems in human liver epithelial cells

    doi: 10.1152/ajpgi.90399.2008

    Figure Lengend Snippet: Quantitative PCR analysis of siRNA-treated HepG2 cells. Quantitative real-time PCR (qPCR) was performed on reverse transcribed total RNA isolated from control HepG2 cells and those pretreated with gene-specific short interfering RNA (siRNA). A : hSVCT1-specific

    Article Snippet: RNA from HepG2 cells and human liver RNA (Clontech, Mountain View, CA) was isolated using TriZOL (Invitrogen, Carlsbad, CA), following the manufacturer's instructions.

    Techniques: Real-time Polymerase Chain Reaction, Isolation, Small Interfering RNA

    MA plot (log-ratio of the expression intensities versus the mean log-expression of the intensities) for a typical ToxArray™ hybridization containing a mouse liver experimental RNA sample (Cy5-labeled) and Stratagene Universal Reference RNA (Cy3-labeled), each with A. thaliana spike-in control RNA added prior to labelling. The green circles indicate the mouse genes and red circles are the Rpl5 gene which reached scanner saturation in the Cy3 channel at many spots. The EC series covers the full range of signal intensities with no signal gaps. The LOWESS fit shown is through the external controls only, with a span of 0.3.

    Journal: BMC Genomics

    Article Title: Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray(TM)

    doi: 10.1186/1471-2164-7-266

    Figure Lengend Snippet: MA plot (log-ratio of the expression intensities versus the mean log-expression of the intensities) for a typical ToxArray™ hybridization containing a mouse liver experimental RNA sample (Cy5-labeled) and Stratagene Universal Reference RNA (Cy3-labeled), each with A. thaliana spike-in control RNA added prior to labelling. The green circles indicate the mouse genes and red circles are the Rpl5 gene which reached scanner saturation in the Cy3 channel at many spots. The EC series covers the full range of signal intensities with no signal gaps. The LOWESS fit shown is through the external controls only, with a span of 0.3.

    Article Snippet: For analysis of differential expression following PB exposures, 5 ng of EC RNA was spiked into 5 μg of liver RNA sample and mouse reference RNA (Stratagene, La Jolla, CA, USA).

    Techniques: Expressing, Hybridization, Labeling

    A treatment/control experimental design. Ten mice were treated with IL-1β ( n = 5), or saline ( n = 5; referred to as untreated). Four hours after treatment, the mice were sacrificed, liver samples were collected, and total RNA was extracted from the tissue. At this point, aliquots of the same RNA sample were sequenced on both an Illumina HiSeq 2500 and an Ion Torrent Proton. Next, RNA-Seq reads from each platform were aligned using three alignment algorithms: 1) GSNAP, 2) STAR, and 3) STAR, followed by Bowtie2 to align reads not mapped by STAR (STAR + Bowtie2). Lastly, all aligned data were normalized using the P ipeline O f R NA-Seq T ransformations (PORT)

    Journal: BMC Genomics

    Article Title: A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

    doi: 10.1186/s12864-017-4011-0

    Figure Lengend Snippet: A treatment/control experimental design. Ten mice were treated with IL-1β ( n = 5), or saline ( n = 5; referred to as untreated). Four hours after treatment, the mice were sacrificed, liver samples were collected, and total RNA was extracted from the tissue. At this point, aliquots of the same RNA sample were sequenced on both an Illumina HiSeq 2500 and an Ion Torrent Proton. Next, RNA-Seq reads from each platform were aligned using three alignment algorithms: 1) GSNAP, 2) STAR, and 3) STAR, followed by Bowtie2 to align reads not mapped by STAR (STAR + Bowtie2). Lastly, all aligned data were normalized using the P ipeline O f R NA-Seq T ransformations (PORT)

    Article Snippet: Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms.

    Techniques: Mouse Assay, RNA Sequencing Assay