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    Zymo Research direct zol rna miniprep
    Nkx2.1Cre + -IN specific transcriptome a. Volcano plot of differentially expressed (DE) genes in the pulldown <t>RNA</t> of Fmr1 −/− -mCherry mice (n=8) compared to WT-mCherry control group (n=3). A few genes are annotated (because of their role in IN and synapse function) amongst significantly downregulated (blue) or upregulated genes (red). b. Top 10 ‘GO terms’ using the biological process package for DE genes in Fmr1 −/− -mCherry mice compared to WT-mCherry control group (see Methods). c. Volcano plot of DE genes in the pulldown RNA of Fmr1 −/− -hM3Dq mice (n=6) compared to WT-mCherry controls. d. Top 10 ‘GO terms’ using the biological process package for differentially expressed genes in Fmr1 −/− -hM3Dq mice compared to WT-mCherry control group (see Methods). e. Top: The total number of down- and up-regulated genes (compared to WT-mCherry controls) was higher in Fmr1 −/− -hM3Dq mice than in Fmr1 −/− -mCherry mice. Bottom: Density plot showing how the log 2 fold change was affected by the DREADD manipulation (more genes are different from WT mice in the Fmr1 −/− -hM3Dq group). f. List of genes associated with different subclasses of MGE-INs for which expression was changed by DREADDs (dark green: basket cells; light green: Chandelier cells; brown: SST cells; black: global MGE-IN markers. Scale bar represents the log 2 CPM (count per millions).
    Direct Zol Rna Miniprep, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Improvement of sensory deficits in Fragile X mice by increasing cortical interneuron activity after the critical period"

    Article Title: Improvement of sensory deficits in Fragile X mice by increasing cortical interneuron activity after the critical period

    Journal: bioRxiv

    doi: 10.1101/2022.05.17.492368

    Nkx2.1Cre + -IN specific transcriptome a. Volcano plot of differentially expressed (DE) genes in the pulldown RNA of Fmr1 −/− -mCherry mice (n=8) compared to WT-mCherry control group (n=3). A few genes are annotated (because of their role in IN and synapse function) amongst significantly downregulated (blue) or upregulated genes (red). b. Top 10 ‘GO terms’ using the biological process package for DE genes in Fmr1 −/− -mCherry mice compared to WT-mCherry control group (see Methods). c. Volcano plot of DE genes in the pulldown RNA of Fmr1 −/− -hM3Dq mice (n=6) compared to WT-mCherry controls. d. Top 10 ‘GO terms’ using the biological process package for differentially expressed genes in Fmr1 −/− -hM3Dq mice compared to WT-mCherry control group (see Methods). e. Top: The total number of down- and up-regulated genes (compared to WT-mCherry controls) was higher in Fmr1 −/− -hM3Dq mice than in Fmr1 −/− -mCherry mice. Bottom: Density plot showing how the log 2 fold change was affected by the DREADD manipulation (more genes are different from WT mice in the Fmr1 −/− -hM3Dq group). f. List of genes associated with different subclasses of MGE-INs for which expression was changed by DREADDs (dark green: basket cells; light green: Chandelier cells; brown: SST cells; black: global MGE-IN markers. Scale bar represents the log 2 CPM (count per millions).
    Figure Legend Snippet: Nkx2.1Cre + -IN specific transcriptome a. Volcano plot of differentially expressed (DE) genes in the pulldown RNA of Fmr1 −/− -mCherry mice (n=8) compared to WT-mCherry control group (n=3). A few genes are annotated (because of their role in IN and synapse function) amongst significantly downregulated (blue) or upregulated genes (red). b. Top 10 ‘GO terms’ using the biological process package for DE genes in Fmr1 −/− -mCherry mice compared to WT-mCherry control group (see Methods). c. Volcano plot of DE genes in the pulldown RNA of Fmr1 −/− -hM3Dq mice (n=6) compared to WT-mCherry controls. d. Top 10 ‘GO terms’ using the biological process package for differentially expressed genes in Fmr1 −/− -hM3Dq mice compared to WT-mCherry control group (see Methods). e. Top: The total number of down- and up-regulated genes (compared to WT-mCherry controls) was higher in Fmr1 −/− -hM3Dq mice than in Fmr1 −/− -mCherry mice. Bottom: Density plot showing how the log 2 fold change was affected by the DREADD manipulation (more genes are different from WT mice in the Fmr1 −/− -hM3Dq group). f. List of genes associated with different subclasses of MGE-INs for which expression was changed by DREADDs (dark green: basket cells; light green: Chandelier cells; brown: SST cells; black: global MGE-IN markers. Scale bar represents the log 2 CPM (count per millions).

    Techniques Used: Mouse Assay, Expressing

    Chronic chemogenetic activation of Nkx2.1-INs mitigates PV-IN loss and gene dysregulation in neonatal Fmr1 −/− mice, but not S1 circuit dynamics. a. Experimental design for chronic chemogenetic activation of Nkx2.1-INs (from P5 to P9) in Fmr1 −/− mice to assess Nkx2.1-specific Ribotag RNA-seq at P15, density of PVALB+ INs at P15, and in vivo 2P calcium imaging at P21. b. Cartoon of Ribotag approach for RNA-seq in both bulk samples and pull-down. c. Left: Volcano plot of differentially expressed (DE) genes in the bulk RNA of Fmr1 −/− -mCherry mice (n=6) compared to WT-mCherry control group (n=8). A few genes are annotated (because of their role in IN and synapse function) amongst significantly downregulated (blue) or upregulated genes (red). Right: Top 10 ‘GO terms’ using the biological process package (see Methods). d. Volcano plot of DE genes in the bulk RNA of Fmr1 −/− -hM3Dq mice (n=7) compared to WT-mCherry controls (n=8). Genes from c that were fully or partially corrected by the DREADD manipulation are in gray or light color font, respectively. e. Top: The total number of down- and up-regulated genes (compared to WT-mCherry controls) was smaller in Fmr1 −/− -hM3Dq mice than in Fmr1 −/− -mCherry. The expression of 435 genes was ‘corrected’ by the chronic chemogenetic treatment in Fmr1 −/− -hM3Dq mice. Bottom: Density plot showing how the log 2 fold change was affected by the DREADD manipulation (fewer genes are different from WT mice in the Fmr1 −/− -hM3Dq group). f. Correlation plot of genes affected in the Fmr1 −/− -mCherry and Fmr1 −/− -hM3Dq. Red and purple dots denote DE genes that are uniquely and significantly different from WT controls in Fmr1 −/− -mCherry and Fmr1 −/− -hM3Dq mice, respectively. Grey dots are shared DE genes in both groups. Note that purple genes are on average less different from WT than red genes. g. Representative examples of how DREADD manipulation affected genes for the “synapse organization” GO term (gray), or different subclasses of MGE-INs (dark green: basket cells; light green: Chandelier cells; brown: SST cells; black: global MGE-IN markers. Scale bar represents the log 2 CPM (count per millions). h. Quantification of total PVALB + cell density at P15 in the barrel field of S1 of WT-mCherry, Fmr1 −/− - mCherry and Fmr1 −/− -h3MDq mice. (160.9 ± 6.5 cells/mm 2 , 87.4 ± 5.5, and 118.6 ± 9.0, n=6, 7, and 8, respectively). i. Example field of view of Pyr neurons expressing AAV-GCaMP6s in S1 of Nkx2.1-Cre +/− ; Fmr1 −/− (scale bar= 100 μm). j. Mean Z-scores for spontaneous activity of Pyr cells are lower in Fmr1 −/− -hM3Dq mice compared to Fmr1 −/− -mCherry mice after chronic C21 injections. (spontaneous: 1.47 ± 0.25 vs. 0.85 ± 0.08, p=0.065, n=8 per group) k. Mean Z-scores for whisker-evoked activity (right) of Pyr cells are significantly lower in Fmr1 −/− - hM3Dq mice compared to Fmr1 −/− -mCherry mice after chronic C21 injections. (1.58 ± 0.29 vs. 0.84 ± 0.06, p=0.028, MW t-test, n=8 per group). l. The proportion of whisker-responsive Pyr cells was not changed by DREADDs in Fmr1 −/− mice. (14.4 ± 4.4% vs. 15.3 ± 3.3%, p=0.875, unpaired t-test) m. The neuronal adaptation index of Pyr cells to repetitive whisker stimulation was not changed by chemogenetics. (0.19 ± 0.00 for WT vs. 0.03 ± 0.01 for Fmr1 −/− ; p=0.652, unpaired t-test).
    Figure Legend Snippet: Chronic chemogenetic activation of Nkx2.1-INs mitigates PV-IN loss and gene dysregulation in neonatal Fmr1 −/− mice, but not S1 circuit dynamics. a. Experimental design for chronic chemogenetic activation of Nkx2.1-INs (from P5 to P9) in Fmr1 −/− mice to assess Nkx2.1-specific Ribotag RNA-seq at P15, density of PVALB+ INs at P15, and in vivo 2P calcium imaging at P21. b. Cartoon of Ribotag approach for RNA-seq in both bulk samples and pull-down. c. Left: Volcano plot of differentially expressed (DE) genes in the bulk RNA of Fmr1 −/− -mCherry mice (n=6) compared to WT-mCherry control group (n=8). A few genes are annotated (because of their role in IN and synapse function) amongst significantly downregulated (blue) or upregulated genes (red). Right: Top 10 ‘GO terms’ using the biological process package (see Methods). d. Volcano plot of DE genes in the bulk RNA of Fmr1 −/− -hM3Dq mice (n=7) compared to WT-mCherry controls (n=8). Genes from c that were fully or partially corrected by the DREADD manipulation are in gray or light color font, respectively. e. Top: The total number of down- and up-regulated genes (compared to WT-mCherry controls) was smaller in Fmr1 −/− -hM3Dq mice than in Fmr1 −/− -mCherry. The expression of 435 genes was ‘corrected’ by the chronic chemogenetic treatment in Fmr1 −/− -hM3Dq mice. Bottom: Density plot showing how the log 2 fold change was affected by the DREADD manipulation (fewer genes are different from WT mice in the Fmr1 −/− -hM3Dq group). f. Correlation plot of genes affected in the Fmr1 −/− -mCherry and Fmr1 −/− -hM3Dq. Red and purple dots denote DE genes that are uniquely and significantly different from WT controls in Fmr1 −/− -mCherry and Fmr1 −/− -hM3Dq mice, respectively. Grey dots are shared DE genes in both groups. Note that purple genes are on average less different from WT than red genes. g. Representative examples of how DREADD manipulation affected genes for the “synapse organization” GO term (gray), or different subclasses of MGE-INs (dark green: basket cells; light green: Chandelier cells; brown: SST cells; black: global MGE-IN markers. Scale bar represents the log 2 CPM (count per millions). h. Quantification of total PVALB + cell density at P15 in the barrel field of S1 of WT-mCherry, Fmr1 −/− - mCherry and Fmr1 −/− -h3MDq mice. (160.9 ± 6.5 cells/mm 2 , 87.4 ± 5.5, and 118.6 ± 9.0, n=6, 7, and 8, respectively). i. Example field of view of Pyr neurons expressing AAV-GCaMP6s in S1 of Nkx2.1-Cre +/− ; Fmr1 −/− (scale bar= 100 μm). j. Mean Z-scores for spontaneous activity of Pyr cells are lower in Fmr1 −/− -hM3Dq mice compared to Fmr1 −/− -mCherry mice after chronic C21 injections. (spontaneous: 1.47 ± 0.25 vs. 0.85 ± 0.08, p=0.065, n=8 per group) k. Mean Z-scores for whisker-evoked activity (right) of Pyr cells are significantly lower in Fmr1 −/− - hM3Dq mice compared to Fmr1 −/− -mCherry mice after chronic C21 injections. (1.58 ± 0.29 vs. 0.84 ± 0.06, p=0.028, MW t-test, n=8 per group). l. The proportion of whisker-responsive Pyr cells was not changed by DREADDs in Fmr1 −/− mice. (14.4 ± 4.4% vs. 15.3 ± 3.3%, p=0.875, unpaired t-test) m. The neuronal adaptation index of Pyr cells to repetitive whisker stimulation was not changed by chemogenetics. (0.19 ± 0.00 for WT vs. 0.03 ± 0.01 for Fmr1 −/− ; p=0.652, unpaired t-test).

    Techniques Used: Activation Assay, Mouse Assay, RNA Sequencing Assay, In Vivo, Imaging, Expressing, Activity Assay, Whisker Assay

    2) Product Images from "Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids"

    Article Title: Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids

    Journal: bioRxiv

    doi: 10.1101/2022.06.09.495585

    RNA sequencing of HNoV-infected 3D-HIE. 3D-HIE were infected with filter stool positive for GII.4 (#20942) for 2hrs at 37°C or kept uninfected. 3D-HIE were then washed twice in PBS, seeded in BME and cultured for 2d in the presence of GCDCA (500µM) and ruxolitinib (2µM). RNA was extracted with Direct-Zol RNA mini-kit and after quality control, the RNA was sequenced with the Illumina Hi-Seq 2500 platform. A) Viral reads were aligned to a consensus GII.4 Sydney (GenBank accession no. JX459908.1 ) and the counts were plotted in Graph Pad Prism. Each dot represents a biological replicate. B) Principal component analysis was performed to compare the biological replicates. Circles represents the independent repeats with the infected samples RC4, RC5 and RC-6 with the corresponding uninfected RC1, RC2 and RC3. C) Volcano plot of differentially expressed genes. On the y-axis, it’s the -Log 10 p-value. Above the dotted line lay genes with significant p-value (p-value
    Figure Legend Snippet: RNA sequencing of HNoV-infected 3D-HIE. 3D-HIE were infected with filter stool positive for GII.4 (#20942) for 2hrs at 37°C or kept uninfected. 3D-HIE were then washed twice in PBS, seeded in BME and cultured for 2d in the presence of GCDCA (500µM) and ruxolitinib (2µM). RNA was extracted with Direct-Zol RNA mini-kit and after quality control, the RNA was sequenced with the Illumina Hi-Seq 2500 platform. A) Viral reads were aligned to a consensus GII.4 Sydney (GenBank accession no. JX459908.1 ) and the counts were plotted in Graph Pad Prism. Each dot represents a biological replicate. B) Principal component analysis was performed to compare the biological replicates. Circles represents the independent repeats with the infected samples RC4, RC5 and RC-6 with the corresponding uninfected RC1, RC2 and RC3. C) Volcano plot of differentially expressed genes. On the y-axis, it’s the -Log 10 p-value. Above the dotted line lay genes with significant p-value (p-value

    Techniques Used: RNA Sequencing Assay, Infection, Cell Culture

    3) Product Images from "Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids"

    Article Title: Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids

    Journal: bioRxiv

    doi: 10.1101/2022.06.09.495585

    RNA sequencing of HNoV-infected 3D-HIE. 3D-HIE were infected with filter stool positive for GII.4 (#20942) for 2hrs at 37°C or kept uninfected. 3D-HIE were then washed twice in PBS, seeded in BME and cultured for 2d in the presence of GCDCA (500µM) and ruxolitinib (2µM). RNA was extracted with Direct-Zol RNA mini-kit and after quality control, the RNA was sequenced with the Illumina Hi-Seq 2500 platform. A) Viral reads were aligned to a consensus GII.4 Sydney (GenBank accession no. JX459908.1 ) and the counts were plotted in Graph Pad Prism. Each dot represents a biological replicate. B) Principal component analysis was performed to compare the biological replicates. Circles represents the independent repeats with the infected samples RC4, RC5 and RC-6 with the corresponding uninfected RC1, RC2 and RC3. C) Volcano plot of differentially expressed genes. On the y-axis, it’s the -Log 10 p-value. Above the dotted line lay genes with significant p-value (p-value
    Figure Legend Snippet: RNA sequencing of HNoV-infected 3D-HIE. 3D-HIE were infected with filter stool positive for GII.4 (#20942) for 2hrs at 37°C or kept uninfected. 3D-HIE were then washed twice in PBS, seeded in BME and cultured for 2d in the presence of GCDCA (500µM) and ruxolitinib (2µM). RNA was extracted with Direct-Zol RNA mini-kit and after quality control, the RNA was sequenced with the Illumina Hi-Seq 2500 platform. A) Viral reads were aligned to a consensus GII.4 Sydney (GenBank accession no. JX459908.1 ) and the counts were plotted in Graph Pad Prism. Each dot represents a biological replicate. B) Principal component analysis was performed to compare the biological replicates. Circles represents the independent repeats with the infected samples RC4, RC5 and RC-6 with the corresponding uninfected RC1, RC2 and RC3. C) Volcano plot of differentially expressed genes. On the y-axis, it’s the -Log 10 p-value. Above the dotted line lay genes with significant p-value (p-value

    Techniques Used: RNA Sequencing Assay, Infection, Cell Culture

    4) Product Images from "A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax-infected patients"

    Article Title: A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax-infected patients

    Journal: Scientific Reports

    doi: 10.1038/s41598-021-84607-w

    qRT-PCR of P. vivax total RNA samples. qRT-PCR amplification of housekeeping genes seryl tRNA synthetase ( a , d ), DNA repair helicase ( b , e ) and gamma-glutamylcysteine synthetase ( c , f ) , from the RNA samples of one Pv-iRT field-isolate (10 3 in light gray to 10 6 in dark gray), preserved in RNAlater or TRI Reagent and extracted by RNeasy Micro kit ( a – c ) or Direct-zol RNA MiniPrep ( d – f ), respectively. Bars and error bars represent the mean Cq and standard deviations (SD), respectively. Black square marks represent average Cq of RT- reactions, when amplification was observed before the last (45th) cycle stage. Blue diamond marks represent mean Cq amplification of human TLR9 gene for host contamination detection. Black * indicate when the mean Cq for each sample is higher than the limit of detection (3 times the Cq SDs from the correspondent RT- mean Cq) and blue § indicate when the mean Cq is higher than the mean Cq for host contamination detection (3 times the Cq SDs from the correspondent TLR9 mean Cq).
    Figure Legend Snippet: qRT-PCR of P. vivax total RNA samples. qRT-PCR amplification of housekeeping genes seryl tRNA synthetase ( a , d ), DNA repair helicase ( b , e ) and gamma-glutamylcysteine synthetase ( c , f ) , from the RNA samples of one Pv-iRT field-isolate (10 3 in light gray to 10 6 in dark gray), preserved in RNAlater or TRI Reagent and extracted by RNeasy Micro kit ( a – c ) or Direct-zol RNA MiniPrep ( d – f ), respectively. Bars and error bars represent the mean Cq and standard deviations (SD), respectively. Black square marks represent average Cq of RT- reactions, when amplification was observed before the last (45th) cycle stage. Blue diamond marks represent mean Cq amplification of human TLR9 gene for host contamination detection. Black * indicate when the mean Cq for each sample is higher than the limit of detection (3 times the Cq SDs from the correspondent RT- mean Cq) and blue § indicate when the mean Cq is higher than the mean Cq for host contamination detection (3 times the Cq SDs from the correspondent TLR9 mean Cq).

    Techniques Used: Quantitative RT-PCR, Amplification

    5) Product Images from "An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo"

    Article Title: An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo

    Journal: Science Translational Medicine

    doi: 10.1126/scitranslmed.abn7737

    Engineered ACE2 neutralizes authentic Omicron and confers protection in hamsters and hACE2 transgenic mice. ( A ) Sensitivity of engineered ACE2 to the Wuhan and Omicron strains was compared by using each infectious virus in Vero E6/TMPRSS2 cells. RNA copy number was analyzed by qRT-PCR against nucleocapsid. n = 3 technical replicates. ( B ) Experimental scheme for the hamster model of SARS-CoV-2. ( C ) Quantification of viral RNA in the lungs of treated or untreated hamsters at day 5 post infection with the SARS-CoV-2 Omicron strain was performed by qRT-PCR against nucleocapsid. (n=4 per group). ( D ) Gene expression of inflammatory cytokines and chemokines was quantified by qRT-PCR in the hamsters. The expression of the gene encoding β-actin was used for normalization. (n=4). ( E ) A survival curve is shown for CAG-hACE2 Tg mice infected with the Omicron strain with or without 3N39v4 ACE2 decoy treatment (control: 2 male, 2 female, treated: 3 male and 3 female). P -values were determined by Mann-Whitney U test (C), one-way ANOVA and Tukey's multiple comparison test (D) and log-rank test (E).
    Figure Legend Snippet: Engineered ACE2 neutralizes authentic Omicron and confers protection in hamsters and hACE2 transgenic mice. ( A ) Sensitivity of engineered ACE2 to the Wuhan and Omicron strains was compared by using each infectious virus in Vero E6/TMPRSS2 cells. RNA copy number was analyzed by qRT-PCR against nucleocapsid. n = 3 technical replicates. ( B ) Experimental scheme for the hamster model of SARS-CoV-2. ( C ) Quantification of viral RNA in the lungs of treated or untreated hamsters at day 5 post infection with the SARS-CoV-2 Omicron strain was performed by qRT-PCR against nucleocapsid. (n=4 per group). ( D ) Gene expression of inflammatory cytokines and chemokines was quantified by qRT-PCR in the hamsters. The expression of the gene encoding β-actin was used for normalization. (n=4). ( E ) A survival curve is shown for CAG-hACE2 Tg mice infected with the Omicron strain with or without 3N39v4 ACE2 decoy treatment (control: 2 male, 2 female, treated: 3 male and 3 female). P -values were determined by Mann-Whitney U test (C), one-way ANOVA and Tukey's multiple comparison test (D) and log-rank test (E).

    Techniques Used: Transgenic Assay, Mouse Assay, Quantitative RT-PCR, Infection, Expressing, MANN-WHITNEY

    6) Product Images from "A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax-infected patients"

    Article Title: A suitable RNA preparation methodology for whole transcriptome shotgun sequencing harvested from Plasmodium vivax-infected patients

    Journal: Scientific Reports

    doi: 10.1038/s41598-021-84607-w

    qRT-PCR of P. vivax total RNA samples. qRT-PCR amplification of housekeeping genes seryl tRNA synthetase ( a , d ), DNA repair helicase ( b , e ) and gamma-glutamylcysteine synthetase ( c , f ) , from the RNA samples of one Pv-iRT field-isolate (10 3 in light gray to 10 6 in dark gray), preserved in RNAlater or TRI Reagent and extracted by RNeasy Micro kit ( a – c ) or Direct-zol RNA MiniPrep ( d – f ), respectively. Bars and error bars represent the mean Cq and standard deviations (SD), respectively. Black square marks represent average Cq of RT- reactions, when amplification was observed before the last (45th) cycle stage. Blue diamond marks represent mean Cq amplification of human TLR9 gene for host contamination detection. Black * indicate when the mean Cq for each sample is higher than the limit of detection (3 times the Cq SDs from the correspondent RT- mean Cq) and blue § indicate when the mean Cq is higher than the mean Cq for host contamination detection (3 times the Cq SDs from the correspondent TLR9 mean Cq).
    Figure Legend Snippet: qRT-PCR of P. vivax total RNA samples. qRT-PCR amplification of housekeeping genes seryl tRNA synthetase ( a , d ), DNA repair helicase ( b , e ) and gamma-glutamylcysteine synthetase ( c , f ) , from the RNA samples of one Pv-iRT field-isolate (10 3 in light gray to 10 6 in dark gray), preserved in RNAlater or TRI Reagent and extracted by RNeasy Micro kit ( a – c ) or Direct-zol RNA MiniPrep ( d – f ), respectively. Bars and error bars represent the mean Cq and standard deviations (SD), respectively. Black square marks represent average Cq of RT- reactions, when amplification was observed before the last (45th) cycle stage. Blue diamond marks represent mean Cq amplification of human TLR9 gene for host contamination detection. Black * indicate when the mean Cq for each sample is higher than the limit of detection (3 times the Cq SDs from the correspondent RT- mean Cq) and blue § indicate when the mean Cq is higher than the mean Cq for host contamination detection (3 times the Cq SDs from the correspondent TLR9 mean Cq).

    Techniques Used: Quantitative RT-PCR, Amplification

    7) Product Images from "Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids"

    Article Title: Human norovirus efficiently replicates in differentiated 3D-human intestinal enteroids

    Journal: bioRxiv

    doi: 10.1101/2022.06.09.495585

    RNA sequencing of HNoV-infected 3D-HIE. 3D-HIE were infected with filter stool positive for GII.4 (#20942) for 2hrs at 37°C or kept uninfected. 3D-HIE were then washed twice in PBS, seeded in BME and cultured for 2d in the presence of GCDCA (500µM) and ruxolitinib (2µM). RNA was extracted with Direct-Zol RNA mini-kit and after quality control, the RNA was sequenced with the Illumina Hi-Seq 2500 platform. A) Viral reads were aligned to a consensus GII.4 Sydney (GenBank accession no. JX459908.1 ) and the counts were plotted in Graph Pad Prism. Each dot represents a biological replicate. B) Principal component analysis was performed to compare the biological replicates. Circles represents the independent repeats with the infected samples RC4, RC5 and RC-6 with the corresponding uninfected RC1, RC2 and RC3. C) Volcano plot of differentially expressed genes. On the y-axis, it’s the -Log 10 p-value. Above the dotted line lay genes with significant p-value (p-value
    Figure Legend Snippet: RNA sequencing of HNoV-infected 3D-HIE. 3D-HIE were infected with filter stool positive for GII.4 (#20942) for 2hrs at 37°C or kept uninfected. 3D-HIE were then washed twice in PBS, seeded in BME and cultured for 2d in the presence of GCDCA (500µM) and ruxolitinib (2µM). RNA was extracted with Direct-Zol RNA mini-kit and after quality control, the RNA was sequenced with the Illumina Hi-Seq 2500 platform. A) Viral reads were aligned to a consensus GII.4 Sydney (GenBank accession no. JX459908.1 ) and the counts were plotted in Graph Pad Prism. Each dot represents a biological replicate. B) Principal component analysis was performed to compare the biological replicates. Circles represents the independent repeats with the infected samples RC4, RC5 and RC-6 with the corresponding uninfected RC1, RC2 and RC3. C) Volcano plot of differentially expressed genes. On the y-axis, it’s the -Log 10 p-value. Above the dotted line lay genes with significant p-value (p-value

    Techniques Used: RNA Sequencing Assay, Infection, Cell Culture

    8) Product Images from "Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer"

    Article Title: Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer

    Journal: bioRxiv

    doi: 10.1101/2022.05.20.492866

    A large-scale transcriptome screen as a platform for splicing discovery. A) Experimental workflow for RNA-seq analysis of lung adenocarcinoma genes and variants. B) Transcriptome profiles of cells expressing different gene constructs. Dimensionality reduction performed using t-distributed stochastic neighbor embedding (t-SNE) ( Van Der Maaten and Hinton 2008 ). Each point represents an experimental replicate. Genes and alleles of particular interest are colored and labeled. Controls are circles colored in black. Circle = wild-type allele. Diamond = variant allele. C) Gene set analysis with GOseq of up-or down-regulated transcripts in MYC, KRAS, FBXW7, and negative control cells. Hallmark gene sets from mSigDB.
    Figure Legend Snippet: A large-scale transcriptome screen as a platform for splicing discovery. A) Experimental workflow for RNA-seq analysis of lung adenocarcinoma genes and variants. B) Transcriptome profiles of cells expressing different gene constructs. Dimensionality reduction performed using t-distributed stochastic neighbor embedding (t-SNE) ( Van Der Maaten and Hinton 2008 ). Each point represents an experimental replicate. Genes and alleles of particular interest are colored and labeled. Controls are circles colored in black. Circle = wild-type allele. Diamond = variant allele. C) Gene set analysis with GOseq of up-or down-regulated transcripts in MYC, KRAS, FBXW7, and negative control cells. Hallmark gene sets from mSigDB.

    Techniques Used: RNA Sequencing Assay, Expressing, Construct, Labeling, Variant Assay, Negative Control

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    Zymo Research zr rna miniprep
    Relative quantity of gDNA contamination of GAPDH and ACTB genes in <t>RNA</t> samples extracted using three methods. Comparison between ZR RNA <t>MiniPrep,</t> TRIzol, and GENEzol. *Very significant difference ( P
    Zr Rna Miniprep, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Relative quantity of gDNA contamination of GAPDH and ACTB genes in RNA samples extracted using three methods. Comparison between ZR RNA MiniPrep, TRIzol, and GENEzol. *Very significant difference ( P

    Journal: Journal of Equine Science

    Article Title: Comparison of commercial RNA extraction kits and qPCR master mixes for studying gene expression in small biopsy tissue samples from the equine gastric epithelium

    doi: 10.1294/jes.28.135

    Figure Lengend Snippet: Relative quantity of gDNA contamination of GAPDH and ACTB genes in RNA samples extracted using three methods. Comparison between ZR RNA MiniPrep, TRIzol, and GENEzol. *Very significant difference ( P

    Article Snippet: The 260/280 ratio of RNA extracted from ZR RNA MiniPrep was highest and closest to 2.0, followed by GENEzol and TRIzol.

    Techniques: