total mrna Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Thermo Fisher dynabeads mrna purification kit
    Optimization of TRAP immunoprecipitation. The amount of antibody required for the TRAP IP was determined by titration. 500 μl hippocampal lysate was incubated with varying amounts of anti-HA antibody from 2.5 to 12.5 μg, followed by pull down of the <t>antibody-ribosome-mRNA</t> complex with protein A <t>dynabeads.</t> After washing, half the beads were used for protein extraction while the other half were used RNA isolation. ( A ) Protein concentration in the input lysate and remaining in the supernatant after IP (Post-IP Lysate) as well as the amount of protein eluted from the beads was determined by Western blotting. Western blots for the ribosomal protein RPP0 and the HA-tagged RPL22 ribosomal protein are shown (i) along with the quantification of the protein bands (ii). ( B ) Concentration of RNA eluted from the beads is shown for each IP. Based on these combined results 10 μg antibody per 500 μl lysate was determined to be the optimal concentration to ensure maximal depletion of the HA-tagged polysomes and give the best signal-to-noise.
    Dynabeads Mrna Purification Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4350 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dynabeads mrna purification kit/product/Thermo Fisher
    Average 99 stars, based on 4350 article reviews
    Price from $9.99 to $1999.99
    dynabeads mrna purification kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Millipore mrna quantification total rna
    Zag gene expression in adipose tissue of ob/ob and lean mice. Total <t>RNA</t> was extracted from subcutaneous and epididymal fat pads of lean ( ob/ + ) and ob/ob mice, and <t>mRNA</t> levels of (A) Zag and (B) leptin were measured by real-time PCR and normalised to β-actin. Results are expressed as means± s.e.m. for groups of 6. * P
    Mrna Quantification Total Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mrna quantification total rna/product/Millipore
    Average 99 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    mrna quantification total rna - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    93
    Bio-Rad total mrna
    Expression of genes in the protective arm of RAS is increased in the <t>CD34</t> + cells of diabetic individuals resistant to the development of microvascular complications, despite poor glycemic control. Quantitative RT-PCR revealed a significant increase in the <t>mRNA</t> levels of ACE2 ( A ) and Mas receptor ( B ) (Mann-Whitney test; n = 5) in the CD34 + cells of patients with longstanding diabetes without microvascular complications (D −MV) compared with cells from either control or patients with diabetes with microvascular complications (D +MV). Datum was expressed as relative mRNA expression normalized to β-actin as a housekeeping gene. C : Migration in response to SDF was higher in CD34 + cells from patients with diabetes without microvascular complications (D −MV) or control cells. Compared with controls, this response was decreased in cells from patients with diabetes with microvascular complications (D +MV) ( n = 5, one-way ANOVA, Newman-Keuls posttest).
    Total Mrna, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 93/100, based on 637 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total mrna/product/Bio-Rad
    Average 93 stars, based on 637 article reviews
    Price from $9.99 to $1999.99
    total mrna - by Bioz Stars, 2020-09
    93/100 stars
      Buy from Supplier

    95
    Thermo Fisher total mrna
    Expression analyses of <t>TMEM33</t> transcripts in normal human tissues and human cancer cell lines. The <t>mRNA</t> blots (Clontech) were sequentially probed with a radiolabeled TMEM33 cDNA probe, followed by β - actin or GAPDH cDNA probe. S.M., smooth muscle; PBL, peripheral blood lymphocytes; HL-60, promyelogenous leukemia; K-562, chronic myelogenous leukemia; MOLT-4, lymphoblastic leukemia; BL-Raji, Burkitt’s lymphoma; SW480, colorectal adenocarcinoma; A549, lung carcinoma; G361, melanoma; DU-145, prostate cancer
    Total Mrna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 8163 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total mrna/product/Thermo Fisher
    Average 95 stars, based on 8163 article reviews
    Price from $9.99 to $1999.99
    total mrna - by Bioz Stars, 2020-09
    95/100 stars
      Buy from Supplier

    93
    Illumina Inc total mrna
    Gene identification in translatome and transcriptome sequencing, in comparison with SILAC-based mass spectrometry. ( A and B ) Number of genes and proteins identified with RNA-seq (lighter circles) and MS (dark circle), respectively, in A549 cells (A) and HBE cells (B). ( C and D ) <t>RNC-mRNA</t> abundance distribution in A549 cells (C) and HBE cells (D). Genes were step-wise classified, based on abundances of quantified RNC-mRNA. Each bar indicates gene number of detection in its respective category. In each category, the percentage of the number of MS quantifiable protein to the number of genes that are detected by RNC-mRNA sequencing is shown with a dot. ( E ) Validation of gene detection in RNC-mRNA, extracted from A549 and HBE cells, respectively. Six randomly selected genes were subjected to RT-PCR assays and indicated by HGNC gene names.
    Total Mrna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 403 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total mrna/product/Illumina Inc
    Average 93 stars, based on 403 article reviews
    Price from $9.99 to $1999.99
    total mrna - by Bioz Stars, 2020-09
    93/100 stars
      Buy from Supplier

    mrna  (TaKaRa)
    95
    TaKaRa mrna
    Gene identification in translatome and transcriptome sequencing, in comparison with SILAC-based mass spectrometry. ( A and B ) Number of genes and proteins identified with RNA-seq (lighter circles) and MS (dark circle), respectively, in A549 cells (A) and HBE cells (B). ( C and D ) <t>RNC-mRNA</t> abundance distribution in A549 cells (C) and HBE cells (D). Genes were step-wise classified, based on abundances of quantified RNC-mRNA. Each bar indicates gene number of detection in its respective category. In each category, the percentage of the number of MS quantifiable protein to the number of genes that are detected by RNC-mRNA sequencing is shown with a dot. ( E ) Validation of gene detection in RNC-mRNA, extracted from A549 and HBE cells, respectively. Six randomly selected genes were subjected to RT-PCR assays and indicated by HGNC gene names.
    Mrna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 95/100, based on 12805 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mrna/product/TaKaRa
    Average 95 stars, based on 12805 article reviews
    Price from $9.99 to $1999.99
    mrna - by Bioz Stars, 2020-09
    95/100 stars
      Buy from Supplier

    92
    tiangen biotech co total mrna
    Gene identification in translatome and transcriptome sequencing, in comparison with SILAC-based mass spectrometry. ( A and B ) Number of genes and proteins identified with RNA-seq (lighter circles) and MS (dark circle), respectively, in A549 cells (A) and HBE cells (B). ( C and D ) <t>RNC-mRNA</t> abundance distribution in A549 cells (C) and HBE cells (D). Genes were step-wise classified, based on abundances of quantified RNC-mRNA. Each bar indicates gene number of detection in its respective category. In each category, the percentage of the number of MS quantifiable protein to the number of genes that are detected by RNC-mRNA sequencing is shown with a dot. ( E ) Validation of gene detection in RNC-mRNA, extracted from A549 and HBE cells, respectively. Six randomly selected genes were subjected to RT-PCR assays and indicated by HGNC gene names.
    Total Mrna, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 92/100, based on 116 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total mrna/product/tiangen biotech co
    Average 92 stars, based on 116 article reviews
    Price from $9.99 to $1999.99
    total mrna - by Bioz Stars, 2020-09
    92/100 stars
      Buy from Supplier

    99
    Millipore genelute mrna prep kit
    Gene identification in translatome and transcriptome sequencing, in comparison with SILAC-based mass spectrometry. ( A and B ) Number of genes and proteins identified with RNA-seq (lighter circles) and MS (dark circle), respectively, in A549 cells (A) and HBE cells (B). ( C and D ) <t>RNC-mRNA</t> abundance distribution in A549 cells (C) and HBE cells (D). Genes were step-wise classified, based on abundances of quantified RNC-mRNA. Each bar indicates gene number of detection in its respective category. In each category, the percentage of the number of MS quantifiable protein to the number of genes that are detected by RNC-mRNA sequencing is shown with a dot. ( E ) Validation of gene detection in RNC-mRNA, extracted from A549 and HBE cells, respectively. Six randomly selected genes were subjected to RT-PCR assays and indicated by HGNC gene names.
    Genelute Mrna Prep Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/genelute mrna prep kit/product/Millipore
    Average 99 stars, based on 25 article reviews
    Price from $9.99 to $1999.99
    genelute mrna prep kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Promega maxwell 16 cell lev total rna purification kit
    Gene identification in translatome and transcriptome sequencing, in comparison with SILAC-based mass spectrometry. ( A and B ) Number of genes and proteins identified with RNA-seq (lighter circles) and MS (dark circle), respectively, in A549 cells (A) and HBE cells (B). ( C and D ) <t>RNC-mRNA</t> abundance distribution in A549 cells (C) and HBE cells (D). Genes were step-wise classified, based on abundances of quantified RNC-mRNA. Each bar indicates gene number of detection in its respective category. In each category, the percentage of the number of MS quantifiable protein to the number of genes that are detected by RNC-mRNA sequencing is shown with a dot. ( E ) Validation of gene detection in RNC-mRNA, extracted from A549 and HBE cells, respectively. Six randomly selected genes were subjected to RT-PCR assays and indicated by HGNC gene names.
    Maxwell 16 Cell Lev Total Rna Purification Kit, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/maxwell 16 cell lev total rna purification kit/product/Promega
    Average 99 stars, based on 25 article reviews
    Price from $9.99 to $1999.99
    maxwell 16 cell lev total rna purification kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    99
    Thermo Fisher mmp 9 mrna total rna
    PRP on <t>mRNA</t> expression of <t>MMP-9</t> in RT-PCR PRP, platelet-rich plasma; MMP, matrix metalloproteinase; RT-PCR, reverse transcription polymerase chain reaction.
    Mmp 9 Mrna Total Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mmp 9 mrna total rna/product/Thermo Fisher
    Average 99 stars, based on 34 article reviews
    Price from $9.99 to $1999.99
    mmp 9 mrna total rna - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    92
    Stratagene total mrna
    Unique responses to I-IFNs by lung DC subsets determine virus replication. A. Sorting strategy for lung DCs. Lung DCs are defined as CD45 + CD11c + MHC-II + Siglec-F - Ly6C - cells (gates I-IV). From gate IV individual DC subsets were further gated into CD103 + DC (gate V) and CD11b high DC (gate VI) for separation by cell sorting. B. qPCR analysis of Ifnar genes and signaling related genes in lung CD103 + DCs (blue bars) and lung CD11b high DCs isolated from IFNAR +/+ naïve mice. C. qPCR analysis of ISG expression by MLN CD103 + DCs (blue bars) or MLN CD11b high DCs (green bars) sorted from either IFNAR -/- or IFNAR +/+ PR8-infected mice at 4 dpi. D. Expression of viral NP <t>mRNA</t> was determined by qPCR for individual sorted MLN DC subsets as in (C). E. CD103 + DCs and CD11b high DCs isolated from the lungs of IFNAR -/- or IFNAR +/+ mice during the course of PR8 infection were assayed for viral NP mRNA by qPCR. F. Total MLN <t>cDNA</t> obtained from PR8-infected IFNAR -/- mice, at different time points after infection, was analyzed for mRNA of the 8 segments of influenza virus (NP, HA, M, NS1, NA, PB1, PB2, PA) by qPCR. Error bars represent mean +/− SD, * p
    Total Mrna, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 102 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/total mrna/product/Stratagene
    Average 92 stars, based on 102 article reviews
    Price from $9.99 to $1999.99
    total mrna - by Bioz Stars, 2020-09
    92/100 stars
      Buy from Supplier

    99
    Illumina Inc truseq mrna stranded library preparation kit
    Unique responses to I-IFNs by lung DC subsets determine virus replication. A. Sorting strategy for lung DCs. Lung DCs are defined as CD45 + CD11c + MHC-II + Siglec-F - Ly6C - cells (gates I-IV). From gate IV individual DC subsets were further gated into CD103 + DC (gate V) and CD11b high DC (gate VI) for separation by cell sorting. B. qPCR analysis of Ifnar genes and signaling related genes in lung CD103 + DCs (blue bars) and lung CD11b high DCs isolated from IFNAR +/+ naïve mice. C. qPCR analysis of ISG expression by MLN CD103 + DCs (blue bars) or MLN CD11b high DCs (green bars) sorted from either IFNAR -/- or IFNAR +/+ PR8-infected mice at 4 dpi. D. Expression of viral NP <t>mRNA</t> was determined by qPCR for individual sorted MLN DC subsets as in (C). E. CD103 + DCs and CD11b high DCs isolated from the lungs of IFNAR -/- or IFNAR +/+ mice during the course of PR8 infection were assayed for viral NP mRNA by qPCR. F. Total MLN <t>cDNA</t> obtained from PR8-infected IFNAR -/- mice, at different time points after infection, was analyzed for mRNA of the 8 segments of influenza virus (NP, HA, M, NS1, NA, PB1, PB2, PA) by qPCR. Error bars represent mean +/− SD, * p
    Truseq Mrna Stranded Library Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq mrna stranded library preparation kit/product/Illumina Inc
    Average 99 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    truseq mrna stranded library preparation kit - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    91
    TaKaRa bovine kidney mrna
    Unique responses to I-IFNs by lung DC subsets determine virus replication. A. Sorting strategy for lung DCs. Lung DCs are defined as CD45 + CD11c + MHC-II + Siglec-F - Ly6C - cells (gates I-IV). From gate IV individual DC subsets were further gated into CD103 + DC (gate V) and CD11b high DC (gate VI) for separation by cell sorting. B. qPCR analysis of Ifnar genes and signaling related genes in lung CD103 + DCs (blue bars) and lung CD11b high DCs isolated from IFNAR +/+ naïve mice. C. qPCR analysis of ISG expression by MLN CD103 + DCs (blue bars) or MLN CD11b high DCs (green bars) sorted from either IFNAR -/- or IFNAR +/+ PR8-infected mice at 4 dpi. D. Expression of viral NP <t>mRNA</t> was determined by qPCR for individual sorted MLN DC subsets as in (C). E. CD103 + DCs and CD11b high DCs isolated from the lungs of IFNAR -/- or IFNAR +/+ mice during the course of PR8 infection were assayed for viral NP mRNA by qPCR. F. Total MLN <t>cDNA</t> obtained from PR8-infected IFNAR -/- mice, at different time points after infection, was analyzed for mRNA of the 8 segments of influenza virus (NP, HA, M, NS1, NA, PB1, PB2, PA) by qPCR. Error bars represent mean +/− SD, * p
    Bovine Kidney Mrna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bovine kidney mrna/product/TaKaRa
    Average 91 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    bovine kidney mrna - by Bioz Stars, 2020-09
    91/100 stars
      Buy from Supplier

    99
    Thermo Fisher human brain mrna
    Absolute <t>LRRK1</t> and LRRK2 <t>mRNA</t> expression levels in human control brain. Copy numbers for LRRK1 and LRRK2 were calculated by comparison to a standard curve of co-amplified plasmids encoding full length Lrrk1 or Lrrk2 proteins.
    Human Brain Mrna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human brain mrna/product/Thermo Fisher
    Average 99 stars, based on 21 article reviews
    Price from $9.99 to $1999.99
    human brain mrna - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    85
    Tel Test Inc rna stat 60 total rna mrna isolation reagent
    Expression of mouse Dlx4 <t>mRNA</t> in E10.5 yolk sac-derived blood, E13.5 fetal liver, adult bone marrow, and adult reticulocytes. One µg of total <t>RNA</t> of mouse yolk sac blood, fetal liver blood, adult bone marrow (BM), and adult reticulocytes was subjected
    Rna Stat 60 Total Rna Mrna Isolation Reagent, supplied by Tel Test Inc, used in various techniques. Bioz Stars score: 85/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna stat 60 total rna mrna isolation reagent/product/Tel Test Inc
    Average 85 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    rna stat 60 total rna mrna isolation reagent - by Bioz Stars, 2020-09
    85/100 stars
      Buy from Supplier

    Image Search Results


    Optimization of TRAP immunoprecipitation. The amount of antibody required for the TRAP IP was determined by titration. 500 μl hippocampal lysate was incubated with varying amounts of anti-HA antibody from 2.5 to 12.5 μg, followed by pull down of the antibody-ribosome-mRNA complex with protein A dynabeads. After washing, half the beads were used for protein extraction while the other half were used RNA isolation. ( A ) Protein concentration in the input lysate and remaining in the supernatant after IP (Post-IP Lysate) as well as the amount of protein eluted from the beads was determined by Western blotting. Western blots for the ribosomal protein RPP0 and the HA-tagged RPL22 ribosomal protein are shown (i) along with the quantification of the protein bands (ii). ( B ) Concentration of RNA eluted from the beads is shown for each IP. Based on these combined results 10 μg antibody per 500 μl lysate was determined to be the optimal concentration to ensure maximal depletion of the HA-tagged polysomes and give the best signal-to-noise.

    Journal: eLife

    Article Title: FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory

    doi: 10.7554/eLife.46919

    Figure Lengend Snippet: Optimization of TRAP immunoprecipitation. The amount of antibody required for the TRAP IP was determined by titration. 500 μl hippocampal lysate was incubated with varying amounts of anti-HA antibody from 2.5 to 12.5 μg, followed by pull down of the antibody-ribosome-mRNA complex with protein A dynabeads. After washing, half the beads were used for protein extraction while the other half were used RNA isolation. ( A ) Protein concentration in the input lysate and remaining in the supernatant after IP (Post-IP Lysate) as well as the amount of protein eluted from the beads was determined by Western blotting. Western blots for the ribosomal protein RPP0 and the HA-tagged RPL22 ribosomal protein are shown (i) along with the quantification of the protein bands (ii). ( B ) Concentration of RNA eluted from the beads is shown for each IP. Based on these combined results 10 μg antibody per 500 μl lysate was determined to be the optimal concentration to ensure maximal depletion of the HA-tagged polysomes and give the best signal-to-noise.

    Article Snippet: Sequencing libraries were prepared using Poly(A) RNA selection (Dynabeads mRNA Purification Kit, ThermoFisher Scientific) and the TruSeq RNA Library Prep Kit (Illumina).

    Techniques: Immunoprecipitation, Titration, Incubation, Protein Extraction, Isolation, Protein Concentration, Western Blot, Concentration Assay

    A, Heat map of correlation coefficient from test group and control group. The colours in the panel represent the correlation coefficient of the two samples. Blue shows the two samples have a low correlation coefficient, and red shows the high similarity of the two samples. The plots are performed in R gplots package. B, Venn diagram of the genes number. The plot shows the number of genes methylated in both groups and the number of specific methylated genes. These plots are performed in R VennDiagram package. C, Scatter plot between two groups. RPM values of all identified methylated genes are plotted. The values of X and Y axes in the scatter plot are the averaged RPM values from each group (log2‐scaled). Genes above the top line (red dots, up‐regulation) or below the bottom line (blue dots, down‐regulation) indicate more than 2.0 fold change (default fold change value is 2.0) between the two compared groups. Brown dots indicate methylation level without differentially expression. D, Heat map of gene expression. The heat map shows the 500 genes with the largest coefficient of variation (CV) based on RPM counts. Each row represents one gene, and all the 500 genes are categorized into 10 clusters based on K‐means clustering. Each column represents one sample. The colour in the panel represents the relative expression level (log2‐transformed). The colour scale is shown below: blue represents an expression level below the mean; red represents an expression level above the mean. The coloured bar top at the top panel showed the sample group, and the coloured bar at the right side of the panel indicates the 10 divisions which were performed using K‐means. These plots were performed in R heatmap2 package. E, Volcano plot for test vs control. Red/blue curves indicate 2.0 fold change of differentially methylated gene with statistical significance (red: up‐regulated; blue: down‐regulated). Brown curve indicates non‐differentially methylated gene; fc or q ‐value is not satisfied. The values of X and Y axes in the volcano plot are the fold change (log2‐transformed) and P ‐value (‐log10‐transformed) between the two groups, respectively. F, m6A peak distribution. Transcriptome‐wide distribution of m6A peaks. Pie chart shows the percentage of non‐IP reads (top) and m6A peaks (bottom) within distinct regions of RNA; NP stands for non–protein‐coding genes, whereas PR stands for protein‐coding genes. Distribution of m6A peaks along mRNA (no figure if not all of 5’UTRs, CDSs and 3’UTRs exist). 5’UTRs, CDSs and 3’UTRs of each transcript are separately binned regions spanning 1% of their total lengths; Y‐coordinates represent percentage of m6A peaks located in each bin. Correlation between gene expression level and m6A peak enrichment. The peak enrichment value relative to the transcript abundance within the input RNA is plotted

    Journal: Journal of Cellular and Molecular Medicine

    Article Title: RNA demethylase ALKBH5 promotes ovarian carcinogenesis in a simulated tumour microenvironment through stimulating NF‐ κB pathway. RNA demethylase ALKBH5 promotes ovarian carcinogenesis in a simulated tumour microenvironment through stimulating NF‐ κB pathway

    doi: 10.1111/jcmm.15228

    Figure Lengend Snippet: A, Heat map of correlation coefficient from test group and control group. The colours in the panel represent the correlation coefficient of the two samples. Blue shows the two samples have a low correlation coefficient, and red shows the high similarity of the two samples. The plots are performed in R gplots package. B, Venn diagram of the genes number. The plot shows the number of genes methylated in both groups and the number of specific methylated genes. These plots are performed in R VennDiagram package. C, Scatter plot between two groups. RPM values of all identified methylated genes are plotted. The values of X and Y axes in the scatter plot are the averaged RPM values from each group (log2‐scaled). Genes above the top line (red dots, up‐regulation) or below the bottom line (blue dots, down‐regulation) indicate more than 2.0 fold change (default fold change value is 2.0) between the two compared groups. Brown dots indicate methylation level without differentially expression. D, Heat map of gene expression. The heat map shows the 500 genes with the largest coefficient of variation (CV) based on RPM counts. Each row represents one gene, and all the 500 genes are categorized into 10 clusters based on K‐means clustering. Each column represents one sample. The colour in the panel represents the relative expression level (log2‐transformed). The colour scale is shown below: blue represents an expression level below the mean; red represents an expression level above the mean. The coloured bar top at the top panel showed the sample group, and the coloured bar at the right side of the panel indicates the 10 divisions which were performed using K‐means. These plots were performed in R heatmap2 package. E, Volcano plot for test vs control. Red/blue curves indicate 2.0 fold change of differentially methylated gene with statistical significance (red: up‐regulated; blue: down‐regulated). Brown curve indicates non‐differentially methylated gene; fc or q ‐value is not satisfied. The values of X and Y axes in the volcano plot are the fold change (log2‐transformed) and P ‐value (‐log10‐transformed) between the two groups, respectively. F, m6A peak distribution. Transcriptome‐wide distribution of m6A peaks. Pie chart shows the percentage of non‐IP reads (top) and m6A peaks (bottom) within distinct regions of RNA; NP stands for non–protein‐coding genes, whereas PR stands for protein‐coding genes. Distribution of m6A peaks along mRNA (no figure if not all of 5’UTRs, CDSs and 3’UTRs exist). 5’UTRs, CDSs and 3’UTRs of each transcript are separately binned regions spanning 1% of their total lengths; Y‐coordinates represent percentage of m6A peaks located in each bin. Correlation between gene expression level and m6A peak enrichment. The peak enrichment value relative to the transcript abundance within the input RNA is plotted

    Article Snippet: 2.7 m6A‐SeqTotal RNA was extracted from the co‐cultured ovarian cancer cell lines (HO8910 and A2780) and their controls using TRIzol reagent (Ambion). mRNA was further purified using a dynabeads mRNA purification kit (Ambion, catalog no. 61006) and then submitted to further analysis conducted by Kangchen Biological Engineering Co. Fragmented RNA was subjected to m6A immunoprecipitation (m6A IP) using anti‐m6A rabbit polyclonal antibody (Synaptic Systems; catalog No. 202003) followed by RNA‐Seq.

    Techniques: Methylation, Expressing, Transformation Assay

    osk RNAs engage in direct interactions in the oocyte. Egg chambers from osk RNA null flies [;; osk A87 /Df(3R)p XT103 ] expressing full-length transgenic osk mRNA under the control of pCog and nos -Gal4 drivers. ( A – A ″, B – B ″) RNA expressed from oskWT ( A – A ″) and oskAA ( B – B ″) transgenes is transported into the oocyte (stage 6) and localizes at the posterior pole of stage 9 egg chambers ( oskWT , 93%; oskAA , 91%). In a subset of the egg chambers ( oskWT , 30%; oskAA , 39%), ectopic osk mRNA is additionally detected. Staufen protein is equally enriched at the posterior pole of egg chambers. As established by qRT-PCR, oskWT and oskAA were overexpressed to similar levels in comparison to osk levels of w 1118 flies. osk RNAs were detected using an osk (coding region)–antisense probe (red) immuno-stained with anti-Staufen antibodies (white). ( C – C ″, D – D ″) Egg chambers coexpressing oskAA with either egfp-WT or egfp-UU . Both reporter RNAs enrich in young oocytes ( C , D ), but posterior pole accumulation of the egfp-WT is strongly reduced ( C′ ) (16% ± 13%) compared with the egfp-UU ( D′ ) (91% ± 5%) at stage 9 of oogenesis. Staufen enriches equally in the presence of either RNA ( C″ , D″ ). A summary of reporter3′UTR RNA hitchhiking at stage 9 of oogenesis is shown below . All egg chambers were simultaneously stained with egfp -antisense probe (red) to specifically detect the reporter RNAs and anti-Staufen antibodies (white) to also detect full-length osk mRNA. The accumulation of egfp -reporter RNA at the posterior pole was scored in at least two independent experiments, analyzing at least 15 egg chambers per experiment. All egg chambers were stained for RNA (red) by whole-mount in situ hybridization and counterstained with DAPI (blue). Bar, 50 μm.

    Journal: RNA

    Article Title: Dimerization of oskar 3? UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte

    doi: 10.1261/rna.2686411

    Figure Lengend Snippet: osk RNAs engage in direct interactions in the oocyte. Egg chambers from osk RNA null flies [;; osk A87 /Df(3R)p XT103 ] expressing full-length transgenic osk mRNA under the control of pCog and nos -Gal4 drivers. ( A – A ″, B – B ″) RNA expressed from oskWT ( A – A ″) and oskAA ( B – B ″) transgenes is transported into the oocyte (stage 6) and localizes at the posterior pole of stage 9 egg chambers ( oskWT , 93%; oskAA , 91%). In a subset of the egg chambers ( oskWT , 30%; oskAA , 39%), ectopic osk mRNA is additionally detected. Staufen protein is equally enriched at the posterior pole of egg chambers. As established by qRT-PCR, oskWT and oskAA were overexpressed to similar levels in comparison to osk levels of w 1118 flies. osk RNAs were detected using an osk (coding region)–antisense probe (red) immuno-stained with anti-Staufen antibodies (white). ( C – C ″, D – D ″) Egg chambers coexpressing oskAA with either egfp-WT or egfp-UU . Both reporter RNAs enrich in young oocytes ( C , D ), but posterior pole accumulation of the egfp-WT is strongly reduced ( C′ ) (16% ± 13%) compared with the egfp-UU ( D′ ) (91% ± 5%) at stage 9 of oogenesis. Staufen enriches equally in the presence of either RNA ( C″ , D″ ). A summary of reporter3′UTR RNA hitchhiking at stage 9 of oogenesis is shown below . All egg chambers were simultaneously stained with egfp -antisense probe (red) to specifically detect the reporter RNAs and anti-Staufen antibodies (white) to also detect full-length osk mRNA. The accumulation of egfp -reporter RNA at the posterior pole was scored in at least two independent experiments, analyzing at least 15 egg chambers per experiment. All egg chambers were stained for RNA (red) by whole-mount in situ hybridization and counterstained with DAPI (blue). Bar, 50 μm.

    Article Snippet: Total ovary RNA was isolated (TRIzol; Invitrogen), poly(A) RNAs were enriched (mRNA Purification Kit; DynaBeads), and cDNAs were generated (Superscript First Strand Synthesis; Invitrogen).

    Techniques: Expressing, Transgenic Assay, Quantitative RT-PCR, Staining, In Situ Hybridization

    The dimerization domain promotes osk RNA interaction during hitchhiking in vivo. ( A ) Schematic representation of the reporter constructs used in this panel. ( A′–Q ). Egg chambers from w 1118 flies expressing egfp-WT, -UU , or -GNRA under the control of a mat-α4-tub -Gal4 driver. ( A′ ) qRT-PCR experiment probing the relative levels of gene expression of egfp-WT , egfp-UU , and egfp-GNRA RNAs. RNA expression is shown as the percentage of the egfp-WT RNA level. All RNA levels were normalized to rp49 RNA. ( B–P , R , S ) Reporter RNAs are detected using an egfp -antisense probe, endogenous osk is visualized using a probe antisense to the osk coding sequence, and Osk protein is stained with anti-Osk antibodies. All egg chambers shown were counterstained with DAPI (blue). Bar, 50 μm. The panels highlighting the posterior pole of different oocytes (D–F , I–K , N–P ) show images at the same magnification as C , H , and M . ( B , G , L ) egfp-WT , - UU , and GNRA reporter RNAs accumulate in young oocytes (stage 6). ( C , H , M ) Posterior accumulation of mutant egfp-UU and -GNRA reporter RNAs is strongly reduced in comparison with egfp-WT RNA at stage 9. The arrow in C indicates the position of the posterior pole. ( D , I , N ) egfp-WT , and to a lesser degree also egfp-UU and - GNRA , RNAs are present at the posterior pole of stage 10 oocytes. ( E , J , O ) Endogenous osk mRNA at stage 9 is localized in the presence of reporter RNAs. ( F , K , P ) Osk protein is expressed in stage 9 oocytes in the presence of reporter RNAs. ( Q ) Percentage of oocytes showing a posterior accumulation of egfp-WT , - UU , or -GNRA reporter RNAs in stage 9 egg chambers. The accumulation of egfp RNAs was scored in at least two independent experiments ( egfp-WT : n = 127; egfp-UU : n = 61; egfp-GNRA : n = 71). ( R , S ) w 1118 control flies, which do not express transgenic reporter3′UTR , were also stained for osk mRNA and Osk protein for comparison.

    Journal: RNA

    Article Title: Dimerization of oskar 3? UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte

    doi: 10.1261/rna.2686411

    Figure Lengend Snippet: The dimerization domain promotes osk RNA interaction during hitchhiking in vivo. ( A ) Schematic representation of the reporter constructs used in this panel. ( A′–Q ). Egg chambers from w 1118 flies expressing egfp-WT, -UU , or -GNRA under the control of a mat-α4-tub -Gal4 driver. ( A′ ) qRT-PCR experiment probing the relative levels of gene expression of egfp-WT , egfp-UU , and egfp-GNRA RNAs. RNA expression is shown as the percentage of the egfp-WT RNA level. All RNA levels were normalized to rp49 RNA. ( B–P , R , S ) Reporter RNAs are detected using an egfp -antisense probe, endogenous osk is visualized using a probe antisense to the osk coding sequence, and Osk protein is stained with anti-Osk antibodies. All egg chambers shown were counterstained with DAPI (blue). Bar, 50 μm. The panels highlighting the posterior pole of different oocytes (D–F , I–K , N–P ) show images at the same magnification as C , H , and M . ( B , G , L ) egfp-WT , - UU , and GNRA reporter RNAs accumulate in young oocytes (stage 6). ( C , H , M ) Posterior accumulation of mutant egfp-UU and -GNRA reporter RNAs is strongly reduced in comparison with egfp-WT RNA at stage 9. The arrow in C indicates the position of the posterior pole. ( D , I , N ) egfp-WT , and to a lesser degree also egfp-UU and - GNRA , RNAs are present at the posterior pole of stage 10 oocytes. ( E , J , O ) Endogenous osk mRNA at stage 9 is localized in the presence of reporter RNAs. ( F , K , P ) Osk protein is expressed in stage 9 oocytes in the presence of reporter RNAs. ( Q ) Percentage of oocytes showing a posterior accumulation of egfp-WT , - UU , or -GNRA reporter RNAs in stage 9 egg chambers. The accumulation of egfp RNAs was scored in at least two independent experiments ( egfp-WT : n = 127; egfp-UU : n = 61; egfp-GNRA : n = 71). ( R , S ) w 1118 control flies, which do not express transgenic reporter3′UTR , were also stained for osk mRNA and Osk protein for comparison.

    Article Snippet: Total ovary RNA was isolated (TRIzol; Invitrogen), poly(A) RNAs were enriched (mRNA Purification Kit; DynaBeads), and cDNAs were generated (Superscript First Strand Synthesis; Invitrogen).

    Techniques: In Vivo, Construct, Expressing, Quantitative RT-PCR, RNA Expression, Sequencing, Staining, Mutagenesis, Transgenic Assay

    dPNUTS is a nuclear protein that colocalises with transcriptionally active RNAPII on salivary gland polytene chromosomes. A) Distribution of dPNUTS transcripts detected by RNA in situ hybridization; dPNUTS transcripts are maternally provided (top left) and are ubiquitously distributed in embryos at cellularisation (top right). At gastrulation, d PNUTS mRNA levels are enriched in the germband and in the fore- and hind-gut (fg and hg, respectively). Later, d PNUTS is highly expressed in the brain (br) and ventral nerve cord (vnc). Embryonic stage and approximate age, hours post fertilization (hpf), are indicated. B) 3 rd instar wing discs stained to reveal the distribution of ectopically expressed Myc-tagged dPNUTS (green in merge), Histone H3S10ph (red in merge, marking mitotic nuclei) and DNA. C) Images of whole mount salivary gland and magnified images of an individual nucleus (below), stained to show the localization of Myc-tagged dPNUTS (green in merge) and DNA (magenta in merge). D) Line scans of images in C) reveal that Myc-tagged dPNUTS is localised to interbands that stain weakly for DNA. Fluorescence intensity of anti-Myc antibody and TOPRO-3 staining was measured along a line through the indicated chromosomal region in the images shown. The profile plot below shows that the peaks of Myc-PNUTS and DNA of staining do not overlap. E) Polytene chromosomes from salivary gland squashes showing that dPNUTS localises to a number of discrete bands that are broadly distributed. F) Merging of the green signal representing dPNUTS with the red signal representing RNAPII Ser2-P (H5) identifies sites where these two proteins co-localize (example indicated with arrow). The relative signals of dPNUTS and RNAPII Ser2-P vary between sites, but the majority dPNUTS loci colocalize with RNAPII Ser2-P staining (star indicates example where only dPNUTS staining is visible).

    Journal: PLoS Genetics

    Article Title: PNUTS/PP1 Regulates RNAPII-Mediated Gene Expression and Is Necessary for Developmental Growth

    doi: 10.1371/journal.pgen.1003885

    Figure Lengend Snippet: dPNUTS is a nuclear protein that colocalises with transcriptionally active RNAPII on salivary gland polytene chromosomes. A) Distribution of dPNUTS transcripts detected by RNA in situ hybridization; dPNUTS transcripts are maternally provided (top left) and are ubiquitously distributed in embryos at cellularisation (top right). At gastrulation, d PNUTS mRNA levels are enriched in the germband and in the fore- and hind-gut (fg and hg, respectively). Later, d PNUTS is highly expressed in the brain (br) and ventral nerve cord (vnc). Embryonic stage and approximate age, hours post fertilization (hpf), are indicated. B) 3 rd instar wing discs stained to reveal the distribution of ectopically expressed Myc-tagged dPNUTS (green in merge), Histone H3S10ph (red in merge, marking mitotic nuclei) and DNA. C) Images of whole mount salivary gland and magnified images of an individual nucleus (below), stained to show the localization of Myc-tagged dPNUTS (green in merge) and DNA (magenta in merge). D) Line scans of images in C) reveal that Myc-tagged dPNUTS is localised to interbands that stain weakly for DNA. Fluorescence intensity of anti-Myc antibody and TOPRO-3 staining was measured along a line through the indicated chromosomal region in the images shown. The profile plot below shows that the peaks of Myc-PNUTS and DNA of staining do not overlap. E) Polytene chromosomes from salivary gland squashes showing that dPNUTS localises to a number of discrete bands that are broadly distributed. F) Merging of the green signal representing dPNUTS with the red signal representing RNAPII Ser2-P (H5) identifies sites where these two proteins co-localize (example indicated with arrow). The relative signals of dPNUTS and RNAPII Ser2-P vary between sites, but the majority dPNUTS loci colocalize with RNAPII Ser2-P staining (star indicates example where only dPNUTS staining is visible).

    Article Snippet: Total RNA quality and quantity was verified on a NanoDrop1000 spectrophotometer (Thermofisher) and Bioanalyzer 2100. mRNA was polyA selected using Dynabeads mRNA Purification Kit for mRNA Purification from Total RNA Preps (Invitrogen).

    Techniques: RNA In Situ Hybridization, Staining, Fluorescence

    Zag gene expression in adipose tissue of ob/ob and lean mice. Total RNA was extracted from subcutaneous and epididymal fat pads of lean ( ob/ + ) and ob/ob mice, and mRNA levels of (A) Zag and (B) leptin were measured by real-time PCR and normalised to β-actin. Results are expressed as means± s.e.m. for groups of 6. * P

    Journal: The Journal of Endocrinology

    Article Title: Downregulation of zinc-?2-glycoprotein in adipose tissue and liver of obese ob/ob mice and by tumour necrosis factor-? in adipocytes

    doi: 10.1677/JOE-09-0299

    Figure Lengend Snippet: Zag gene expression in adipose tissue of ob/ob and lean mice. Total RNA was extracted from subcutaneous and epididymal fat pads of lean ( ob/ + ) and ob/ob mice, and mRNA levels of (A) Zag and (B) leptin were measured by real-time PCR and normalised to β-actin. Results are expressed as means± s.e.m. for groups of 6. * P

    Article Snippet: Real-time PCR for mRNA quantification Total RNA was extracted from tissues and cells using TRI reagent (Sigma), and the RNA concentration was determined from the absorbance at 260 nm.

    Techniques: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction

    Tnfα gene expression in adipose tissue and liver of ob/ob and lean mice. Total RNA was extracted from epididymal fat pad and liver of lean ( ob/ + ) and ob/ob mice, and Tnfα mRNA levels in (A) epididymal adipose tissue and (B) liver were measured by real-time PCR and normalised to β-actin. Results are expressed as means± s.e.m. for groups of 6. * P

    Journal: The Journal of Endocrinology

    Article Title: Downregulation of zinc-?2-glycoprotein in adipose tissue and liver of obese ob/ob mice and by tumour necrosis factor-? in adipocytes

    doi: 10.1677/JOE-09-0299

    Figure Lengend Snippet: Tnfα gene expression in adipose tissue and liver of ob/ob and lean mice. Total RNA was extracted from epididymal fat pad and liver of lean ( ob/ + ) and ob/ob mice, and Tnfα mRNA levels in (A) epididymal adipose tissue and (B) liver were measured by real-time PCR and normalised to β-actin. Results are expressed as means± s.e.m. for groups of 6. * P

    Article Snippet: Real-time PCR for mRNA quantification Total RNA was extracted from tissues and cells using TRI reagent (Sigma), and the RNA concentration was determined from the absorbance at 260 nm.

    Techniques: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction

    Expression of genes in the protective arm of RAS is increased in the CD34 + cells of diabetic individuals resistant to the development of microvascular complications, despite poor glycemic control. Quantitative RT-PCR revealed a significant increase in the mRNA levels of ACE2 ( A ) and Mas receptor ( B ) (Mann-Whitney test; n = 5) in the CD34 + cells of patients with longstanding diabetes without microvascular complications (D −MV) compared with cells from either control or patients with diabetes with microvascular complications (D +MV). Datum was expressed as relative mRNA expression normalized to β-actin as a housekeeping gene. C : Migration in response to SDF was higher in CD34 + cells from patients with diabetes without microvascular complications (D −MV) or control cells. Compared with controls, this response was decreased in cells from patients with diabetes with microvascular complications (D +MV) ( n = 5, one-way ANOVA, Newman-Keuls posttest).

    Journal: Diabetes

    Article Title: Activation of the ACE2/Angiotensin-(1-7)/Mas Receptor Axis Enhances the Reparative Function of Dysfunctional Diabetic Endothelial Progenitors

    doi: 10.2337/db12-0808

    Figure Lengend Snippet: Expression of genes in the protective arm of RAS is increased in the CD34 + cells of diabetic individuals resistant to the development of microvascular complications, despite poor glycemic control. Quantitative RT-PCR revealed a significant increase in the mRNA levels of ACE2 ( A ) and Mas receptor ( B ) (Mann-Whitney test; n = 5) in the CD34 + cells of patients with longstanding diabetes without microvascular complications (D −MV) compared with cells from either control or patients with diabetes with microvascular complications (D +MV). Datum was expressed as relative mRNA expression normalized to β-actin as a housekeeping gene. C : Migration in response to SDF was higher in CD34 + cells from patients with diabetes without microvascular complications (D −MV) or control cells. Compared with controls, this response was decreased in cells from patients with diabetes with microvascular complications (D +MV) ( n = 5, one-way ANOVA, Newman-Keuls posttest).

    Article Snippet: Total mRNA of human CD34+ cells was isolated using the Aurum Total RNA Mini Kit (Bio-Rad), and the purity of RNA was determined by NanoDrop (ND-1000 UV-Vis spectrophotometer; NanoDrop Technologies).

    Techniques: Expressing, Quantitative RT-PCR, MANN-WHITNEY, Migration

    Expression analyses of TMEM33 transcripts in normal human tissues and human cancer cell lines. The mRNA blots (Clontech) were sequentially probed with a radiolabeled TMEM33 cDNA probe, followed by β - actin or GAPDH cDNA probe. S.M., smooth muscle; PBL, peripheral blood lymphocytes; HL-60, promyelogenous leukemia; K-562, chronic myelogenous leukemia; MOLT-4, lymphoblastic leukemia; BL-Raji, Burkitt’s lymphoma; SW480, colorectal adenocarcinoma; A549, lung carcinoma; G361, melanoma; DU-145, prostate cancer

    Journal: Breast Cancer Research and Treatment

    Article Title: TMEM33: a new stress-inducible endoplasmic reticulum transmembrane protein and modulator of the unfolded protein response signaling

    doi: 10.1007/s10549-015-3536-7

    Figure Lengend Snippet: Expression analyses of TMEM33 transcripts in normal human tissues and human cancer cell lines. The mRNA blots (Clontech) were sequentially probed with a radiolabeled TMEM33 cDNA probe, followed by β - actin or GAPDH cDNA probe. S.M., smooth muscle; PBL, peripheral blood lymphocytes; HL-60, promyelogenous leukemia; K-562, chronic myelogenous leukemia; MOLT-4, lymphoblastic leukemia; BL-Raji, Burkitt’s lymphoma; SW480, colorectal adenocarcinoma; A549, lung carcinoma; G361, melanoma; DU-145, prostate cancer

    Article Snippet: Construction of Myc -TMEM33 expression vector TMEM33 cDNA (741 bp) was amplified by RT-PCR using total mRNA from human testes (Ambion, Foster City, CA) and cloned into the pCR2.1 vector (Invitrogen).

    Techniques: Expressing

    TMEM33 is an ER stress-inducible molecule. a HeLa cells were treated with indicated doses of thapsigargin (TG) or tunicamycin (TU) for various times, followed by immunoblotting with anti-TMEM33 antibody. The blots were reprobed with anti-GAPDH antibody. The expression levels of TMEM33 were quantified using ImageQuant software (Molecular Dynamics), and normalized against GAPDH in corresponding lanes. The fold open triangle indicates TMEM33 level at various doses or time points relative to control lane. Data shown are representative of two to three independent experiments. b HeLa cells were grown in high glucose (25 mM) DMEM containing 10 % FBS. The medium was switched to low glucose (5.5 mM) DMEM containing 10 % FBS for the times indicated, followed by sequential immunoblotting with anti-TMEM33 antibody and anti-GAPDH antibody. Normalized expression levels of TMEM33 were quantified as in panel a . Data shown are representative of two independent experiments. c Northern blot analysis of TMEM33 mRNA in HeLa cells treated with thapsigargin as shown. The blot was reprobed with radiolabeled GAPDH cDNA. The normalized expression levels of 7.7 kb TMEM33 transcript at various time points were quantified using ImageQuant software (Molecular Dynamics)

    Journal: Breast Cancer Research and Treatment

    Article Title: TMEM33: a new stress-inducible endoplasmic reticulum transmembrane protein and modulator of the unfolded protein response signaling

    doi: 10.1007/s10549-015-3536-7

    Figure Lengend Snippet: TMEM33 is an ER stress-inducible molecule. a HeLa cells were treated with indicated doses of thapsigargin (TG) or tunicamycin (TU) for various times, followed by immunoblotting with anti-TMEM33 antibody. The blots were reprobed with anti-GAPDH antibody. The expression levels of TMEM33 were quantified using ImageQuant software (Molecular Dynamics), and normalized against GAPDH in corresponding lanes. The fold open triangle indicates TMEM33 level at various doses or time points relative to control lane. Data shown are representative of two to three independent experiments. b HeLa cells were grown in high glucose (25 mM) DMEM containing 10 % FBS. The medium was switched to low glucose (5.5 mM) DMEM containing 10 % FBS for the times indicated, followed by sequential immunoblotting with anti-TMEM33 antibody and anti-GAPDH antibody. Normalized expression levels of TMEM33 were quantified as in panel a . Data shown are representative of two independent experiments. c Northern blot analysis of TMEM33 mRNA in HeLa cells treated with thapsigargin as shown. The blot was reprobed with radiolabeled GAPDH cDNA. The normalized expression levels of 7.7 kb TMEM33 transcript at various time points were quantified using ImageQuant software (Molecular Dynamics)

    Article Snippet: Construction of Myc -TMEM33 expression vector TMEM33 cDNA (741 bp) was amplified by RT-PCR using total mRNA from human testes (Ambion, Foster City, CA) and cloned into the pCR2.1 vector (Invitrogen).

    Techniques: Expressing, Software, Northern Blot

    Gene identification in translatome and transcriptome sequencing, in comparison with SILAC-based mass spectrometry. ( A and B ) Number of genes and proteins identified with RNA-seq (lighter circles) and MS (dark circle), respectively, in A549 cells (A) and HBE cells (B). ( C and D ) RNC-mRNA abundance distribution in A549 cells (C) and HBE cells (D). Genes were step-wise classified, based on abundances of quantified RNC-mRNA. Each bar indicates gene number of detection in its respective category. In each category, the percentage of the number of MS quantifiable protein to the number of genes that are detected by RNC-mRNA sequencing is shown with a dot. ( E ) Validation of gene detection in RNC-mRNA, extracted from A549 and HBE cells, respectively. Six randomly selected genes were subjected to RT-PCR assays and indicated by HGNC gene names.

    Journal: Nucleic Acids Research

    Article Title: Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

    doi: 10.1093/nar/gkt178

    Figure Lengend Snippet: Gene identification in translatome and transcriptome sequencing, in comparison with SILAC-based mass spectrometry. ( A and B ) Number of genes and proteins identified with RNA-seq (lighter circles) and MS (dark circle), respectively, in A549 cells (A) and HBE cells (B). ( C and D ) RNC-mRNA abundance distribution in A549 cells (C) and HBE cells (D). Genes were step-wise classified, based on abundances of quantified RNC-mRNA. Each bar indicates gene number of detection in its respective category. In each category, the percentage of the number of MS quantifiable protein to the number of genes that are detected by RNC-mRNA sequencing is shown with a dot. ( E ) Validation of gene detection in RNC-mRNA, extracted from A549 and HBE cells, respectively. Six randomly selected genes were subjected to RT-PCR assays and indicated by HGNC gene names.

    Article Snippet: Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina).

    Techniques: Sequencing, Mass Spectrometry, RNA Sequencing Assay, Reverse Transcription Polymerase Chain Reaction

    Biased TRs of BDP1 splice variants in A549 and HBE cells. ( A and B ) BDP1 splice variants detected in mRNA (A) and RNC-mRNA (B) of A549 and HBE cells, respectively. The bars represent the normalized number of reads that were mapped to specific splicing junctions of different variants. ( C ) TR of these splice variants in A549 and HBE cells, respectively.

    Journal: Nucleic Acids Research

    Article Title: Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

    doi: 10.1093/nar/gkt178

    Figure Lengend Snippet: Biased TRs of BDP1 splice variants in A549 and HBE cells. ( A and B ) BDP1 splice variants detected in mRNA (A) and RNC-mRNA (B) of A549 and HBE cells, respectively. The bars represent the normalized number of reads that were mapped to specific splicing junctions of different variants. ( C ) TR of these splice variants in A549 and HBE cells, respectively.

    Article Snippet: Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina).

    Techniques:

    Distribution and correlation analysis of mRNA TRs, comparing A549 cells with HBE cells. ( A ) Correlation of mRNA and RNC-mRNA abundances in A549 and HBE cells, respectively. ( B ) Correlation of mRNA ratio (A549/HBE) and RNC-mRNA ratio (A549/HBE). ( C ) Correlation of TRs and mRNA lengths. ( D ) Correlation of TR fold changes (A549/HBE) and mRNA lengths. The genes with TR ratio changes greater than 4 folds are indicated by green dots.

    Journal: Nucleic Acids Research

    Article Title: Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

    doi: 10.1093/nar/gkt178

    Figure Lengend Snippet: Distribution and correlation analysis of mRNA TRs, comparing A549 cells with HBE cells. ( A ) Correlation of mRNA and RNC-mRNA abundances in A549 and HBE cells, respectively. ( B ) Correlation of mRNA ratio (A549/HBE) and RNC-mRNA ratio (A549/HBE). ( C ) Correlation of TRs and mRNA lengths. ( D ) Correlation of TR fold changes (A549/HBE) and mRNA lengths. The genes with TR ratio changes greater than 4 folds are indicated by green dots.

    Article Snippet: Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina).

    Techniques:

    Multivariate linear correlation among the relative abundances of mRNA, RNC-mRNA and protein. ( A and B ) Bivariate correlation comparing mRNA (A) and RNC-mRNA ratios (A549/HBE) (B) with SILAC ratio (A549/HBE), respectively. ( C and D ) Multivariate linear model, fitting SILAC ratio (A549/HBE), mRNA length and RNC-mRNA ratio (A549/HBE), calculated based on rpkM (C) and edgeR (D) normalizations regarding RNA-seq data. The viewpoints were on the fitted planes.

    Journal: Nucleic Acids Research

    Article Title: Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

    doi: 10.1093/nar/gkt178

    Figure Lengend Snippet: Multivariate linear correlation among the relative abundances of mRNA, RNC-mRNA and protein. ( A and B ) Bivariate correlation comparing mRNA (A) and RNC-mRNA ratios (A549/HBE) (B) with SILAC ratio (A549/HBE), respectively. ( C and D ) Multivariate linear model, fitting SILAC ratio (A549/HBE), mRNA length and RNC-mRNA ratio (A549/HBE), calculated based on rpkM (C) and edgeR (D) normalizations regarding RNA-seq data. The viewpoints were on the fitted planes.

    Article Snippet: Briefly, the polyA+ mRNA in the total mRNA or RNC-mRNA samples was isolated using the RNA Purification Beads (Illumina).

    Techniques: RNA Sequencing Assay

    PRP on mRNA expression of MMP-9 in RT-PCR PRP, platelet-rich plasma; MMP, matrix metalloproteinase; RT-PCR, reverse transcription polymerase chain reaction.

    Journal: Archives of Plastic Surgery

    Article Title: The Effect of Platelet-rich Plasma on Wounds of OLETF Rats Using Expression of Matrix Metalloproteinase-2 and -9 mRNA

    doi: 10.5999/aps.2012.39.2.106

    Figure Lengend Snippet: PRP on mRNA expression of MMP-9 in RT-PCR PRP, platelet-rich plasma; MMP, matrix metalloproteinase; RT-PCR, reverse transcription polymerase chain reaction.

    Article Snippet: RT-PCR of MMP-2, MMP-9 mRNA Total RNA was isolated from the tissues of wounds using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions.

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction

    Unique responses to I-IFNs by lung DC subsets determine virus replication. A. Sorting strategy for lung DCs. Lung DCs are defined as CD45 + CD11c + MHC-II + Siglec-F - Ly6C - cells (gates I-IV). From gate IV individual DC subsets were further gated into CD103 + DC (gate V) and CD11b high DC (gate VI) for separation by cell sorting. B. qPCR analysis of Ifnar genes and signaling related genes in lung CD103 + DCs (blue bars) and lung CD11b high DCs isolated from IFNAR +/+ naïve mice. C. qPCR analysis of ISG expression by MLN CD103 + DCs (blue bars) or MLN CD11b high DCs (green bars) sorted from either IFNAR -/- or IFNAR +/+ PR8-infected mice at 4 dpi. D. Expression of viral NP mRNA was determined by qPCR for individual sorted MLN DC subsets as in (C). E. CD103 + DCs and CD11b high DCs isolated from the lungs of IFNAR -/- or IFNAR +/+ mice during the course of PR8 infection were assayed for viral NP mRNA by qPCR. F. Total MLN cDNA obtained from PR8-infected IFNAR -/- mice, at different time points after infection, was analyzed for mRNA of the 8 segments of influenza virus (NP, HA, M, NS1, NA, PB1, PB2, PA) by qPCR. Error bars represent mean +/− SD, * p

    Journal: PLoS Pathogens

    Article Title: Unique Type I Interferon Responses Determine the Functional Fate of Migratory Lung Dendritic Cells during Influenza Virus Infection

    doi: 10.1371/journal.ppat.1002345

    Figure Lengend Snippet: Unique responses to I-IFNs by lung DC subsets determine virus replication. A. Sorting strategy for lung DCs. Lung DCs are defined as CD45 + CD11c + MHC-II + Siglec-F - Ly6C - cells (gates I-IV). From gate IV individual DC subsets were further gated into CD103 + DC (gate V) and CD11b high DC (gate VI) for separation by cell sorting. B. qPCR analysis of Ifnar genes and signaling related genes in lung CD103 + DCs (blue bars) and lung CD11b high DCs isolated from IFNAR +/+ naïve mice. C. qPCR analysis of ISG expression by MLN CD103 + DCs (blue bars) or MLN CD11b high DCs (green bars) sorted from either IFNAR -/- or IFNAR +/+ PR8-infected mice at 4 dpi. D. Expression of viral NP mRNA was determined by qPCR for individual sorted MLN DC subsets as in (C). E. CD103 + DCs and CD11b high DCs isolated from the lungs of IFNAR -/- or IFNAR +/+ mice during the course of PR8 infection were assayed for viral NP mRNA by qPCR. F. Total MLN cDNA obtained from PR8-infected IFNAR -/- mice, at different time points after infection, was analyzed for mRNA of the 8 segments of influenza virus (NP, HA, M, NS1, NA, PB1, PB2, PA) by qPCR. Error bars represent mean +/− SD, * p

    Article Snippet: Total mRNA was converted to cDNA by RT-PCR using oligo-dT reaction (Affinity Script, Stratagene). cDNA was diluted 50 times in water and triplicate reactions were setup in 384-well plates. qPCR reactions based on SYBR green detection, were performed using a Lightcycler equipment (Roche, USA) all reactions were normalized to α-tubulin as previously described . qPCR reactions with sorted DCs required mRNA amplification.

    Techniques: FACS, Real-time Polymerase Chain Reaction, Isolation, Mouse Assay, Expressing, Infection

    Ag-bearing DC migration is associated with localized viral mRNA and virus replication in the MLNs. A. Total MLN cDNA obtained from PR8-infected mice, at different time points after infection, was analyzed by qPCR for the 8 segments of influenza viral mRNA (NP (nucleoprotein), HA (hemagglutinin), M (matrix protein), NS1 (non-structural protein 1), NA (neuraminidase), PB1 (polymerase PB1), PB2 (polymerase PB2), and PA (polymerase PA) B. MLNs were isolated from PR8-infected mice and titers of infectious virus were determined. C. Cryostat sections of MLNs isolated from PR8-infected mice were fixed, permeabilized and stained for CD11c (green), NP, M (red) and B220 (blue), and visualized with an immunofluorescence microscope at 20x and 100x magnification. White arrows indicate Ag-bearing CD11c + cells at 20x magnification that were then zoomed and photographed at 100x.

    Journal: PLoS Pathogens

    Article Title: Unique Type I Interferon Responses Determine the Functional Fate of Migratory Lung Dendritic Cells during Influenza Virus Infection

    doi: 10.1371/journal.ppat.1002345

    Figure Lengend Snippet: Ag-bearing DC migration is associated with localized viral mRNA and virus replication in the MLNs. A. Total MLN cDNA obtained from PR8-infected mice, at different time points after infection, was analyzed by qPCR for the 8 segments of influenza viral mRNA (NP (nucleoprotein), HA (hemagglutinin), M (matrix protein), NS1 (non-structural protein 1), NA (neuraminidase), PB1 (polymerase PB1), PB2 (polymerase PB2), and PA (polymerase PA) B. MLNs were isolated from PR8-infected mice and titers of infectious virus were determined. C. Cryostat sections of MLNs isolated from PR8-infected mice were fixed, permeabilized and stained for CD11c (green), NP, M (red) and B220 (blue), and visualized with an immunofluorescence microscope at 20x and 100x magnification. White arrows indicate Ag-bearing CD11c + cells at 20x magnification that were then zoomed and photographed at 100x.

    Article Snippet: Total mRNA was converted to cDNA by RT-PCR using oligo-dT reaction (Affinity Script, Stratagene). cDNA was diluted 50 times in water and triplicate reactions were setup in 384-well plates. qPCR reactions based on SYBR green detection, were performed using a Lightcycler equipment (Roche, USA) all reactions were normalized to α-tubulin as previously described . qPCR reactions with sorted DCs required mRNA amplification.

    Techniques: Migration, Infection, Mouse Assay, Real-time Polymerase Chain Reaction, Isolation, Staining, Immunofluorescence, Microscopy

    Absolute LRRK1 and LRRK2 mRNA expression levels in human control brain. Copy numbers for LRRK1 and LRRK2 were calculated by comparison to a standard curve of co-amplified plasmids encoding full length Lrrk1 or Lrrk2 proteins.

    Journal: Mechanisms of ageing and development

    Article Title: Heterodimerization of Lrrk1-Lrrk2: Implications for LRRK2-associated Parkinson disease

    doi: 10.1016/j.mad.2010.01.009

    Figure Lengend Snippet: Absolute LRRK1 and LRRK2 mRNA expression levels in human control brain. Copy numbers for LRRK1 and LRRK2 were calculated by comparison to a standard curve of co-amplified plasmids encoding full length Lrrk1 or Lrrk2 proteins.

    Article Snippet: Full-length LRRK1 was reverse transcribed from human brain mRNA and Topo-cloned into the pcDNA3.1/V5-His TOPO TA® expression vector (Invitrogen).

    Techniques: Expressing, Amplification

    Expression of mouse Dlx4 mRNA in E10.5 yolk sac-derived blood, E13.5 fetal liver, adult bone marrow, and adult reticulocytes. One µg of total RNA of mouse yolk sac blood, fetal liver blood, adult bone marrow (BM), and adult reticulocytes was subjected

    Journal:

    Article Title: BP1 motif in the human ?-globin promoter affects ?-globin expression during embryonic/fetal erythropoiesis in transgenic mice bearing the human ?-globin gene

    doi: 10.1016/j.bcmd.2008.05.008

    Figure Lengend Snippet: Expression of mouse Dlx4 mRNA in E10.5 yolk sac-derived blood, E13.5 fetal liver, adult bone marrow, and adult reticulocytes. One µg of total RNA of mouse yolk sac blood, fetal liver blood, adult bone marrow (BM), and adult reticulocytes was subjected

    Article Snippet: Total RNA was isolated from human or mouse cells using RNA STAT-60 total RNA/mRNA isolation reagent (Tel-Test, Inc., Friendswood, TX) according to the manufacturer’s protocol and quantitated by absorbance at 260 nm.

    Techniques: Expressing, Derivative Assay