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  • mrna  (Qiagen)
    99
    Qiagen mrna
    Mrna, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 21522 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs mrna
    Mrna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4498 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore cas9 mrnas
    RGEN-induced Prkdc gene disruption in mice. ( A ) Representative T7E1 assays demonstrating mutagenesis efficiencies of <t>Cas9</t> <t>mRNA</t> plus Prkdc -specific sgRNA that were delivered via intracytoplasmic injection into one-cell-stage mouse embryos. Numbers indicate
    Cas9 Mrnas, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Shanghai Generay Biotech mrnas
    RGEN-induced Prkdc gene disruption in mice. ( A ) Representative T7E1 assays demonstrating mutagenesis efficiencies of <t>Cas9</t> <t>mRNA</t> plus Prkdc -specific sgRNA that were delivered via intracytoplasmic injection into one-cell-stage mouse embryos. Numbers indicate
    Mrnas, supplied by Shanghai Generay Biotech, used in various techniques. Bioz Stars score: 94/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa mrnas
    RNA-Seq and miRNA-Seq validated by RT-qPCR. a Validation of four DE <t>circRNAs.</t> b Validation of four DE <t>mRNAs.</t> c Validation of four DE miRNAs
    Mrnas, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 1921 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher mrnas
    Host cell mRNA synthesis and translation are unaffected by compound JMN3-003. A ) Relative TaqMan RT-PCR-based quantitation of three unstable cellular <t>mRNAs</t> (MCL1, <t>ASB7,</t> MKP-1) after exposure of cells to JMN3-003 for six hours. Controls were treated with Actinomycine D (Act D) for comparison. C T values are expressed relative to vehicle-treated samples and reflect averages of three independent experiments, each analyzed in triplicate, ± SD. B–D ) Expression of virus-encoded but not host cell or plasmid-encoded viral proteins is blocked by JMN3-003. Immunodetection of transiently expressed MeV-F ( B ), virus-encoded MeV-F ( C ), and virus-encoded influenza A/WSN M2 ( D ) in cell lysates after incubation of cells in the presence of compound or vehicle only (DMSO) for 30 hours. As internal cellular standard, membranes were probed for GAPDH in parallel. Numbers correspond to average densitometric quantitations ± SD of three experiments, representative immunoblots are shown. (ND: not determined).
    Mrnas, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 14442 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Horizon Discovery mrnas
    Host cell mRNA synthesis and translation are unaffected by compound JMN3-003. A ) Relative TaqMan RT-PCR-based quantitation of three unstable cellular <t>mRNAs</t> (MCL1, <t>ASB7,</t> MKP-1) after exposure of cells to JMN3-003 for six hours. Controls were treated with Actinomycine D (Act D) for comparison. C T values are expressed relative to vehicle-treated samples and reflect averages of three independent experiments, each analyzed in triplicate, ± SD. B–D ) Expression of virus-encoded but not host cell or plasmid-encoded viral proteins is blocked by JMN3-003. Immunodetection of transiently expressed MeV-F ( B ), virus-encoded MeV-F ( C ), and virus-encoded influenza A/WSN M2 ( D ) in cell lysates after incubation of cells in the presence of compound or vehicle only (DMSO) for 30 hours. As internal cellular standard, membranes were probed for GAPDH in parallel. Numbers correspond to average densitometric quantitations ± SD of three experiments, representative immunoblots are shown. (ND: not determined).
    Mrnas, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 99/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Pacific Biosciences mrnas
    Schematic diagram of the <t>TeloPrime</t> and SMARTer cDNA synthesis technologies. (A) SMARTer does not distinguish between truncated and full-length transcripts. (B) TeloPrime enriches for full-length transcripts by affinity of the 5’ adapter to the 5’ cap structure of full-length <t>mRNAs</t> during cDNA synthesis. Red and pink rectangular shapes are the 5’ adapters provided by each kit, respectively. Green rectangular boxes are the oligos priming cDNA synthesis of poly-A transcripts.
    Mrnas, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    SAS institute mrnas
    Schematic diagram of the <t>TeloPrime</t> and SMARTer cDNA synthesis technologies. (A) SMARTer does not distinguish between truncated and full-length transcripts. (B) TeloPrime enriches for full-length transcripts by affinity of the 5’ adapter to the 5’ cap structure of full-length <t>mRNAs</t> during cDNA synthesis. Red and pink rectangular shapes are the 5’ adapters provided by each kit, respectively. Green rectangular boxes are the oligos priming cDNA synthesis of poly-A transcripts.
    Mrnas, supplied by SAS institute, used in various techniques. Bioz Stars score: 90/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Agilent technologies mrnas
    Expression profiles and enrichment Analysis of <t>mRNAs/lncRNAs</t> regulated by let-7e. (a) The percentage of down-regulated mRNAs (lncRNAs) in all regulated mRNAs (lncRNAs) in HUVECs treated by let-7e mimic or inhibitor. ★ p
    Mrnas, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 537 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Cell Matrix Inc mrnas
    Expression profiles and enrichment Analysis of <t>mRNAs/lncRNAs</t> regulated by let-7e. (a) The percentage of down-regulated mRNAs (lncRNAs) in all regulated mRNAs (lncRNAs) in HUVECs treated by let-7e mimic or inhibitor. ★ p
    Mrnas, supplied by Cell Matrix Inc, used in various techniques. Bioz Stars score: 89/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore mrnas
    Expression profiles and enrichment Analysis of <t>mRNAs/lncRNAs</t> regulated by let-7e. (a) The percentage of down-regulated mRNAs (lncRNAs) in all regulated mRNAs (lncRNAs) in HUVECs treated by let-7e mimic or inhibitor. ★ p
    Mrnas, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 566 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ValueGene mrnas
    Expression profiles and enrichment Analysis of <t>mRNAs/lncRNAs</t> regulated by let-7e. (a) The percentage of down-regulated mRNAs (lncRNAs) in all regulated mRNAs (lncRNAs) in HUVECs treated by let-7e mimic or inhibitor. ★ p
    Mrnas, supplied by ValueGene, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    VANGL2 LTD mrnas
    Maternal <t>Vangl2</t> and aPKC depletion disrupts the pattern of expression of specific zygotic genes. ( A ) Relative expression levels of Siamois , Xnr3 and Foxi1e <t>mRNAs</t> in control (Uninj) and Vangl2-depleted (VG–) embryos at the late blastula (st9) and
    Mrnas, supplied by VANGL2 LTD, used in various techniques. Bioz Stars score: 99/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Sangon Biotech mrnas
    Maternal <t>Vangl2</t> and aPKC depletion disrupts the pattern of expression of specific zygotic genes. ( A ) Relative expression levels of Siamois , Xnr3 and Foxi1e <t>mRNAs</t> in control (Uninj) and Vangl2-depleted (VG–) embryos at the late blastula (st9) and
    Mrnas, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 99/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Stratagene mrnas
    Steady-state levels of mitochondrial <t>mRNAs,</t> <t>rRNAs</t> and tRNAs. (A) qRT-PCR analyses on mitochondrial mRNAs normalized to the nuclear ribosomal protein 49 ( rp49 ) transcript levels in control (white and gray bars) and DmLrpprc2 KD (black bars) third-instar larvae or 6-day-old adults of the Lrpprc2 RNAi#2 line ( n = 4–5). Error bars indicate mean ± 1 SD. Student's t -test was applied, * P
    Mrnas, supplied by Stratagene, used in various techniques. Bioz Stars score: 93/100, based on 376 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Waters Corporation mrnas
    Steady-state levels of mitochondrial <t>mRNAs,</t> <t>rRNAs</t> and tRNAs. (A) qRT-PCR analyses on mitochondrial mRNAs normalized to the nuclear ribosomal protein 49 ( rp49 ) transcript levels in control (white and gray bars) and DmLrpprc2 KD (black bars) third-instar larvae or 6-day-old adults of the Lrpprc2 RNAi#2 line ( n = 4–5). Error bars indicate mean ± 1 SD. Student's t -test was applied, * P
    Mrnas, supplied by Waters Corporation, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Bio-Rad mrnas
    Expression levels of FSHβ (A, B) and LHβ (C, <t>D)mRNAs</t> in Nile tilapia pituitaries cultured with different concentrations of NKB (A, C) or NKBRP (B, D) peptides. Relative abundance of the mRNAs was normalized to the amount of <t>GAPDH</t> by the comparative threshold cycle method using qRTPCR. Results are means ± SEM (n=5–8). * indicates significant difference from 0 μM group (P
    Mrnas, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 1187 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Stemgent mrnas
    Schematic representation of iPSC derivation protocol and the generation of iPSCs from HSF and HUVECs. (A) On day 0, the parent cells, HSF and HVECs cells were treated separately with Stemcircle, a plasmid containing <t>Oct4,</t> Nanog, Sox2 and Lin28 for 24 hours and subsequently, a cocktail of <t>mRNAs</t> containing Oct4, Sox2, Klf4, cMyc, Lin28 for up to day 12. The colonies were allowed to expand in between day 13 and 16. On day 17, the fully expanded colonies were picked and grown. HSF-Human skin fibroblast, HUVECs-Human umbilical vein endothelial cells, D-day. (B1) Phage contrast microscopic image of iPSC-derived from HSF (hf-iPSCs). (B2) Live staining of Tra1-60+ cells from hf-iPSCs. (C1) Phage contrast microscopic image of iPSC-derived from HUVECs (he-iPSCs). (C2) Live staining of Tra1-60+ cells from he-iPSCs. (D) Transfection efficiency of iPSCs generated from HSF by flow cytometry analysis at passage 0 (P0). The data show 4% of cells were positive for either Oct4 or Sox2. (E) Quantification of Tra1-60+ cells by flow cytometry at P9. The data show 73.2% of cells are Tra1-60+. Data shown are representative of three independent experiments, **p
    Mrnas, supplied by Stemgent, used in various techniques. Bioz Stars score: 92/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Unigene mrnas
    Tag-mapping of experimental tags to X. tropicalis genome and transcript databases. All different experimental tags (23,766 tags) were mapped first to the genome of X. tropicalis and those without a match (311 tags) were discarded from further analysis. The remaining experimental tags that presented one or more matches to the genome (23,455 tags; 100%) were then mapped to the Ensembl modified database, and only those tags found in the first or second positions from the 3'-end of the RNA sequence or belonging to the <t>polyA-next</t> category (see Materials and methods for details) were selected and reported as mapping to this transcript database (5,615 tags; 23.9%; red). The remaining tags that did not exhibit a match to the transcripts in the Ensembl modified database (17,840; 76.1%) were then searched with the same restraints mentioned above in the joint set composed of the NCBI <t>(mRNAs),</t> Unigene (clusters of mRNAs and ESTs) and Gurdon databases (clusters of ESTs). A total of 7,172 tags (30.6%) were found to match to positions 1, 2 or poly-A next in the transcripts from this set (green). The remaining tags without a match to these databases (10,668; 45.5%) were then re-mapped against the complete set of transcripts (a complete joint set of RNAs composed of Ensembl, NCBI, Unigene and Gurdon databases), but with the restraint that the mapping must occur to position 3 or above in a transcript. A total of 5,011 tags (21.4%) that fulfilled these conditions were obtained (blue). The remaining 5,657 (24.1%) tags mapped to the genome, but did not map to any known transcript (yellow).
    Mrnas, supplied by Unigene, used in various techniques. Bioz Stars score: 91/100, based on 157 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Horizon Discovery mrna preparation mrna fragments
    Axonal levels of <t>amphoterin</t> <t>mRNA</t> do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and
    Mrna Preparation Mrna Fragments, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 78/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    TriLink mrna delivery cas9 mrna
    Axonal levels of <t>amphoterin</t> <t>mRNA</t> do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and
    Mrna Delivery Cas9 Mrna, supplied by TriLink, used in various techniques. Bioz Stars score: 93/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa nucleotrap mrna mini kits
    Axonal levels of <t>amphoterin</t> <t>mRNA</t> do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and
    Nucleotrap Mrna Mini Kits, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore direct mrna isolation kit
    Axonal levels of <t>amphoterin</t> <t>mRNA</t> do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and
    Direct Mrna Isolation Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa nucleotrap mrna midi kit
    Axonal levels of <t>amphoterin</t> <t>mRNA</t> do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and
    Nucleotrap Mrna Midi Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    TriLink ccr7 mrnas
    Axonal levels of <t>amphoterin</t> <t>mRNA</t> do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and
    Ccr7 Mrnas, supplied by TriLink, used in various techniques. Bioz Stars score: 77/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Agilent technologies mrna
    3.2. Comparative <t>mRNA</t> and <t>miRNA</t> profiles
    Mrna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 3086 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Kapa Biosystems mrna
    Sex-determining region Y box 2 (SOX2) gene expression in the peripheral blood of children with retinoblastoma (Rb). The quantification of the quantitative reverse transcription polymerase chain reactions were plotted into histograms. (A) Relative expression of SOX2 <t>mRNA</t> in the peripheral blood of control individuals and Rb patients. * P
    Mrna, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 99/100, based on 176 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Ribobio mrna
    Sex-determining region Y box 2 (SOX2) gene expression in the peripheral blood of children with retinoblastoma (Rb). The quantification of the quantitative reverse transcription polymerase chain reactions were plotted into histograms. (A) Relative expression of SOX2 <t>mRNA</t> in the peripheral blood of control individuals and Rb patients. * P
    Mrna, supplied by Ribobio, used in various techniques. Bioz Stars score: 96/100, based on 65 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    RGEN-induced Prkdc gene disruption in mice. ( A ) Representative T7E1 assays demonstrating mutagenesis efficiencies of Cas9 mRNA plus Prkdc -specific sgRNA that were delivered via intracytoplasmic injection into one-cell-stage mouse embryos. Numbers indicate

    Journal: Genome Research

    Article Title: Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases

    doi: 10.1101/gr.163394.113

    Figure Lengend Snippet: RGEN-induced Prkdc gene disruption in mice. ( A ) Representative T7E1 assays demonstrating mutagenesis efficiencies of Cas9 mRNA plus Prkdc -specific sgRNA that were delivered via intracytoplasmic injection into one-cell-stage mouse embryos. Numbers indicate

    Article Snippet: Cas9 mRNA and sgRNAs in M2 medium (Sigma-Aldrich) were injected into the cytoplasm of fertilized eggs with well-recognized pronuclei using a Piezo-driven micromanipulator (Prime Tech).

    Techniques: Mouse Assay, Mutagenesis, Injection

    Characterization of a transgenic (Tg) mouse line (NFCas9-2) expressing humanized Cas9 systemically. ( a ) Schematic of the NFCas9 transgene construct, which confers ubiquitous Cas9 expression under the chicken β-actin promoter, CAG. N and F indicate the SV40-derived nuclear location signal (NLS) and FLAG sequences, respectively. ( b ) Quantitation of Cas9 mRNA expression in the major organs. Relative Cas9 mRNA copy number was determined by real-time qPCR. ( c ) Body weight change of both male and female mice aged 4 to 10 weeks. ( d ) Organs were collected from 10-week-old Cas9/+ and +/+ mice (n = 3 each). Representative images are shown. Scale bar = 100 μm. ( e ) Evaluation of serum levels of blood urea nitrogen (BUN), creatinine (Cr), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) in 10-week-old Tg mice (Cas9/+ female, n = 8; Cas9/+ male, n = 11) and their non-Tg littermates (+/+ male, n = 9; +/+ female, n = 10). Data are represented as the mean ± standard deviation (SD).

    Journal: Scientific Reports

    Article Title: A non-inheritable maternal Cas9-based multiple-gene editing system in mice

    doi: 10.1038/srep20011

    Figure Lengend Snippet: Characterization of a transgenic (Tg) mouse line (NFCas9-2) expressing humanized Cas9 systemically. ( a ) Schematic of the NFCas9 transgene construct, which confers ubiquitous Cas9 expression under the chicken β-actin promoter, CAG. N and F indicate the SV40-derived nuclear location signal (NLS) and FLAG sequences, respectively. ( b ) Quantitation of Cas9 mRNA expression in the major organs. Relative Cas9 mRNA copy number was determined by real-time qPCR. ( c ) Body weight change of both male and female mice aged 4 to 10 weeks. ( d ) Organs were collected from 10-week-old Cas9/+ and +/+ mice (n = 3 each). Representative images are shown. Scale bar = 100 μm. ( e ) Evaluation of serum levels of blood urea nitrogen (BUN), creatinine (Cr), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) in 10-week-old Tg mice (Cas9/+ female, n = 8; Cas9/+ male, n = 11) and their non-Tg littermates (+/+ male, n = 9; +/+ female, n = 10). Data are represented as the mean ± standard deviation (SD).

    Article Snippet: Cas9 mRNA expression levels in Tg mice were measured by qRT-PCR using Cas9E-S and Cas9cla-A primers and NFCas9 RNA copy standard curves, as well as by CAG1620-S/Cas9215-A and Ramp3-S/Ramp3-A qRT-PCRs and western blotting with anti-FLAG; F1804, Sigma-Aldrich; St. Louis, MO, USA). mRNA copy number standard templates were prepared in a solution containing total RNA (50 ng) isolated from a wild-type 13.5-dpc embryo and serially diluted (10, 102 , 103 , 104 , and 105 copies) in vitro -synthesized Cas9 RNA (sequence length: 4146 nucleotides; 0.18 pg corresponding to 105 copies).

    Techniques: Transgenic Assay, Expressing, Construct, Derivative Assay, Quantitation Assay, Real-time Polymerase Chain Reaction, Mouse Assay, AST Assay, Standard Deviation

    RNA-Seq and miRNA-Seq validated by RT-qPCR. a Validation of four DE circRNAs. b Validation of four DE mRNAs. c Validation of four DE miRNAs

    Journal: Journal of Translational Medicine

    Article Title: Crosstalk in competing endogenous RNA networks reveals new circular RNAs involved in the pathogenesis of early HIV infection

    doi: 10.1186/s12967-018-1706-1

    Figure Lengend Snippet: RNA-Seq and miRNA-Seq validated by RT-qPCR. a Validation of four DE circRNAs. b Validation of four DE mRNAs. c Validation of four DE miRNAs

    Article Snippet: The circRNAs and mRNAs were reverse transcribed using a Primpscript® RT reagent kit (TAKARA), and miRNAs were reverse transcribed using a Mir-X™ miRNA First Strand Synthesis Kit (TAKARA) following the manufacturer’s instructions.

    Techniques: RNA Sequencing Assay, Quantitative RT-PCR

    The Profiling and Characteristics of mRNAs and circRNAs in EHI. a Circos plot showing the mRNAs and circRNAs on human chromosomes. From the outside in, the first layer of the Circos plot is a chromosome map of the human genome; black and white bars are chromosome cytobands, and red bars represent centromeres. The second layer shows the 20 most significantly up-regulated and 20 most significantly down-regulated mRNAs. All DE mRNAs and circRNAs are marked in red and blue in the third layer. The fourth and fifth layers show the fold change of all DE mRNAs and circRNAs. b The counts of DE circRNAs based on their categories. c The distribution of the DE circRNAs based on the length of nucleic acids

    Journal: Journal of Translational Medicine

    Article Title: Crosstalk in competing endogenous RNA networks reveals new circular RNAs involved in the pathogenesis of early HIV infection

    doi: 10.1186/s12967-018-1706-1

    Figure Lengend Snippet: The Profiling and Characteristics of mRNAs and circRNAs in EHI. a Circos plot showing the mRNAs and circRNAs on human chromosomes. From the outside in, the first layer of the Circos plot is a chromosome map of the human genome; black and white bars are chromosome cytobands, and red bars represent centromeres. The second layer shows the 20 most significantly up-regulated and 20 most significantly down-regulated mRNAs. All DE mRNAs and circRNAs are marked in red and blue in the third layer. The fourth and fifth layers show the fold change of all DE mRNAs and circRNAs. b The counts of DE circRNAs based on their categories. c The distribution of the DE circRNAs based on the length of nucleic acids

    Article Snippet: The circRNAs and mRNAs were reverse transcribed using a Primpscript® RT reagent kit (TAKARA), and miRNAs were reverse transcribed using a Mir-X™ miRNA First Strand Synthesis Kit (TAKARA) following the manufacturer’s instructions.

    Techniques:

    Host cell mRNA synthesis and translation are unaffected by compound JMN3-003. A ) Relative TaqMan RT-PCR-based quantitation of three unstable cellular mRNAs (MCL1, ASB7, MKP-1) after exposure of cells to JMN3-003 for six hours. Controls were treated with Actinomycine D (Act D) for comparison. C T values are expressed relative to vehicle-treated samples and reflect averages of three independent experiments, each analyzed in triplicate, ± SD. B–D ) Expression of virus-encoded but not host cell or plasmid-encoded viral proteins is blocked by JMN3-003. Immunodetection of transiently expressed MeV-F ( B ), virus-encoded MeV-F ( C ), and virus-encoded influenza A/WSN M2 ( D ) in cell lysates after incubation of cells in the presence of compound or vehicle only (DMSO) for 30 hours. As internal cellular standard, membranes were probed for GAPDH in parallel. Numbers correspond to average densitometric quantitations ± SD of three experiments, representative immunoblots are shown. (ND: not determined).

    Journal: PLoS ONE

    Article Title: Potent Host-Directed Small-Molecule Inhibitors of Myxovirus RNA-Dependent RNA-Polymerases

    doi: 10.1371/journal.pone.0020069

    Figure Lengend Snippet: Host cell mRNA synthesis and translation are unaffected by compound JMN3-003. A ) Relative TaqMan RT-PCR-based quantitation of three unstable cellular mRNAs (MCL1, ASB7, MKP-1) after exposure of cells to JMN3-003 for six hours. Controls were treated with Actinomycine D (Act D) for comparison. C T values are expressed relative to vehicle-treated samples and reflect averages of three independent experiments, each analyzed in triplicate, ± SD. B–D ) Expression of virus-encoded but not host cell or plasmid-encoded viral proteins is blocked by JMN3-003. Immunodetection of transiently expressed MeV-F ( B ), virus-encoded MeV-F ( C ), and virus-encoded influenza A/WSN M2 ( D ) in cell lysates after incubation of cells in the presence of compound or vehicle only (DMSO) for 30 hours. As internal cellular standard, membranes were probed for GAPDH in parallel. Numbers correspond to average densitometric quantitations ± SD of three experiments, representative immunoblots are shown. (ND: not determined).

    Article Snippet: Quantitative TaqMan RT-PCR was again achieved using the TaqMan Fast Master Mix (Applied Biosystems) combined with proprietary primer and probe sets specific for Induced myeloid leukemia cell differentiation protein 1- (MCL1), MAPK phosphatase 1 (MKP1), and ankyrin repeat and SOCS box-containing protein 7- (ASB7) encoding mRNAs (Applied Biosystems).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Quantitation Assay, Activated Clotting Time Assay, Expressing, Plasmid Preparation, Immunodetection, Incubation, Western Blot

    Schematic diagram of the TeloPrime and SMARTer cDNA synthesis technologies. (A) SMARTer does not distinguish between truncated and full-length transcripts. (B) TeloPrime enriches for full-length transcripts by affinity of the 5’ adapter to the 5’ cap structure of full-length mRNAs during cDNA synthesis. Red and pink rectangular shapes are the 5’ adapters provided by each kit, respectively. Green rectangular boxes are the oligos priming cDNA synthesis of poly-A transcripts.

    Journal: PLoS ONE

    Article Title: cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing

    doi: 10.1371/journal.pone.0157779

    Figure Lengend Snippet: Schematic diagram of the TeloPrime and SMARTer cDNA synthesis technologies. (A) SMARTer does not distinguish between truncated and full-length transcripts. (B) TeloPrime enriches for full-length transcripts by affinity of the 5’ adapter to the 5’ cap structure of full-length mRNAs during cDNA synthesis. Red and pink rectangular shapes are the 5’ adapters provided by each kit, respectively. Green rectangular boxes are the oligos priming cDNA synthesis of poly-A transcripts.

    Article Snippet: To enrich for real full-length transcripts we implemented the TeloPrime Full-Length cDNA Amplification Kit, which selectively synthesises cDNA molecules from mRNAs carrying a 5’ cap, to the standard Pacific Biosciences cDNA library preparation protocol.

    Techniques:

    Expression profiles and enrichment Analysis of mRNAs/lncRNAs regulated by let-7e. (a) The percentage of down-regulated mRNAs (lncRNAs) in all regulated mRNAs (lncRNAs) in HUVECs treated by let-7e mimic or inhibitor. ★ p

    Journal: Scientific Reports

    Article Title: Let-7e modulates the inflammatory response in vascular endothelial cells through ceRNA crosstalk

    doi: 10.1038/srep42498

    Figure Lengend Snippet: Expression profiles and enrichment Analysis of mRNAs/lncRNAs regulated by let-7e. (a) The percentage of down-regulated mRNAs (lncRNAs) in all regulated mRNAs (lncRNAs) in HUVECs treated by let-7e mimic or inhibitor. ★ p

    Article Snippet: Expression data of mRNAs and lncRNAs were filtered and normalized (ArrayExpress accession number: E-MTAB-4971), and then the lncRNAs and mRNAs regulated by let-7e were identified using GeneSpring GX 11.5 (Agilent, CA).

    Techniques: Expressing

    Maternal Vangl2 and aPKC depletion disrupts the pattern of expression of specific zygotic genes. ( A ) Relative expression levels of Siamois , Xnr3 and Foxi1e mRNAs in control (Uninj) and Vangl2-depleted (VG–) embryos at the late blastula (st9) and

    Journal: Development (Cambridge, England)

    Article Title: The roles of maternal Vangl2 and aPKC in Xenopus oocyte and embryo patterning

    doi: 10.1242/dev.068866

    Figure Lengend Snippet: Maternal Vangl2 and aPKC depletion disrupts the pattern of expression of specific zygotic genes. ( A ) Relative expression levels of Siamois , Xnr3 and Foxi1e mRNAs in control (Uninj) and Vangl2-depleted (VG–) embryos at the late blastula (st9) and

    Article Snippet: The roles of PCP and ABP pathway components have not been examined in vertebrate oocytes, although real-time RT-PCR analysis shows that their mRNAs (including Vangl2, Celsr1, Disheveled, frizzled, prickle, PTK7, aPKC, scribble, Par3 and Par6 ) are expressed (data not shown).

    Techniques: Expressing

    Steady-state levels of mitochondrial mRNAs, rRNAs and tRNAs. (A) qRT-PCR analyses on mitochondrial mRNAs normalized to the nuclear ribosomal protein 49 ( rp49 ) transcript levels in control (white and gray bars) and DmLrpprc2 KD (black bars) third-instar larvae or 6-day-old adults of the Lrpprc2 RNAi#2 line ( n = 4–5). Error bars indicate mean ± 1 SD. Student's t -test was applied, * P

    Journal: Nucleic Acids Research

    Article Title: Drosophila melanogaster LRPPRC2 is involved in coordination of mitochondrial translation

    doi: 10.1093/nar/gku1132

    Figure Lengend Snippet: Steady-state levels of mitochondrial mRNAs, rRNAs and tRNAs. (A) qRT-PCR analyses on mitochondrial mRNAs normalized to the nuclear ribosomal protein 49 ( rp49 ) transcript levels in control (white and gray bars) and DmLrpprc2 KD (black bars) third-instar larvae or 6-day-old adults of the Lrpprc2 RNAi#2 line ( n = 4–5). Error bars indicate mean ± 1 SD. Student's t -test was applied, * P

    Article Snippet: Different mRNAs and rRNAs were detected after hybridization with α-32 P-dCTP-labeled DNA probes, obtained by using the Prime-It II random primer labeling kit (Stratagene).

    Techniques: Quantitative RT-PCR

    Expression levels of FSHβ (A, B) and LHβ (C, D)mRNAs in Nile tilapia pituitaries cultured with different concentrations of NKB (A, C) or NKBRP (B, D) peptides. Relative abundance of the mRNAs was normalized to the amount of GAPDH by the comparative threshold cycle method using qRTPCR. Results are means ± SEM (n=5–8). * indicates significant difference from 0 μM group (P

    Journal: Development & Reproduction

    Article Title: Neurokinin B-related Peptide Suppresses the Expression of GnRH I, Kiss2 and tac3 in the Brain of Mature Female Nile tilapia Oreochromis niloticus

    doi: 10.12717/DR.2016.20.1.051

    Figure Lengend Snippet: Expression levels of FSHβ (A, B) and LHβ (C, D)mRNAs in Nile tilapia pituitaries cultured with different concentrations of NKB (A, C) or NKBRP (B, D) peptides. Relative abundance of the mRNAs was normalized to the amount of GAPDH by the comparative threshold cycle method using qRTPCR. Results are means ± SEM (n=5–8). * indicates significant difference from 0 μM group (P

    Article Snippet: The abundance level of the mRNAs was normalized against the amount of GAPDH and the relative abundance was determined by the comparative threshold cycle method, 2–△△Ct , using CFX Manager™ Software (Bio-Rad).

    Techniques: Expressing, Cell Culture

    Expression levels of GnRH I (A), Kiss2 (B) andtac3 (C) mRNAs in the brains and FSHβ (D) and LHβ (E) mRNAs in the pituitaries of Nile tilapia injected either with LHRH, NKB, NKBRP or PBS. Relative abundance of the mRNAs in the brains was normalized to the amount of GAPDH and β-actin and in the pituitaries was normalized to the amount of GAPDH by the comparative threshold cycle method using qRT-PCR. Results are means ± SEM (n=6–8). * indicates significant difference from PBS group (P

    Journal: Development & Reproduction

    Article Title: Neurokinin B-related Peptide Suppresses the Expression of GnRH I, Kiss2 and tac3 in the Brain of Mature Female Nile tilapia Oreochromis niloticus

    doi: 10.12717/DR.2016.20.1.051

    Figure Lengend Snippet: Expression levels of GnRH I (A), Kiss2 (B) andtac3 (C) mRNAs in the brains and FSHβ (D) and LHβ (E) mRNAs in the pituitaries of Nile tilapia injected either with LHRH, NKB, NKBRP or PBS. Relative abundance of the mRNAs in the brains was normalized to the amount of GAPDH and β-actin and in the pituitaries was normalized to the amount of GAPDH by the comparative threshold cycle method using qRT-PCR. Results are means ± SEM (n=6–8). * indicates significant difference from PBS group (P

    Article Snippet: The abundance level of the mRNAs was normalized against the amount of GAPDH and the relative abundance was determined by the comparative threshold cycle method, 2–△△Ct , using CFX Manager™ Software (Bio-Rad).

    Techniques: Expressing, Injection, Quantitative RT-PCR

    Schematic representation of iPSC derivation protocol and the generation of iPSCs from HSF and HUVECs. (A) On day 0, the parent cells, HSF and HVECs cells were treated separately with Stemcircle, a plasmid containing Oct4, Nanog, Sox2 and Lin28 for 24 hours and subsequently, a cocktail of mRNAs containing Oct4, Sox2, Klf4, cMyc, Lin28 for up to day 12. The colonies were allowed to expand in between day 13 and 16. On day 17, the fully expanded colonies were picked and grown. HSF-Human skin fibroblast, HUVECs-Human umbilical vein endothelial cells, D-day. (B1) Phage contrast microscopic image of iPSC-derived from HSF (hf-iPSCs). (B2) Live staining of Tra1-60+ cells from hf-iPSCs. (C1) Phage contrast microscopic image of iPSC-derived from HUVECs (he-iPSCs). (C2) Live staining of Tra1-60+ cells from he-iPSCs. (D) Transfection efficiency of iPSCs generated from HSF by flow cytometry analysis at passage 0 (P0). The data show 4% of cells were positive for either Oct4 or Sox2. (E) Quantification of Tra1-60+ cells by flow cytometry at P9. The data show 73.2% of cells are Tra1-60+. Data shown are representative of three independent experiments, **p

    Journal: PLoS ONE

    Article Title: Generation of Functional Cardiomyocytes from Efficiently Generated Human iPSCs and a Novel Method of Measuring Contractility

    doi: 10.1371/journal.pone.0134093

    Figure Lengend Snippet: Schematic representation of iPSC derivation protocol and the generation of iPSCs from HSF and HUVECs. (A) On day 0, the parent cells, HSF and HVECs cells were treated separately with Stemcircle, a plasmid containing Oct4, Nanog, Sox2 and Lin28 for 24 hours and subsequently, a cocktail of mRNAs containing Oct4, Sox2, Klf4, cMyc, Lin28 for up to day 12. The colonies were allowed to expand in between day 13 and 16. On day 17, the fully expanded colonies were picked and grown. HSF-Human skin fibroblast, HUVECs-Human umbilical vein endothelial cells, D-day. (B1) Phage contrast microscopic image of iPSC-derived from HSF (hf-iPSCs). (B2) Live staining of Tra1-60+ cells from hf-iPSCs. (C1) Phage contrast microscopic image of iPSC-derived from HUVECs (he-iPSCs). (C2) Live staining of Tra1-60+ cells from he-iPSCs. (D) Transfection efficiency of iPSCs generated from HSF by flow cytometry analysis at passage 0 (P0). The data show 4% of cells were positive for either Oct4 or Sox2. (E) Quantification of Tra1-60+ cells by flow cytometry at P9. The data show 73.2% of cells are Tra1-60+. Data shown are representative of three independent experiments, **p

    Article Snippet: Then the cells were followed by a cocktail of mRNAs (Stemgent) containing Oct4, Sox2, Klf4, cMyc and Lin28 every day for 11 days using Lipofectamine (Invitrogen) as a transfection agent.

    Techniques: Plasmid Preparation, Derivative Assay, Staining, Transfection, Generated, Flow Cytometry, Cytometry

    Tag-mapping of experimental tags to X. tropicalis genome and transcript databases. All different experimental tags (23,766 tags) were mapped first to the genome of X. tropicalis and those without a match (311 tags) were discarded from further analysis. The remaining experimental tags that presented one or more matches to the genome (23,455 tags; 100%) were then mapped to the Ensembl modified database, and only those tags found in the first or second positions from the 3'-end of the RNA sequence or belonging to the polyA-next category (see Materials and methods for details) were selected and reported as mapping to this transcript database (5,615 tags; 23.9%; red). The remaining tags that did not exhibit a match to the transcripts in the Ensembl modified database (17,840; 76.1%) were then searched with the same restraints mentioned above in the joint set composed of the NCBI (mRNAs), Unigene (clusters of mRNAs and ESTs) and Gurdon databases (clusters of ESTs). A total of 7,172 tags (30.6%) were found to match to positions 1, 2 or poly-A next in the transcripts from this set (green). The remaining tags without a match to these databases (10,668; 45.5%) were then re-mapped against the complete set of transcripts (a complete joint set of RNAs composed of Ensembl, NCBI, Unigene and Gurdon databases), but with the restraint that the mapping must occur to position 3 or above in a transcript. A total of 5,011 tags (21.4%) that fulfilled these conditions were obtained (blue). The remaining 5,657 (24.1%) tags mapped to the genome, but did not map to any known transcript (yellow).

    Journal: Genome Biology

    Article Title: Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression

    doi: 10.1186/gb-2009-10-2-r15

    Figure Lengend Snippet: Tag-mapping of experimental tags to X. tropicalis genome and transcript databases. All different experimental tags (23,766 tags) were mapped first to the genome of X. tropicalis and those without a match (311 tags) were discarded from further analysis. The remaining experimental tags that presented one or more matches to the genome (23,455 tags; 100%) were then mapped to the Ensembl modified database, and only those tags found in the first or second positions from the 3'-end of the RNA sequence or belonging to the polyA-next category (see Materials and methods for details) were selected and reported as mapping to this transcript database (5,615 tags; 23.9%; red). The remaining tags that did not exhibit a match to the transcripts in the Ensembl modified database (17,840; 76.1%) were then searched with the same restraints mentioned above in the joint set composed of the NCBI (mRNAs), Unigene (clusters of mRNAs and ESTs) and Gurdon databases (clusters of ESTs). A total of 7,172 tags (30.6%) were found to match to positions 1, 2 or poly-A next in the transcripts from this set (green). The remaining tags without a match to these databases (10,668; 45.5%) were then re-mapped against the complete set of transcripts (a complete joint set of RNAs composed of Ensembl, NCBI, Unigene and Gurdon databases), but with the restraint that the mapping must occur to position 3 or above in a transcript. A total of 5,011 tags (21.4%) that fulfilled these conditions were obtained (blue). The remaining 5,657 (24.1%) tags mapped to the genome, but did not map to any known transcript (yellow).

    Article Snippet: Experimental tags with no match to positions 1, 2 or polyA-next in the Ensembl modified database were mapped to mRNAs from NCBI, EST cluster sequences from Unigene and full-length ESTs from the Gurdon Institute.

    Techniques: Modification, Sequencing

    Axonal levels of amphoterin mRNA do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and

    Journal: The Journal of Neuroscience

    Article Title: Axonal Amphoterin mRNA Is Regulated by Translational Control and Enhances Axon Outgrowth

    doi: 10.1523/JNEUROSCI.3397-14.2015

    Figure Lengend Snippet: Axonal levels of amphoterin mRNA do not change with injury. A , B , Neuronal cultures prepared from 7 d injury-conditioned versus naive DRGs were used for fractionation of cell body versus axonal RNA. RT-qPCR shows β-actin in both cell body and

    Article Snippet: siRNAs targeting four sequences in rat amphoterin mRNA were initially used to deplete the mRNA (Dharmacon).

    Techniques: Fractionation, Quantitative RT-PCR

    Overexpression of axonally targeted amphoterin mRNA increases axon growth. A , B , Representative montage images of NF-H-immunostained DRG neurons are shown in A for transfections with GFP, AMPH-GFP-5′/3′-amph 738–1238 , AMPH-GFP-5′amph/3′gfp.

    Journal: The Journal of Neuroscience

    Article Title: Axonal Amphoterin mRNA Is Regulated by Translational Control and Enhances Axon Outgrowth

    doi: 10.1523/JNEUROSCI.3397-14.2015

    Figure Lengend Snippet: Overexpression of axonally targeted amphoterin mRNA increases axon growth. A , B , Representative montage images of NF-H-immunostained DRG neurons are shown in A for transfections with GFP, AMPH-GFP-5′/3′-amph 738–1238 , AMPH-GFP-5′amph/3′gfp.

    Article Snippet: siRNAs targeting four sequences in rat amphoterin mRNA were initially used to deplete the mRNA (Dharmacon).

    Techniques: Over Expression, Transfection

    Amphoterin depletion decreases axonal outgrowth. A , B , siAmph mRNA-transfected DRG neuron cultures show significantly decreased amphoterin mRNA by RT-qPCR compared with nontargeting control (siCon) ( A ); there is also a clear decrease in amphoterin protein

    Journal: The Journal of Neuroscience

    Article Title: Axonal Amphoterin mRNA Is Regulated by Translational Control and Enhances Axon Outgrowth

    doi: 10.1523/JNEUROSCI.3397-14.2015

    Figure Lengend Snippet: Amphoterin depletion decreases axonal outgrowth. A , B , siAmph mRNA-transfected DRG neuron cultures show significantly decreased amphoterin mRNA by RT-qPCR compared with nontargeting control (siCon) ( A ); there is also a clear decrease in amphoterin protein

    Article Snippet: siRNAs targeting four sequences in rat amphoterin mRNA were initially used to deplete the mRNA (Dharmacon).

    Techniques: Transfection, Quantitative RT-PCR

    3.2. Comparative mRNA and miRNA profiles

    Journal: Toxicology

    Article Title: Differential Programming of p53-Deficient Embryonic Cells During Rotenone Block

    doi: 10.1016/j.tox.2011.08.013

    Figure Lengend Snippet: 3.2. Comparative mRNA and miRNA profiles

    Article Snippet: Various QA/QC metrics for mRNA (Agilent) and miRNA (Exiqon) profiling included internal positive (spike-in) and negative (unexpressed) controls.

    Techniques:

    Sex-determining region Y box 2 (SOX2) gene expression in the peripheral blood of children with retinoblastoma (Rb). The quantification of the quantitative reverse transcription polymerase chain reactions were plotted into histograms. (A) Relative expression of SOX2 mRNA in the peripheral blood of control individuals and Rb patients. * P

    Journal: Oncology Letters

    Article Title: Enhanced SOX2 expression in retinoblastoma tissues and peripheral blood is associated with the clinicopathological characteristics of the disease

    doi: 10.3892/ol.2015.2857

    Figure Lengend Snippet: Sex-determining region Y box 2 (SOX2) gene expression in the peripheral blood of children with retinoblastoma (Rb). The quantification of the quantitative reverse transcription polymerase chain reactions were plotted into histograms. (A) Relative expression of SOX2 mRNA in the peripheral blood of control individuals and Rb patients. * P

    Article Snippet: The quantitative reverse transcription polymerase chain reaction (qRT-PCR) kit for mRNA was purchased from Kapa Biosystems, Inc. (Wilmington, MA, USA).

    Techniques: Expressing