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  • 99
    New England Biolabs nebnext ultra rna library prep kit for illumina
    Nebnext Ultra Rna Library Prep Kit For Illumina, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nebnext ultra rna library prep kit for illumina/product/New England Biolabs
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    99
    Millipore rna preparation
    Rna Preparation, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 563 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc truseq rna sample preparation kit
    Truseq Rna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 11357 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq rna sample preparation kit/product/Illumina Inc
    Average 99 stars, based on 11357 article reviews
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    99
    Illumina Inc rna seq library preparation
    Percentage of pseudogenes (blue), protein-coding (green) and non-coding RNAs (red) for 1 μ g <t>TruSeq</t> samples (A) and 100 ng TruSeq samples (B). Note that mRNA samples are on the left side and total <t>RNA</t> samples are on the right side for each figure.
    Rna Seq Library Preparation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1713 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna seq library preparation/product/Illumina Inc
    Average 99 stars, based on 1713 article reviews
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    99
    Illumina Inc truseq small rna sample preparation kit
    Percentage of pseudogenes (blue), protein-coding (green) and non-coding RNAs (red) for 1 μ g <t>TruSeq</t> samples (A) and 100 ng TruSeq samples (B). Note that mRNA samples are on the left side and total <t>RNA</t> samples are on the right side for each figure.
    Truseq Small Rna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 2225 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq small rna sample preparation kit/product/Illumina Inc
    Average 99 stars, based on 2225 article reviews
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    99
    Illumina Inc truseq stranded total rna sample preparation kit
    Percentage of pseudogenes (blue), protein-coding (green) and non-coding RNAs (red) for 1 μ g <t>TruSeq</t> samples (A) and 100 ng TruSeq samples (B). Note that mRNA samples are on the left side and total <t>RNA</t> samples are on the right side for each figure.
    Truseq Stranded Total Rna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1212 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq stranded total rna sample preparation kit/product/Illumina Inc
    Average 99 stars, based on 1212 article reviews
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    93
    Agilent technologies rna preparations
    Comparison of the gene expressions of SYM-I cells infected with Ni, Ni-CE, and CE(NiN) strains using a <t>DNA</t> microarray. SYM-I cells were infected with Ni, Ni-CE, and CE(NiN) strains at an MOI of 2. After 24 h, the total cellular <t>RNA</t> was extracted and used for DNA microarray analysis. The data were normalized by GeneSpring GX software. (A) Cluster analysis of genes of SYM-I cells infected with each virus. The expression pattern of genes involved in “host-pathogen interaction” is represented as a hierarchical clustering, using Cluster and Java TreeView. Genes shown in red are upregulated, and those shown in green are downregulated relative to mock-infected cells. (B) Expression levels of 10 host immunity-related genes, most of which were differentially expressed in Ni-CE- and CE(NiN)-infected cells. Each bar represents the fold change in expression compared to the expression level of each gene in mock-infected cells.
    Rna Preparations, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 981 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna preparations/product/Agilent technologies
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    92
    Illumina Inc rna library preparation
    —Northern blot analysis of 3′ terminal ribonucleotide modifications. A small <t>RNA</t> sample purified from 96-h drone larvae was either subjected (+) or not subjected (−) to beta-elimination. Northern blots were probed for the predicted <t>piRNA</t> P4 ( supplementary table S2 , Supplementary Material online) and ame-mir-71. Beta-elimination did not affect the migration rate of the predicted piRNA, but did induce a faster migration of ame-mir-71 indicating that the former is modified at the 3′ end. ( A ) piRNA P4, unaltered after beta-elimination, ( B ) ame-mir-71, ( C ) short ame-mir-71 isomiR, ( D ) shortened ame-mir-71 after beta-elimination, ( E ) shortened isomiR.
    Rna Library Preparation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 605 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna library preparation/product/Illumina Inc
    Average 92 stars, based on 605 article reviews
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    rna library preparation - by Bioz Stars, 2020-09
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    92
    Illumina Inc scriptseq v2 rna seq library preparation kit
    Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit <t>ScriptSeq</t> v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.
    Scriptseq V2 Rna Seq Library Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 559 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/scriptseq v2 rna seq library preparation kit/product/Illumina Inc
    Average 92 stars, based on 559 article reviews
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    91
    Illumina Inc truseq rna sample preparation v2 guide
    Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit <t>ScriptSeq</t> v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.
    Truseq Rna Sample Preparation V2 Guide, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 491 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/truseq rna sample preparation v2 guide/product/Illumina Inc
    Average 91 stars, based on 491 article reviews
    Price from $9.99 to $1999.99
    truseq rna sample preparation v2 guide - by Bioz Stars, 2020-09
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    90
    Agilent technologies sureselect strand specific rna library preparation kit
    Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit <t>ScriptSeq</t> v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.
    Sureselect Strand Specific Rna Library Preparation Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 303 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sureselect strand specific rna library preparation kit/product/Agilent technologies
    Average 90 stars, based on 303 article reviews
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    Image Search Results


    Percentage of pseudogenes (blue), protein-coding (green) and non-coding RNAs (red) for 1 μ g TruSeq samples (A) and 100 ng TruSeq samples (B). Note that mRNA samples are on the left side and total RNA samples are on the right side for each figure.

    Journal: bioRxiv

    Article Title: Comprehensive analysis of RNA-seq kits for standard, low and ultra-low quantity samples

    doi: 10.1101/524439

    Figure Lengend Snippet: Percentage of pseudogenes (blue), protein-coding (green) and non-coding RNAs (red) for 1 μ g TruSeq samples (A) and 100 ng TruSeq samples (B). Note that mRNA samples are on the left side and total RNA samples are on the right side for each figure.

    Article Snippet: Here, in the light of recent developments and progress in RNA-seq library protocols, we use human input samples to evaluate three different recently developed commercial kits used for RNA-seq library preparation: TruSeq (Illumina), SMARTer (Clontech/Takara Bio) and SMARTer Ultra-Low (Clontech/Takara Bio).

    Techniques:

    Comparison of the gene expressions of SYM-I cells infected with Ni, Ni-CE, and CE(NiN) strains using a DNA microarray. SYM-I cells were infected with Ni, Ni-CE, and CE(NiN) strains at an MOI of 2. After 24 h, the total cellular RNA was extracted and used for DNA microarray analysis. The data were normalized by GeneSpring GX software. (A) Cluster analysis of genes of SYM-I cells infected with each virus. The expression pattern of genes involved in “host-pathogen interaction” is represented as a hierarchical clustering, using Cluster and Java TreeView. Genes shown in red are upregulated, and those shown in green are downregulated relative to mock-infected cells. (B) Expression levels of 10 host immunity-related genes, most of which were differentially expressed in Ni-CE- and CE(NiN)-infected cells. Each bar represents the fold change in expression compared to the expression level of each gene in mock-infected cells.

    Journal: Journal of Virology

    Article Title: Rabies Virus Nucleoprotein Functions To Evade Activation of the RIG-I-Mediated Antiviral Response ▿

    doi: 10.1128/JVI.02220-09

    Figure Lengend Snippet: Comparison of the gene expressions of SYM-I cells infected with Ni, Ni-CE, and CE(NiN) strains using a DNA microarray. SYM-I cells were infected with Ni, Ni-CE, and CE(NiN) strains at an MOI of 2. After 24 h, the total cellular RNA was extracted and used for DNA microarray analysis. The data were normalized by GeneSpring GX software. (A) Cluster analysis of genes of SYM-I cells infected with each virus. The expression pattern of genes involved in “host-pathogen interaction” is represented as a hierarchical clustering, using Cluster and Java TreeView. Genes shown in red are upregulated, and those shown in green are downregulated relative to mock-infected cells. (B) Expression levels of 10 host immunity-related genes, most of which were differentially expressed in Ni-CE- and CE(NiN)-infected cells. Each bar represents the fold change in expression compared to the expression level of each gene in mock-infected cells.

    Article Snippet: RNA preparations used for DNA microarray analysis were analyzed with a lab-on-a-chip Agilent Bioanalyzer (RNA 6000 LabChip kit; Agilent) to confirm the concentration, integrity, and purity.

    Techniques: Infection, Microarray, Software, Expressing

    Validation by real-time RT-PCR of DNA microarray results for IFN -β (A), IFN -λ 1 (B), CXCL10 (C), and CCL5 (D). The assay was performed with the same total RNA used in the DNA microarray experiment. Expression levels of genes were normalized to mRNA levels of GAPDH . Each bar represents the mean (± the SD) of three independent replicates. *, Significant difference ( P

    Journal: Journal of Virology

    Article Title: Rabies Virus Nucleoprotein Functions To Evade Activation of the RIG-I-Mediated Antiviral Response ▿

    doi: 10.1128/JVI.02220-09

    Figure Lengend Snippet: Validation by real-time RT-PCR of DNA microarray results for IFN -β (A), IFN -λ 1 (B), CXCL10 (C), and CCL5 (D). The assay was performed with the same total RNA used in the DNA microarray experiment. Expression levels of genes were normalized to mRNA levels of GAPDH . Each bar represents the mean (± the SD) of three independent replicates. *, Significant difference ( P

    Article Snippet: RNA preparations used for DNA microarray analysis were analyzed with a lab-on-a-chip Agilent Bioanalyzer (RNA 6000 LabChip kit; Agilent) to confirm the concentration, integrity, and purity.

    Techniques: Quantitative RT-PCR, Microarray, Expressing

    H2A.X re-expression inhibits EMT and promotes metastatic colonization in the lung. ( a ) Immunoblot analysis of EMT markers in HCT116 parental cells (WT), H2A.X knockout cells (KO) and H2A.X knockout cells in which H2A.X expression was restored (KO+H2A.X), utilizing actin as a loading control. ( b ) HCT116 parental cells (WT), H2A.X knockout cells (KO) and revertant cells (KO+H2A.X) were analysed for transcripts levels of EMT markers by real-time PCR. Expression values for E-cadherin (CDH1), ZEB1, Slug, Vimentin (VIM), integrin beta 4 (ITGB4) and versican (VCAN) were normalized to 18S RNA (gene/18S ratio). Error bars represent the s.e. ( n =3). Statistical significance was determined by a two-tailed, unpaired Student's t -test. The experiments were repeated three times. ( c ). Immunostaining of the epithelial marker E-cadherin. Nuclei were counterstained in red with propidium iodide; scale bars, 20 μm. Photomicrographs of cells are shown (top panel); scale bar, 100 μm. ( d ) Tail vein injections of HCT116 parental cells (WT) and H2A.X knockout cells (KO) showed similar numbers of lung metastatic foci 4 weeks post injection. Ectopic expression of H2A.X (KO+H2A.X) resulted in a 2.5-fold increase in lung macroscopic metastases. ( e ) Representative haematoxylin- and eosin-stained lung sections from mice injected with HCT116 parental cells (WT), H2A.X knockout cells (KO) and H2A.X knockout cells in which H2A.X expression was restored (KO+H2A.X). Black arrows indicate some macroscopic lung nodules. Scale bars, 1 mm. Statistical significance was determined by a two-tailed, unpaired Student's t -test.

    Journal: Nature Communications

    Article Title: The histone variant H2A.X is a regulator of the epithelial–mesenchymal transition

    doi: 10.1038/ncomms10711

    Figure Lengend Snippet: H2A.X re-expression inhibits EMT and promotes metastatic colonization in the lung. ( a ) Immunoblot analysis of EMT markers in HCT116 parental cells (WT), H2A.X knockout cells (KO) and H2A.X knockout cells in which H2A.X expression was restored (KO+H2A.X), utilizing actin as a loading control. ( b ) HCT116 parental cells (WT), H2A.X knockout cells (KO) and revertant cells (KO+H2A.X) were analysed for transcripts levels of EMT markers by real-time PCR. Expression values for E-cadherin (CDH1), ZEB1, Slug, Vimentin (VIM), integrin beta 4 (ITGB4) and versican (VCAN) were normalized to 18S RNA (gene/18S ratio). Error bars represent the s.e. ( n =3). Statistical significance was determined by a two-tailed, unpaired Student's t -test. The experiments were repeated three times. ( c ). Immunostaining of the epithelial marker E-cadherin. Nuclei were counterstained in red with propidium iodide; scale bars, 20 μm. Photomicrographs of cells are shown (top panel); scale bar, 100 μm. ( d ) Tail vein injections of HCT116 parental cells (WT) and H2A.X knockout cells (KO) showed similar numbers of lung metastatic foci 4 weeks post injection. Ectopic expression of H2A.X (KO+H2A.X) resulted in a 2.5-fold increase in lung macroscopic metastases. ( e ) Representative haematoxylin- and eosin-stained lung sections from mice injected with HCT116 parental cells (WT), H2A.X knockout cells (KO) and H2A.X knockout cells in which H2A.X expression was restored (KO+H2A.X). Black arrows indicate some macroscopic lung nodules. Scale bars, 1 mm. Statistical significance was determined by a two-tailed, unpaired Student's t -test.

    Article Snippet: Quality of RNA preparation, based on the 28S/18S ribosomal RNAs ratio, was assessed using the RNA 6000 Nano Lab-On-chip (Agilent Technologies, Palo Alto, CA, USA).

    Techniques: Expressing, Knock-Out, Real-time Polymerase Chain Reaction, Two Tailed Test, Immunostaining, Marker, Injection, Staining, Mouse Assay

    H2A.X is a key player in the regulation of EMT and in colon cancer metastasis signalling. HCT116 cells were infected with shRNAs against H2A.X (shH2A.X) or scrambled sequences (shCTRL). ( a , b ) Compared with controls, shH2A.X-infected HCT116 cells exhibited decreased H2A.X protein levels ( a , top, immunoblot), mesenchymal-like morphology ( a , bottom, photomicrographs, scale bar, 100 μm) and increased invasion in transwell invasion assays ( b , top, photomicrograph, scale bar, 100 μm; bottom, quantification). Error bars represent the means±s.d. of three independent experiments. Statistical significance was determined by a two-tailed, unpaired Student's t -test. ( c ) Ingenuity Pathway Analysis (IPA) revealed differentially expressed genes (DEGs) in three canonical pathways. Blue bars represent the top three canonical pathways overrepresented in the DEGs. The height of the bar represents the P value. The yellow line indicates the −log ( P value) threshold of significance (1.3), which corresponds to P value of 0.05. Statistical significance was determined by Fisher's test. ( d ) Venn diagram of DEGs assigned to the invasion, migration and metastasis pathways using IPA. DEGs were generated using Partek Genomics Suite software, version 6.6. ( e ) Heat map of the 18 DEGs common to the invasion, migration and metastasis pathways. The numbering refers to independent replicates for either shCTRL sample or shH2A.X sample. ( f ) Verification of differential expression of genes by real-time PCR). Expression values are relative fold change for gene transcripts normalized to 18S RNA (gene/18S ratio). Error bars represent s.d. ( n =3). Statistical significance was determined by a two-tailed, unpaired Student's t -test.

    Journal: Nature Communications

    Article Title: The histone variant H2A.X is a regulator of the epithelial–mesenchymal transition

    doi: 10.1038/ncomms10711

    Figure Lengend Snippet: H2A.X is a key player in the regulation of EMT and in colon cancer metastasis signalling. HCT116 cells were infected with shRNAs against H2A.X (shH2A.X) or scrambled sequences (shCTRL). ( a , b ) Compared with controls, shH2A.X-infected HCT116 cells exhibited decreased H2A.X protein levels ( a , top, immunoblot), mesenchymal-like morphology ( a , bottom, photomicrographs, scale bar, 100 μm) and increased invasion in transwell invasion assays ( b , top, photomicrograph, scale bar, 100 μm; bottom, quantification). Error bars represent the means±s.d. of three independent experiments. Statistical significance was determined by a two-tailed, unpaired Student's t -test. ( c ) Ingenuity Pathway Analysis (IPA) revealed differentially expressed genes (DEGs) in three canonical pathways. Blue bars represent the top three canonical pathways overrepresented in the DEGs. The height of the bar represents the P value. The yellow line indicates the −log ( P value) threshold of significance (1.3), which corresponds to P value of 0.05. Statistical significance was determined by Fisher's test. ( d ) Venn diagram of DEGs assigned to the invasion, migration and metastasis pathways using IPA. DEGs were generated using Partek Genomics Suite software, version 6.6. ( e ) Heat map of the 18 DEGs common to the invasion, migration and metastasis pathways. The numbering refers to independent replicates for either shCTRL sample or shH2A.X sample. ( f ) Verification of differential expression of genes by real-time PCR). Expression values are relative fold change for gene transcripts normalized to 18S RNA (gene/18S ratio). Error bars represent s.d. ( n =3). Statistical significance was determined by a two-tailed, unpaired Student's t -test.

    Article Snippet: Quality of RNA preparation, based on the 28S/18S ribosomal RNAs ratio, was assessed using the RNA 6000 Nano Lab-On-chip (Agilent Technologies, Palo Alto, CA, USA).

    Techniques: Infection, Two Tailed Test, Indirect Immunoperoxidase Assay, Migration, Generated, Software, Expressing, Real-time Polymerase Chain Reaction

    —Northern blot analysis of 3′ terminal ribonucleotide modifications. A small RNA sample purified from 96-h drone larvae was either subjected (+) or not subjected (−) to beta-elimination. Northern blots were probed for the predicted piRNA P4 ( supplementary table S2 , Supplementary Material online) and ame-mir-71. Beta-elimination did not affect the migration rate of the predicted piRNA, but did induce a faster migration of ame-mir-71 indicating that the former is modified at the 3′ end. ( A ) piRNA P4, unaltered after beta-elimination, ( B ) ame-mir-71, ( C ) short ame-mir-71 isomiR, ( D ) shortened ame-mir-71 after beta-elimination, ( E ) shortened isomiR.

    Journal: Genome Biology and Evolution

    Article Title: Contrasting Sex-and Caste-Dependent piRNA Profiles in the Transposon Depleted Haplodiploid Honeybee Apis mellifera

    doi: 10.1093/gbe/evx087

    Figure Lengend Snippet: —Northern blot analysis of 3′ terminal ribonucleotide modifications. A small RNA sample purified from 96-h drone larvae was either subjected (+) or not subjected (−) to beta-elimination. Northern blots were probed for the predicted piRNA P4 ( supplementary table S2 , Supplementary Material online) and ame-mir-71. Beta-elimination did not affect the migration rate of the predicted piRNA, but did induce a faster migration of ame-mir-71 indicating that the former is modified at the 3′ end. ( A ) piRNA P4, unaltered after beta-elimination, ( B ) ame-mir-71, ( C ) short ame-mir-71 isomiR, ( D ) shortened ame-mir-71 after beta-elimination, ( E ) shortened isomiR.

    Article Snippet: RNA Library Preparation for Illumina High-Throughput Sequencing For piRNA and transcriptomics analysis, we made use of a recently developed small RNA and transcriptional dataset generated by our laboratory (GEO NCBI database accession number GSE61253) ( ).

    Techniques: Northern Blot, Purification, Migration, Modification

    —Candidate piRNAs in the honeybee genome. Shaded regions show the minimum/maximum values observed between biological replicates. ( A ) Size distribution of small RNAs of 24 bp and larger mapped to the honeybee genome. A peak between 26 and 31 nt can be observed, consistent with the size of piRNAs in other species. ( B ) Percentage of sequences with a 5′ U. The majority of sequences between 26 and 31 nt have the 5′ U characteristic of piRNAs. ( C ) Size distribution of small RNAs mapped to transposons, the typical piRNA peak between 26 and 31 nt is more pronounced than for the total small RNA population.

    Journal: Genome Biology and Evolution

    Article Title: Contrasting Sex-and Caste-Dependent piRNA Profiles in the Transposon Depleted Haplodiploid Honeybee Apis mellifera

    doi: 10.1093/gbe/evx087

    Figure Lengend Snippet: —Candidate piRNAs in the honeybee genome. Shaded regions show the minimum/maximum values observed between biological replicates. ( A ) Size distribution of small RNAs of 24 bp and larger mapped to the honeybee genome. A peak between 26 and 31 nt can be observed, consistent with the size of piRNAs in other species. ( B ) Percentage of sequences with a 5′ U. The majority of sequences between 26 and 31 nt have the 5′ U characteristic of piRNAs. ( C ) Size distribution of small RNAs mapped to transposons, the typical piRNA peak between 26 and 31 nt is more pronounced than for the total small RNA population.

    Article Snippet: RNA Library Preparation for Illumina High-Throughput Sequencing For piRNA and transcriptomics analysis, we made use of a recently developed small RNA and transcriptional dataset generated by our laboratory (GEO NCBI database accession number GSE61253) ( ).

    Techniques:

    INPP4B regulation of IL-8 and PAK6 is independent of Akt. PC-3 Tet-On #14 cells were cultured for 2 days with or without doxycycline on matrigel coated plates in full medium. (A) INPP4B induction levels were determined by quantitative RT-PCR. (B) Validation of gene expression in samples from (A) : IL-8, COL6A3, HAS2 and PAK6. (C) Negative control, #4, and #14 PC-3 cell lines were treated as in (A) and cellular extracts were analyzed for FLAG-INPP4B, PAK6, and tubulin expression. (D) Negative control, #4, and #14 clines were induced with 0.5 μg/ml of doxycycline for 48 hours in complete medium. Conditioned medium was collected, cleared by centrifugation and concentrations of secreted IL-8 protein were determined using human IL-8-specific capture ELISA kit. Values were calculated as a percent of IL8 expression in negative control PC-3 clone. (E-F) PC-3 cells cultured in growth medium were treated with DMSO (vehicle), 0.5 μM AZD5363, 5 μM AZD5363 or 10 μM LY294002 to inhibit Akt or PI3K respectively. RNA was extracted and analyzed for expression of IL-8 (E) and PAK6 (F) by quantitative PCR and normalized to 18S . (G) Inhibition of PI3K and Akt by LY294002 and AZD5363 was confirmed by analyzing expression and activation status of the ribosomal protein S6 by Western blot analysis of PC-3 clone #14 cells treated with 0.5 or 5 μM AZD5363 (AZD) and 10 μM LY294002 (LY). Tubulin was used as a loading control. Data are presented as means ± SEM. * P

    Journal: Cell Communication and Signaling : CCS

    Article Title: INPP4B suppresses prostate cancer cell invasion

    doi: 10.1186/s12964-014-0061-y

    Figure Lengend Snippet: INPP4B regulation of IL-8 and PAK6 is independent of Akt. PC-3 Tet-On #14 cells were cultured for 2 days with or without doxycycline on matrigel coated plates in full medium. (A) INPP4B induction levels were determined by quantitative RT-PCR. (B) Validation of gene expression in samples from (A) : IL-8, COL6A3, HAS2 and PAK6. (C) Negative control, #4, and #14 PC-3 cell lines were treated as in (A) and cellular extracts were analyzed for FLAG-INPP4B, PAK6, and tubulin expression. (D) Negative control, #4, and #14 clines were induced with 0.5 μg/ml of doxycycline for 48 hours in complete medium. Conditioned medium was collected, cleared by centrifugation and concentrations of secreted IL-8 protein were determined using human IL-8-specific capture ELISA kit. Values were calculated as a percent of IL8 expression in negative control PC-3 clone. (E-F) PC-3 cells cultured in growth medium were treated with DMSO (vehicle), 0.5 μM AZD5363, 5 μM AZD5363 or 10 μM LY294002 to inhibit Akt or PI3K respectively. RNA was extracted and analyzed for expression of IL-8 (E) and PAK6 (F) by quantitative PCR and normalized to 18S . (G) Inhibition of PI3K and Akt by LY294002 and AZD5363 was confirmed by analyzing expression and activation status of the ribosomal protein S6 by Western blot analysis of PC-3 clone #14 cells treated with 0.5 or 5 μM AZD5363 (AZD) and 10 μM LY294002 (LY). Tubulin was used as a loading control. Data are presented as means ± SEM. * P

    Article Snippet: RNA preparation and Illumina microarray hybridization PC-3 Tet-On cells (5×105 ) were grown in triplicate on Matrigel-coated tissue culture dishes for two days with or without 0.5 μg/ml doxycycline prior to harvesting for RNA extraction.

    Techniques: Cell Culture, Quantitative RT-PCR, Expressing, Negative Control, Centrifugation, Enzyme-linked Immunosorbent Assay, Real-time Polymerase Chain Reaction, Inhibition, Activation Assay, Western Blot

    INPP4B regulates IL-8 and PAK6 through PKC signaling in PC-3 cells. (A-B) PC-3 cells cultured in regular growth medium were treated with DMSO (vehicle), 2 μM BIM-I (BIM), or 250 nM PMA to inhibit or activate PKC signaling respectively. RNA was extracted and analyzed for expression of IL-8 (A) and PAK6 (B) by quantitative RT-PCR and normalized to 18S . (C) PC-3 Tet-On Neg and #14 clones were cultured for 2 days ± doxycycline and treated with 250 nM PMA for 4.5 hours prior to RNA extraction and gene analysis for IL-8 . (D) PC-3 Tet-On #14 cells were cultured without Dox (Con), or with Dox for 2 days prior to protein extraction. Lysates were analyzed for phospho-PKCβII S660, phospho-PKCζ T410, FLAG-INPP4B, and tubulin. (E) PC-3 Tet-On #14 cells were cultured with doxycycline for the indication time periods prior to protein extraction. Lysates were analyzed for BIRC5, FLAG-INPP4B, and tubulin protein levels by Western blot analysis. Data in A, B, and C are presented as means ± SEM.

    Journal: Cell Communication and Signaling : CCS

    Article Title: INPP4B suppresses prostate cancer cell invasion

    doi: 10.1186/s12964-014-0061-y

    Figure Lengend Snippet: INPP4B regulates IL-8 and PAK6 through PKC signaling in PC-3 cells. (A-B) PC-3 cells cultured in regular growth medium were treated with DMSO (vehicle), 2 μM BIM-I (BIM), or 250 nM PMA to inhibit or activate PKC signaling respectively. RNA was extracted and analyzed for expression of IL-8 (A) and PAK6 (B) by quantitative RT-PCR and normalized to 18S . (C) PC-3 Tet-On Neg and #14 clones were cultured for 2 days ± doxycycline and treated with 250 nM PMA for 4.5 hours prior to RNA extraction and gene analysis for IL-8 . (D) PC-3 Tet-On #14 cells were cultured without Dox (Con), or with Dox for 2 days prior to protein extraction. Lysates were analyzed for phospho-PKCβII S660, phospho-PKCζ T410, FLAG-INPP4B, and tubulin. (E) PC-3 Tet-On #14 cells were cultured with doxycycline for the indication time periods prior to protein extraction. Lysates were analyzed for BIRC5, FLAG-INPP4B, and tubulin protein levels by Western blot analysis. Data in A, B, and C are presented as means ± SEM.

    Article Snippet: RNA preparation and Illumina microarray hybridization PC-3 Tet-On cells (5×105 ) were grown in triplicate on Matrigel-coated tissue culture dishes for two days with or without 0.5 μg/ml doxycycline prior to harvesting for RNA extraction.

    Techniques: Cell Culture, Expressing, Quantitative RT-PCR, Clone Assay, RNA Extraction, Protein Extraction, Western Blot

    Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.

    Journal: Viruses

    Article Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    doi: 10.3390/v8020053

    Figure Lengend Snippet: Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.

    Article Snippet: ARs are used in the manufacture of the reverse transcriptase FailSafe PCR enzyme (Epicentre, Madison, WI, USA) included in the utilized ScriptSeq v2 RNA-Seq Library Preparation kit (Illumina, San Diego, CA, USA).

    Techniques: RNA Sequencing Assay