rna integrity Search Results


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  • 99
    Thermo Fisher ribonucleic acid rna integrity
    Distributionof vasa , dnd , and ly75 transcripts in Atlantic salmon. A : cDNA from various tissues of adult fish (blood, brain, gill, skeletal muscle, heart, liver, spleen, gall bladder, stomach, pyloric caeca, mid gut, head kidney, kidney, skin, testis, and ovary) were used for semi-quantitative RT-PCR. Actb was used as endogenous reference. Amplicon sizes, in base pairs, are indicated on the right. Expression pattern was determined using two biological replicates. B : Total <t>RNA</t> (400–900 ng) from early embryonic stages (two-cell, eight-cell, early-blastula, late-blastula, mid-gastrula, and 10-somite) was electrophoresed. Both 28S and 18S rRNA, stained with SYBR Safe DNA gel stain, are shown in all stages. C : The changes of both total RNA (white squares) and <t>mRNA</t> (black bars) amount per egg for each developmental stage. The concentration was quantified using three replicates. D : cDNA synthesized from above-mentioned developmental stages were used for semi-quantitative RT-PCR. In order to eliminate a possibility of genomic DNA contamination, −RT (without reverse transcriptase) samples of each counterpart were examined and electrophoresed. Amplicon sizes, in base pairs are indicated on the right.
    Ribonucleic Acid Rna Integrity, supplied by Thermo Fisher, 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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    99
    Millipore rna integrity
    Distributionof vasa , dnd , and ly75 transcripts in Atlantic salmon. A : cDNA from various tissues of adult fish (blood, brain, gill, skeletal muscle, heart, liver, spleen, gall bladder, stomach, pyloric caeca, mid gut, head kidney, kidney, skin, testis, and ovary) were used for semi-quantitative RT-PCR. Actb was used as endogenous reference. Amplicon sizes, in base pairs, are indicated on the right. Expression pattern was determined using two biological replicates. B : Total <t>RNA</t> (400–900 ng) from early embryonic stages (two-cell, eight-cell, early-blastula, late-blastula, mid-gastrula, and 10-somite) was electrophoresed. Both 28S and 18S rRNA, stained with SYBR Safe DNA gel stain, are shown in all stages. C : The changes of both total RNA (white squares) and <t>mRNA</t> (black bars) amount per egg for each developmental stage. The concentration was quantified using three replicates. D : cDNA synthesized from above-mentioned developmental stages were used for semi-quantitative RT-PCR. In order to eliminate a possibility of genomic DNA contamination, −RT (without reverse transcriptase) samples of each counterpart were examined and electrophoresed. Amplicon sizes, in base pairs are indicated on the right.
    Rna Integrity, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 192 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies ribonucleic acid rna integrity
    Relationship between SDV and <t>RIN</t> . Comparison of the SDV and RIN integrity metrics for a panel of seven <t>RNA</t> samples.
    Ribonucleic Acid Rna Integrity, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 3670 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Agilent technologies rna integrity analysis
    Variation of <t>RNA</t> integrity in primary tumors and metastases in a metastatic cancer case A129 ( A ) One primary pancreatic tumor was bread-loafed as indicated by primary tumor section S2 to S6. Each slice was further cut into equally sized small pieces (approximately 1 × 1 cm) and numbered accordingly to generate sample IDs. Samples with high tumor cellularity were used for RNA extraction and determination of RNA integrity. Samples indicated by an asterisk (*) were excluded due to low tumor cellularity or necrosis. ( B ) Each piece of tissue was trisected and RNA extracted (E1,E2,E3). The color code for <t>RIN</t> value is the same as in Figure 1 .
    Rna Integrity Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 96/100, based on 188 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Agilent technologies integrity controlled rna
    Variation of <t>RNA</t> integrity in primary tumors and metastases in a metastatic cancer case A129 ( A ) One primary pancreatic tumor was bread-loafed as indicated by primary tumor section S2 to S6. Each slice was further cut into equally sized small pieces (approximately 1 × 1 cm) and numbered accordingly to generate sample IDs. Samples with high tumor cellularity were used for RNA extraction and determination of RNA integrity. Samples indicated by an asterisk (*) were excluded due to low tumor cellularity or necrosis. ( B ) Each piece of tissue was trisected and RNA extracted (E1,E2,E3). The color code for <t>RIN</t> value is the same as in Figure 1 .
    Integrity Controlled Rna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 87/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Bio-Rad rna integrity rna integrity
    Variation of <t>RNA</t> integrity in primary tumors and metastases in a metastatic cancer case A129 ( A ) One primary pancreatic tumor was bread-loafed as indicated by primary tumor section S2 to S6. Each slice was further cut into equally sized small pieces (approximately 1 × 1 cm) and numbered accordingly to generate sample IDs. Samples with high tumor cellularity were used for RNA extraction and determination of RNA integrity. Samples indicated by an asterisk (*) were excluded due to low tumor cellularity or necrosis. ( B ) Each piece of tissue was trisected and RNA extracted (E1,E2,E3). The color code for <t>RIN</t> value is the same as in Figure 1 .
    Rna Integrity Rna Integrity, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc project integrated rna seq
    Variation of <t>RNA</t> integrity in primary tumors and metastases in a metastatic cancer case A129 ( A ) One primary pancreatic tumor was bread-loafed as indicated by primary tumor section S2 to S6. Each slice was further cut into equally sized small pieces (approximately 1 × 1 cm) and numbered accordingly to generate sample IDs. Samples with high tumor cellularity were used for RNA extraction and determination of RNA integrity. Samples indicated by an asterisk (*) were excluded due to low tumor cellularity or necrosis. ( B ) Each piece of tissue was trisected and RNA extracted (E1,E2,E3). The color code for <t>RIN</t> value is the same as in Figure 1 .
    Project Integrated Rna Seq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Advanced Genomic Technology LLC rna integrity
    Variation of <t>RNA</t> integrity in primary tumors and metastases in a metastatic cancer case A129 ( A ) One primary pancreatic tumor was bread-loafed as indicated by primary tumor section S2 to S6. Each slice was further cut into equally sized small pieces (approximately 1 × 1 cm) and numbered accordingly to generate sample IDs. Samples with high tumor cellularity were used for RNA extraction and determination of RNA integrity. Samples indicated by an asterisk (*) were excluded due to low tumor cellularity or necrosis. ( B ) Each piece of tissue was trisected and RNA extracted (E1,E2,E3). The color code for <t>RIN</t> value is the same as in Figure 1 .
    Rna Integrity, supplied by Advanced Genomic Technology LLC, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Integrity, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 187 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Signal Recovery rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Integrity, supplied by Signal Recovery, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Eppendorf AG rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Integrity, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 94/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    UNICO rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Integrity, supplied by UNICO, used in various techniques. Bioz Stars score: 92/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Rockland Immunochemicals rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Integrity, supplied by Rockland Immunochemicals, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    MOgene rna integrity criteria
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Integrity Criteria, supplied by MOgene, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Angelini rna seq integration
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Seq Integration, supplied by Angelini, used in various techniques. Bioz Stars score: 89/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc beadchip microarray rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Beadchip Microarray Rna Integrity, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher mouse rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Mouse Rna Integrity, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Human Protein Atlas integrated rna seq transcriptomics
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Integrated Rna Seq Transcriptomics, supplied by Human Protein Atlas, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Thermo Fisher rna integrity rin number analysis
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Integrity Rin Number Analysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Agilent technologies rna quality control rna integrity
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Rna Quality Control Rna Integrity, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher standard affymetrix rna integrity metrics
    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of <t>mRNA-seq</t> expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger <t>RNA</t> abundance measured by high-throughput sequencing.
    Standard Affymetrix Rna Integrity Metrics, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 86 stars, based on 5 article reviews
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    92
    Thermo Fisher rna based non integrative sendai virus
    Characterization of HLHS patient specific iPSC lines. ( A ) Brightfield images of two clones derived from each patient using the non-integrative <t>RNA</t> based <t>Sendai</t> virus; ( B ) Representative example of flow cytometric analysis of key pluripotent cell markers, TRA-1-60 and NANOG. A representative example is shown from HLHS1 clone 1, however similar results were obtained for all HLHS and unaffected iPSC lines; ( C ) Elimination of Sendai viral vectors from derived iPSC lines ( KOS stands for KLF4 , OCT4 and SOX2 ); ( D ) Immunofluorescent images showing antibody staining of cells derived from all three germ layers: neuronal class β-III-tubulin staining neuronal cells derived from ectoderm; α-Smooth muscle actin staining smooth muscle cells derived from mesoderm αFP (alpha-fetoprotein) staining endodermal cells. A representative example is shown from HLHS2 clone 1; however similar results were obtained for all HLHS and unaffected iPSC lines. ( E ) In vivo differentiation of HLHS1-clone 1 as a representative example of teratoma forming ability of HLHS patient specific iPSC lines. (A) low power showing heterogeneous structure of the teratoma; (B) neuroepithelium; (C) cartilage; (D) intestinal epithelium. (A: scale bar = 400 µm, B-D: scale bar = 50 µm).
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    Agilent technologies gene custom microarray rna integrity
    CXCR4 <t>RNA</t> and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom <t>microarray.</t> 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    Solexa sequencing rna integrity
    CXCR4 <t>RNA</t> and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom <t>microarray.</t> 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    CeGAT GmbH rna integrity number
    CXCR4 <t>RNA</t> and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom <t>microarray.</t> 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    Novogene rna integrity numbers
    CXCR4 <t>RNA</t> and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom <t>microarray.</t> 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    Aros Applied Biotechnology rna integrity number
    CXCR4 <t>RNA</t> and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom <t>microarray.</t> 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    Pacific Biosciences rna integrity number
    CXCR4 <t>RNA</t> and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom <t>microarray.</t> 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    Thermo Fisher expression array processing rna integrity screening
    CXCR4 <t>RNA</t> and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom <t>microarray.</t> 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    Image Search Results


    Distributionof vasa , dnd , and ly75 transcripts in Atlantic salmon. A : cDNA from various tissues of adult fish (blood, brain, gill, skeletal muscle, heart, liver, spleen, gall bladder, stomach, pyloric caeca, mid gut, head kidney, kidney, skin, testis, and ovary) were used for semi-quantitative RT-PCR. Actb was used as endogenous reference. Amplicon sizes, in base pairs, are indicated on the right. Expression pattern was determined using two biological replicates. B : Total RNA (400–900 ng) from early embryonic stages (two-cell, eight-cell, early-blastula, late-blastula, mid-gastrula, and 10-somite) was electrophoresed. Both 28S and 18S rRNA, stained with SYBR Safe DNA gel stain, are shown in all stages. C : The changes of both total RNA (white squares) and mRNA (black bars) amount per egg for each developmental stage. The concentration was quantified using three replicates. D : cDNA synthesized from above-mentioned developmental stages were used for semi-quantitative RT-PCR. In order to eliminate a possibility of genomic DNA contamination, −RT (without reverse transcriptase) samples of each counterpart were examined and electrophoresed. Amplicon sizes, in base pairs are indicated on the right.

    Journal: Molecular Reproduction and Development

    Article Title: Identification and Migration of Primordial Germ Cells in Atlantic Salmon, Salmo salar: Characterization of Vasa, Dead End, and Lymphocyte Antigen 75 Genes

    doi: 10.1002/mrd.22142

    Figure Lengend Snippet: Distributionof vasa , dnd , and ly75 transcripts in Atlantic salmon. A : cDNA from various tissues of adult fish (blood, brain, gill, skeletal muscle, heart, liver, spleen, gall bladder, stomach, pyloric caeca, mid gut, head kidney, kidney, skin, testis, and ovary) were used for semi-quantitative RT-PCR. Actb was used as endogenous reference. Amplicon sizes, in base pairs, are indicated on the right. Expression pattern was determined using two biological replicates. B : Total RNA (400–900 ng) from early embryonic stages (two-cell, eight-cell, early-blastula, late-blastula, mid-gastrula, and 10-somite) was electrophoresed. Both 28S and 18S rRNA, stained with SYBR Safe DNA gel stain, are shown in all stages. C : The changes of both total RNA (white squares) and mRNA (black bars) amount per egg for each developmental stage. The concentration was quantified using three replicates. D : cDNA synthesized from above-mentioned developmental stages were used for semi-quantitative RT-PCR. In order to eliminate a possibility of genomic DNA contamination, −RT (without reverse transcriptase) samples of each counterpart were examined and electrophoresed. Amplicon sizes, in base pairs are indicated on the right.

    Article Snippet: Total RNA and purified mRNA were electrophoresed on a 1% (w/v) agarose gel to assessed RNA integrity, and were further quantified with a NanoDrop ND-1000 (Thermo Scientific, Saven & Werner AS, Kristiansand, Norway).

    Techniques: Fluorescence In Situ Hybridization, Quantitative RT-PCR, Amplification, Expressing, Staining, Concentration Assay, Synthesized

    Relationship between SDV and RIN . Comparison of the SDV and RIN integrity metrics for a panel of seven RNA samples.

    Journal: BMC Research Notes

    Article Title: Evaluation of a novel approach for the measurement of RNA quality

    doi: 10.1186/1756-0500-3-89

    Figure Lengend Snippet: Relationship between SDV and RIN . Comparison of the SDV and RIN integrity metrics for a panel of seven RNA samples. "Treatment" denotes the duration of thermal degradation treatment used. Each group includes nine observations, except for treatment four which corresponds to a 12-minute incubation at 90°C and, which includes only seven observations. The thicker horizontal line shows the median, boxes show the upper and lower quartiles and whiskers extend to the most distant data point within 1.5 times the interquartile range of the relevant quartile. Values beyond this are shown as individual data points.

    Article Snippet: Comparison with RNA Integrity Number (RIN) RIN is an incremental scale which spans from 0 to 10, with increasing RNA integrity correlating with increasing RIN value.

    Techniques: Incubation

    SDV and RIN chromatograms . Graphical overlay of SDV chromatograms for the analysis of intact (A), and degraded (B) RNA. RIN chromatograms for intact (C) and degraded (D) RNA are shown for comparison.

    Journal: BMC Research Notes

    Article Title: Evaluation of a novel approach for the measurement of RNA quality

    doi: 10.1186/1756-0500-3-89

    Figure Lengend Snippet: SDV and RIN chromatograms . Graphical overlay of SDV chromatograms for the analysis of intact (A), and degraded (B) RNA. RIN chromatograms for intact (C) and degraded (D) RNA are shown for comparison.

    Article Snippet: Comparison with RNA Integrity Number (RIN) RIN is an incremental scale which spans from 0 to 10, with increasing RNA integrity correlating with increasing RIN value.

    Techniques:

    RNA integrity and concentration. A) Gel-eletrophoretic separation of isolated total RNA after DNase digest and clean-up on 1% agarose. B) Gel images of RNA samples generated by the Agilent Bioanalyzer using RNA 6000 Nano Lab Chip. C) RNA concentration and RIN as determined by the Agilent Bioanalyzer. RIN = RNA Integrity Number; L = RNA Ladder. Green line in Figure 4B: Bioanalyzer internal marker.

    Journal: PLoS ONE

    Article Title: Probing Oral Microbial Functionality - Expression of spxB in Plaque Samples

    doi: 10.1371/journal.pone.0086685

    Figure Lengend Snippet: RNA integrity and concentration. A) Gel-eletrophoretic separation of isolated total RNA after DNase digest and clean-up on 1% agarose. B) Gel images of RNA samples generated by the Agilent Bioanalyzer using RNA 6000 Nano Lab Chip. C) RNA concentration and RIN as determined by the Agilent Bioanalyzer. RIN = RNA Integrity Number; L = RNA Ladder. Green line in Figure 4B: Bioanalyzer internal marker.

    Article Snippet: RNA Integrity RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

    Techniques: Concentration Assay, Isolation, Generated, Chromatin Immunoprecipitation, Marker

    Relationship between RNA yield and 260/230 absorbance. a Concentration, yield, RIN, and absorbance ratios of RNA from A459 cells and from PCLS from different species (two slices each). b Correlation between RNA concentration and absorbance ratio 260/230. c RNA yield and absorbance ratio prior to and after the clean up procedure. Results represent the means of ten human PCLS samples

    Journal: BMC Research Notes

    Article Title: RNA isolation from precision-cut lung slices (PCLS) from different species

    doi: 10.1186/s13104-017-2447-6

    Figure Lengend Snippet: Relationship between RNA yield and 260/230 absorbance. a Concentration, yield, RIN, and absorbance ratios of RNA from A459 cells and from PCLS from different species (two slices each). b Correlation between RNA concentration and absorbance ratio 260/230. c RNA yield and absorbance ratio prior to and after the clean up procedure. Results represent the means of ten human PCLS samples

    Article Snippet: RNA integrity (RIN) was evaluated using an Agilent 2100 Bioanalyzer® (Agilent Technologies, Ratingen, Germany).

    Techniques: Concentration Assay

    Experimental overview of the project and the data processing pipeline. Four difference prostate cancer cell lines were grown and the media harvested from these cell lines were used to isolate exosomes. Total RNA was then extracted from both cellular and exosomal sources. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling. Agilent low RNA input linear amplification kit PLUS was used for sample amplification and labeling. After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent feature extraction software. Normalization and further data analysis was performed using GeneSpring v11.5.1 software.

    Journal: Genomics Data

    Article Title: A comparative analysis of lncRNAs in prostate cancer exosomes and their parental cell lines

    doi: 10.1016/j.gdata.2016.05.010

    Figure Lengend Snippet: Experimental overview of the project and the data processing pipeline. Four difference prostate cancer cell lines were grown and the media harvested from these cell lines were used to isolate exosomes. Total RNA was then extracted from both cellular and exosomal sources. Integrity and concentration of RNA were assessed after RNA extraction and prior to sample labeling. Agilent low RNA input linear amplification kit PLUS was used for sample amplification and labeling. After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent feature extraction software. Normalization and further data analysis was performed using GeneSpring v11.5.1 software.

    Article Snippet: 6 Preparation of lncRNAs for hybridization to Agilent arrays RNA Integrity and concentration was assessed post RNA extraction and prior to sample labeling.

    Techniques: Concentration Assay, RNA Extraction, Labeling, Amplification, Microarray, Software

    C57BL/6 macrophages show similar early TLR4-induced responses but higher expression of type I IFN pathway genes, as compared with BALB/c macrophages. ( A ) Tlr4 mRNA expression in C57BL/6 and BALB/c BMDMs at steady-state was determined by qRT-PCR and normalized to Hprt1 mRNA expression. ( B ) C57BL/6 and BALB/c BMDMs were stimulated with LPS for the indicated times and TLR4 expression was analyzed by flow cytometry. ( C ) BMDMs were stimulated with LPS as indicated, and phosphorylation of ERK1/2 and p38 in whole-cell lysates was determined by Western blotting. ( D and E ) C57BL/6 and BALB/c BMDMs were stimulated with B. pseudomallei for 3 or 6 h in triplicate cultures. Total RNA was isolated and processed for microarray analysis as described in Materials and Methods . (D) Genes significantly differentially regulated by B. pseudomallei in C57BL/6 and BALB/c BMDMs were identified by two-way ANOVA analysis ( p

    Journal: The Journal of Immunology Author Choice

    Article Title: Differential Production of Type I IFN Determines the Reciprocal Levels of IL-10 and Proinflammatory Cytokines Produced by C57BL/6 and BALB/c Macrophages

    doi: 10.4049/jimmunol.1501923

    Figure Lengend Snippet: C57BL/6 macrophages show similar early TLR4-induced responses but higher expression of type I IFN pathway genes, as compared with BALB/c macrophages. ( A ) Tlr4 mRNA expression in C57BL/6 and BALB/c BMDMs at steady-state was determined by qRT-PCR and normalized to Hprt1 mRNA expression. ( B ) C57BL/6 and BALB/c BMDMs were stimulated with LPS for the indicated times and TLR4 expression was analyzed by flow cytometry. ( C ) BMDMs were stimulated with LPS as indicated, and phosphorylation of ERK1/2 and p38 in whole-cell lysates was determined by Western blotting. ( D and E ) C57BL/6 and BALB/c BMDMs were stimulated with B. pseudomallei for 3 or 6 h in triplicate cultures. Total RNA was isolated and processed for microarray analysis as described in Materials and Methods . (D) Genes significantly differentially regulated by B. pseudomallei in C57BL/6 and BALB/c BMDMs were identified by two-way ANOVA analysis ( p

    Article Snippet: Microarray processing and analysis RNA quality was confirmed (RNA integrity number, range 9–10) using an Agilent 2100 Bioanalyzer (Agilent Technologies).

    Techniques: Expressing, Quantitative RT-PCR, Flow Cytometry, Cytometry, Western Blot, Isolation, Microarray

    Venn diagram showing the number of genes in the hippocampus of BaP‐exposed Muta ™ Mouse that were differentially expressed (false‐discovery rate‐adjusted P ‐values ≤ 0.05 and fold change ≥ ± 1.5 relative to control) using RNA‐seq and Agilent microarrays.

    Journal: Environmental and Molecular Mutagenesis

    Article Title: Transcriptional profiling of the mouse hippocampus supports an NMDAR‐mediated neurotoxic mode of action for benzo[a]pyrene

    doi: 10.1002/em.22020

    Figure Lengend Snippet: Venn diagram showing the number of genes in the hippocampus of BaP‐exposed Muta ™ Mouse that were differentially expressed (false‐discovery rate‐adjusted P ‐values ≤ 0.05 and fold change ≥ ± 1.5 relative to control) using RNA‐seq and Agilent microarrays.

    Article Snippet: For RNA‐sequencing, 4 µg of RNA with RNA integrity numbers above 7.0 per sample (Agilent 2100 Bioanalyzer) was shipped on dry ice to the McGill University and Génome Québec Innovation Centre (Montréal, Canada), where cDNA libraries were built following the polyA‐enrichment Illumina TruSeq v2 protocol.

    Techniques: RNA Sequencing Assay

    Agilent Bioanalyzer electropherograms as suitable basis for RNA quality assessment. (a-f) Isolated total RNA was loaded on Agilent RNA Pico Chips, which were run in an Agilent 2100 Bioanalyzer. RNA profiles of microdissected rat ( a ) and human ( c ) FF samples show clearly distinguishable 18 S and 28 S rRNA peaks, which are absent in FFPE samples ( b , d-f ). Instead, we examined the shape of the plateau and used the DV200 to judge RNA quality of FFPE samples. In human FFPE samples, prolongation of tissue lysis led to a decrease of high-molecular-weight species, since the peak with an average size of 3,000–4,000 nucleotides ( d,e ; arrows) is no longer present after 10 hours incubation ( f ). Implementation of a 70 °C incubation step after tissue lysis ( e , f ) favoured cross-link reduction as well, noticeable by a reduction of the peak on the right-hand side as compared with corresponding untreated samples ( d ). FU, fluorescent units; nt, nucleotides; DV200, percentage of RNA fragments > 200 nucleotides. (g , h) Overview of RIN and DV200 parameters of rat ( g ) and human (h) FF and FFPE samples to monitor RNA quality. Increasing the lysis time of human tissues (h) from 3 to 10 hours did not significantly affect DV200 values (unpaired two-tailed Student’s t-test; p = 0.2840, t(4) = 1.236), nor did the additional incubation step at 70 °C ( p = 0.7292, t(4) = 0.3714). RIN, RNA integrity number; DV200, percentage of RNA fragments > 200 nucleotides.

    Journal: Scientific Reports

    Article Title: Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples

    doi: 10.1038/s41598-018-24781-6

    Figure Lengend Snippet: Agilent Bioanalyzer electropherograms as suitable basis for RNA quality assessment. (a-f) Isolated total RNA was loaded on Agilent RNA Pico Chips, which were run in an Agilent 2100 Bioanalyzer. RNA profiles of microdissected rat ( a ) and human ( c ) FF samples show clearly distinguishable 18 S and 28 S rRNA peaks, which are absent in FFPE samples ( b , d-f ). Instead, we examined the shape of the plateau and used the DV200 to judge RNA quality of FFPE samples. In human FFPE samples, prolongation of tissue lysis led to a decrease of high-molecular-weight species, since the peak with an average size of 3,000–4,000 nucleotides ( d,e ; arrows) is no longer present after 10 hours incubation ( f ). Implementation of a 70 °C incubation step after tissue lysis ( e , f ) favoured cross-link reduction as well, noticeable by a reduction of the peak on the right-hand side as compared with corresponding untreated samples ( d ). FU, fluorescent units; nt, nucleotides; DV200, percentage of RNA fragments > 200 nucleotides. (g , h) Overview of RIN and DV200 parameters of rat ( g ) and human (h) FF and FFPE samples to monitor RNA quality. Increasing the lysis time of human tissues (h) from 3 to 10 hours did not significantly affect DV200 values (unpaired two-tailed Student’s t-test; p = 0.2840, t(4) = 1.236), nor did the additional incubation step at 70 °C ( p = 0.7292, t(4) = 0.3714). RIN, RNA integrity number; DV200, percentage of RNA fragments > 200 nucleotides.

    Article Snippet: Agilent 2100 Bioanalyzer RNA integrity of samples isolated from fresh mouse tissue was determined by Agilent 2100 Bioanalyzer using Agilent RNA Nano Chips.

    Techniques: Isolation, Formalin-fixed Paraffin-Embedded, Lysis, Molecular Weight, Incubation, Two Tailed Test

    (A) The means of the RNA integrity number (RIN) gradually decrease with increasing delayed freezing time: a P = 0.000; b P = 0.004; c P = 0.011. (B) Case distribution of RIN according to the delayed time.

    Journal: Journal of the Korean Society of Coloproctology

    Article Title: Effects of Delay in the Snap Freezing of Colorectal Cancer Tissues on the Quality of DNA and RNA

    doi: 10.3393/jksc.2010.26.5.316

    Figure Lengend Snippet: (A) The means of the RNA integrity number (RIN) gradually decrease with increasing delayed freezing time: a P = 0.000; b P = 0.004; c P = 0.011. (B) Case distribution of RIN according to the delayed time.

    Article Snippet: The integrity of RNA was evaluated by measuring the 28s and the 18s ribosomal RNA (rRNA) bands shown on agarose gel electrophoresis by using the Multi Gauge V3.0 program (FujiFilm, Tokyo, Japan) and by measuring the RNA integrity number (RIN) through the use of the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Techniques:

    Percentage of samples suitable for gene expression arrays (RNA integrity number [RIN] of ≥7) at different ex-vivo procurement times (time from surgical removal to cryopreservation) for a ≤10 min, b 11–30 min, c 31–60 min, and d > 1 h. For each group, total RNA from 12 fresh-frozen tissue blocks (total of 48) was extracted and RIN determined after electropherogram and analysis on Agilent 2100 Bioanalyzer

    Journal: Annals of surgical oncology

    Article Title: Biobanking of Human Pancreas Cancer Tissue: Impact of Ex-Vivo Procurement Times on RNA Quality

    doi: 10.1245/s10434-010-0959-6

    Figure Lengend Snippet: Percentage of samples suitable for gene expression arrays (RNA integrity number [RIN] of ≥7) at different ex-vivo procurement times (time from surgical removal to cryopreservation) for a ≤10 min, b 11–30 min, c 31–60 min, and d > 1 h. For each group, total RNA from 12 fresh-frozen tissue blocks (total of 48) was extracted and RIN determined after electropherogram and analysis on Agilent 2100 Bioanalyzer

    Article Snippet: To assess RNA integrity, RNA integrity numbers (RINs) are calculated by Agilent software.

    Techniques: Expressing, Ex Vivo

    RNA-Seq analysis of global transcriptome changes based on MCPIP1 expression ( A) Principal component analysis (PCA) of RNA-Seq datasets and ( B ) Venn diagrams show the number of differentially expressed transcripts (adj. P -value

    Journal: Oncotarget

    Article Title: RNA sequencing reveals widespread transcriptome changes in a renal carcinoma cell line

    doi: 10.18632/oncotarget.24269

    Figure Lengend Snippet: RNA-Seq analysis of global transcriptome changes based on MCPIP1 expression ( A) Principal component analysis (PCA) of RNA-Seq datasets and ( B ) Venn diagrams show the number of differentially expressed transcripts (adj. P -value

    Article Snippet: Generation of the transcriptome library and RNA sequencing RNA integrity was assessed with the Agilent RNA 6000 Nano Kit on 2100 Bioanalyzer (Agilent) followed by library preparation with the Ion AmpliSeq Transcriptome Human Gene Expression Panel (Thermo) according to the manufacturer’s protocol [ ].

    Techniques: RNA Sequencing Assay, Expressing

    (A) RNA integrity versus processing time (T p ): FNA-sample RIN scores do not correlate with lag time between aspiration and freezing time (T p ) when specimens are processed for cryopreservation within 1 hour of aspiration. (B) RNA integrity versus frozen time duration (T f ): FNA-sample RIN scores do not correlate with total frozen time (T f ).

    Journal: Cancer cytopathology

    Article Title: Preservation of Fine-Needle Aspiration Specimens for Future Use in RNA-Based Molecular Testing

    doi: 10.1002/cncy.20130

    Figure Lengend Snippet: (A) RNA integrity versus processing time (T p ): FNA-sample RIN scores do not correlate with lag time between aspiration and freezing time (T p ) when specimens are processed for cryopreservation within 1 hour of aspiration. (B) RNA integrity versus frozen time duration (T f ): FNA-sample RIN scores do not correlate with total frozen time (T f ).

    Article Snippet: RNA integrity and yield were evaluated by analysis on the Agilent 2100 bioanalyzer RNA 6000 Pico Chip kit using the RNA Integrity Number (RIN) software (Agilent Technologies, Santa Clara, Calif).

    Techniques:

    Linear regression analysis for RNA integrity compared to postmortem interval for heart, liver, lymph node and adrenal. Results show linear regression lines for each tissue for RIN compared to PMI with 95 % confidence limits. Results show Pearson r values

    Journal: Cell and tissue banking

    Article Title: Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program

    doi: 10.1007/s10561-016-9555-8

    Figure Lengend Snippet: Linear regression analysis for RNA integrity compared to postmortem interval for heart, liver, lymph node and adrenal. Results show linear regression lines for each tissue for RIN compared to PMI with 95 % confidence limits. Results show Pearson r values

    Article Snippet: The Agilent Bioanalyzer RNA integrity number (RIN) has become the accepted standard for assessing the intactness of isolated RNA from all sources ( ).

    Techniques:

    Effect of RIN on expression values of housekeeping normalization genes in RNA samples derived from heart. The results show linear correlation analyses for Ct values compared to RIN values for the genes β2 microglobulin (β2 M) ( a and b

    Journal: Cell and tissue banking

    Article Title: Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program

    doi: 10.1007/s10561-016-9555-8

    Figure Lengend Snippet: Effect of RIN on expression values of housekeeping normalization genes in RNA samples derived from heart. The results show linear correlation analyses for Ct values compared to RIN values for the genes β2 microglobulin (β2 M) ( a and b

    Article Snippet: The Agilent Bioanalyzer RNA integrity number (RIN) has become the accepted standard for assessing the intactness of isolated RNA from all sources ( ).

    Techniques: Expressing, Derivative Assay

    Variation of RNA integrity in primary tumors and metastases in a metastatic cancer case A129 ( A ) One primary pancreatic tumor was bread-loafed as indicated by primary tumor section S2 to S6. Each slice was further cut into equally sized small pieces (approximately 1 × 1 cm) and numbered accordingly to generate sample IDs. Samples with high tumor cellularity were used for RNA extraction and determination of RNA integrity. Samples indicated by an asterisk (*) were excluded due to low tumor cellularity or necrosis. ( B ) Each piece of tissue was trisected and RNA extracted (E1,E2,E3). The color code for RIN value is the same as in Figure 1 .

    Journal: Oncotarget

    Article Title: Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    doi: 10.18632/oncotarget.11836

    Figure Lengend Snippet: Variation of RNA integrity in primary tumors and metastases in a metastatic cancer case A129 ( A ) One primary pancreatic tumor was bread-loafed as indicated by primary tumor section S2 to S6. Each slice was further cut into equally sized small pieces (approximately 1 × 1 cm) and numbered accordingly to generate sample IDs. Samples with high tumor cellularity were used for RNA extraction and determination of RNA integrity. Samples indicated by an asterisk (*) were excluded due to low tumor cellularity or necrosis. ( B ) Each piece of tissue was trisected and RNA extracted (E1,E2,E3). The color code for RIN value is the same as in Figure 1 .

    Article Snippet: RNA integrity analysis The RNA integrity number (RIN) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) with an RNA nano-kit system as described in the manufacturer's instructions.

    Techniques: RNA Extraction

    RNAseq clearly separates a tumor signature from the normal counterpart ( A ) Normalized RNA-seq coverage is plotted against transcript position. ( B ) Fragment length distribution. Representative samples with wide spectrum of RIN are shown in A and B. ( C ) Heat map shows expression profile of top 250 differentially expressed genes. Numbers in parenthesis indicate RIN values. Tumor, tissues from primary pancreatic cancer. Normal, tissue from normal pancreas.

    Journal: Oncotarget

    Article Title: Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    doi: 10.18632/oncotarget.11836

    Figure Lengend Snippet: RNAseq clearly separates a tumor signature from the normal counterpart ( A ) Normalized RNA-seq coverage is plotted against transcript position. ( B ) Fragment length distribution. Representative samples with wide spectrum of RIN are shown in A and B. ( C ) Heat map shows expression profile of top 250 differentially expressed genes. Numbers in parenthesis indicate RIN values. Tumor, tissues from primary pancreatic cancer. Normal, tissue from normal pancreas.

    Article Snippet: RNA integrity analysis The RNA integrity number (RIN) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) with an RNA nano-kit system as described in the manufacturer's instructions.

    Techniques: RNA Sequencing Assay, Expressing

    RNA integrity numbers in patient-matched tissues RIN values from patient-matched tissues were plotted against tissue types. Selected cases from each of the four PMI categories were shown. Samples with low RNA yield leading to unreported or unreliable RIN were assigned to a RIN value of 0 and indicated by a circle. Dashed lines indicate tissues not analysed for that patient. Abbreviations are He, heart; Ki, kidney; Li, liver; Lu, Lung; Pa, pancreas; Ske, skeletal muscle; Ski, skin; Sp, spleen; Pr, primary tumor; LiM, liver mets; LuM, Lung mets.

    Journal: Oncotarget

    Article Title: Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    doi: 10.18632/oncotarget.11836

    Figure Lengend Snippet: RNA integrity numbers in patient-matched tissues RIN values from patient-matched tissues were plotted against tissue types. Selected cases from each of the four PMI categories were shown. Samples with low RNA yield leading to unreported or unreliable RIN were assigned to a RIN value of 0 and indicated by a circle. Dashed lines indicate tissues not analysed for that patient. Abbreviations are He, heart; Ki, kidney; Li, liver; Lu, Lung; Pa, pancreas; Ske, skeletal muscle; Ski, skin; Sp, spleen; Pr, primary tumor; LiM, liver mets; LuM, Lung mets.

    Article Snippet: RNA integrity analysis The RNA integrity number (RIN) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) with an RNA nano-kit system as described in the manufacturer's instructions.

    Techniques:

    Correlations between RNA integrity numbers and post mortem interval by tissue site Scatter plots were generated by plotting RIN values from each normal tissue type or primary tumors against PMI. Linear regression was performed to create curve fits. Samples with low RNA yield leading to unreported or unreliable RIN were assigned to a RIN value of 0 (red stars) and excluded from linear regression analysis.

    Journal: Oncotarget

    Article Title: Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    doi: 10.18632/oncotarget.11836

    Figure Lengend Snippet: Correlations between RNA integrity numbers and post mortem interval by tissue site Scatter plots were generated by plotting RIN values from each normal tissue type or primary tumors against PMI. Linear regression was performed to create curve fits. Samples with low RNA yield leading to unreported or unreliable RIN were assigned to a RIN value of 0 (red stars) and excluded from linear regression analysis.

    Article Snippet: RNA integrity analysis The RNA integrity number (RIN) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) with an RNA nano-kit system as described in the manufacturer's instructions.

    Techniques: Generated

    Correlation between RIN and sample storage time Scatter plots were generated by plotting RIN values from each tissue types against sample storage time. Samples with low RNA yield leading to unreported or unreliable RIN were assigned to a RIN value of 0 and indicated by a red star.

    Journal: Oncotarget

    Article Title: Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    doi: 10.18632/oncotarget.11836

    Figure Lengend Snippet: Correlation between RIN and sample storage time Scatter plots were generated by plotting RIN values from each tissue types against sample storage time. Samples with low RNA yield leading to unreported or unreliable RIN were assigned to a RIN value of 0 and indicated by a red star.

    Article Snippet: RNA integrity analysis The RNA integrity number (RIN) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) with an RNA nano-kit system as described in the manufacturer's instructions.

    Techniques: Generated

    RNA integrity in patient-matched liver metastases and lung metastases ( A ) Numbers listed are the corresponding RIN value for each individual tissue. N/A, data not available due to low RNA yield. ( B ) Scatter plot was generated by plotting RIN values from liver metastases against that from lung metastases. Pearson r and p value s were from correlation analysis.

    Journal: Oncotarget

    Article Title: Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    doi: 10.18632/oncotarget.11836

    Figure Lengend Snippet: RNA integrity in patient-matched liver metastases and lung metastases ( A ) Numbers listed are the corresponding RIN value for each individual tissue. N/A, data not available due to low RNA yield. ( B ) Scatter plot was generated by plotting RIN values from liver metastases against that from lung metastases. Pearson r and p value s were from correlation analysis.

    Article Snippet: RNA integrity analysis The RNA integrity number (RIN) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) with an RNA nano-kit system as described in the manufacturer's instructions.

    Techniques: Generated

    Heat map of RNA integrity numbers by tissue type RIN values from individual tissues were expressed with colored regions as defined by the accompanying legend. Abbreviations are PDA, pancreatic ductal adenocarcinoma; BC, breast cancer; GCT, germ cell tumor; CRC, colorectal cancer; NSCLC, non-small cell lung cancer; UCC, urothelial cell carcinoma; MM, melanoma; He, heart; Ki, kidney; Li, liver; Lu, Lung; Pa, pancreas; Ski, skin; Sp, spleen; Pr, primary tumor; LiM, liver metastasis; LuM, Lung metastasis. PMA, postmortem autolysis; TN, tumor-associated necrosis; fib, fibrosis.

    Journal: Oncotarget

    Article Title: Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    doi: 10.18632/oncotarget.11836

    Figure Lengend Snippet: Heat map of RNA integrity numbers by tissue type RIN values from individual tissues were expressed with colored regions as defined by the accompanying legend. Abbreviations are PDA, pancreatic ductal adenocarcinoma; BC, breast cancer; GCT, germ cell tumor; CRC, colorectal cancer; NSCLC, non-small cell lung cancer; UCC, urothelial cell carcinoma; MM, melanoma; He, heart; Ki, kidney; Li, liver; Lu, Lung; Pa, pancreas; Ski, skin; Sp, spleen; Pr, primary tumor; LiM, liver metastasis; LuM, Lung metastasis. PMA, postmortem autolysis; TN, tumor-associated necrosis; fib, fibrosis.

    Article Snippet: RNA integrity analysis The RNA integrity number (RIN) was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies) with an RNA nano-kit system as described in the manufacturer's instructions.

    Techniques:

    ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of mRNA-seq expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger RNA abundance measured by high-throughput sequencing.

    Journal: Genome Biology

    Article Title: Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

    doi: 10.1186/gb-2012-13-10-r88

    Figure Lengend Snippet: ΔDNase regions are associated with androgen receptor-regulated transcription . (a) Heatmap of mRNA-seq expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger RNA abundance measured by high-throughput sequencing.

    Article Snippet: All RNA used for subsequent library preparation had an RNA integrity number greater than 9.0. mRNA-seq libraries were created using the Illumina mRNA-seq protocol and kit then sequenced on the Illumina GAIIx platform.

    Techniques: Expressing, Microarray, Next-Generation Sequencing

    Characterization of HLHS patient specific iPSC lines. ( A ) Brightfield images of two clones derived from each patient using the non-integrative RNA based Sendai virus; ( B ) Representative example of flow cytometric analysis of key pluripotent cell markers, TRA-1-60 and NANOG. A representative example is shown from HLHS1 clone 1, however similar results were obtained for all HLHS and unaffected iPSC lines; ( C ) Elimination of Sendai viral vectors from derived iPSC lines ( KOS stands for KLF4 , OCT4 and SOX2 ); ( D ) Immunofluorescent images showing antibody staining of cells derived from all three germ layers: neuronal class β-III-tubulin staining neuronal cells derived from ectoderm; α-Smooth muscle actin staining smooth muscle cells derived from mesoderm αFP (alpha-fetoprotein) staining endodermal cells. A representative example is shown from HLHS2 clone 1; however similar results were obtained for all HLHS and unaffected iPSC lines. ( E ) In vivo differentiation of HLHS1-clone 1 as a representative example of teratoma forming ability of HLHS patient specific iPSC lines. (A) low power showing heterogeneous structure of the teratoma; (B) neuroepithelium; (C) cartilage; (D) intestinal epithelium. (A: scale bar = 400 µm, B-D: scale bar = 50 µm).

    Journal: Human Molecular Genetics

    Article Title: Induced pluripotent stem cell modelling of HLHS underlines the contribution of dysfunctional NOTCH signalling to impaired cardiogenesis

    doi: 10.1093/hmg/ddx140

    Figure Lengend Snippet: Characterization of HLHS patient specific iPSC lines. ( A ) Brightfield images of two clones derived from each patient using the non-integrative RNA based Sendai virus; ( B ) Representative example of flow cytometric analysis of key pluripotent cell markers, TRA-1-60 and NANOG. A representative example is shown from HLHS1 clone 1, however similar results were obtained for all HLHS and unaffected iPSC lines; ( C ) Elimination of Sendai viral vectors from derived iPSC lines ( KOS stands for KLF4 , OCT4 and SOX2 ); ( D ) Immunofluorescent images showing antibody staining of cells derived from all three germ layers: neuronal class β-III-tubulin staining neuronal cells derived from ectoderm; α-Smooth muscle actin staining smooth muscle cells derived from mesoderm αFP (alpha-fetoprotein) staining endodermal cells. A representative example is shown from HLHS2 clone 1; however similar results were obtained for all HLHS and unaffected iPSC lines. ( E ) In vivo differentiation of HLHS1-clone 1 as a representative example of teratoma forming ability of HLHS patient specific iPSC lines. (A) low power showing heterogeneous structure of the teratoma; (B) neuroepithelium; (C) cartilage; (D) intestinal epithelium. (A: scale bar = 400 µm, B-D: scale bar = 50 µm).

    Article Snippet: All iPSC clones were derived from reprogramming of dermal fibroblasts using the RNA based non-integrative Sendai virus (Thermo Fisher Cytotune 2 Kit).

    Techniques: Clone Assay, Derivative Assay, Flow Cytometry, Staining, In Vivo

    CXCR4 RNA and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom microarray. 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p

    Journal: Oncotarget

    Article Title: A differential role for CXCR4 in the regulation of normal versus malignant breast stem cell activity

    doi:

    Figure Lengend Snippet: CXCR4 RNA and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom microarray. 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p

    Article Snippet: Agilent gene custom microarray RNA integrity was assessed by microanalysis (Agilent Bioanalyser).

    Techniques: Expressing, Microarray, Quantitative RT-PCR, FACS, Flow Cytometry