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  • 99
    Millipore rna seq library
    Rna Seq Library, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore rna seq library preparation
    Senataxin counteracts the formation of translocations. a Rejoining of distant DSBs were detected by PCR, following DSB induction and repair (+4OHT + IAA 2 h) at breaks recently shown to undergo clustering 31 . DNA sequencing confirmed the nature of the amplified products. b MIS12::TRIM37 and LINC00271::LYRM2 rejoining frequencies were analyzed before or after 4OHT + IAA treatment, by quantitative PCR in AID DIvA cells <t>transfected</t> with control or SETX directed siRNA. Mean and s.e.m. of five biological replicates are shown. P values are indicated (one sample t- test). c MIS12::TRIM37 rejoining frequency was analyzed in control or SETX-depleted AID DIvA cells pretreated or not with DRB prior to 4OHT addition as indicated. Mean and s.e.m. of three biological replicates are shown. P value is indicated (paired t -test). d Model: R-loops form as the <t>RNA</t> Polymerase II progresses across the gene. The induction of a DSB elicits ATM activity which triggers RNA polymerase II stalling at the vicinity of the DSB, hence decreasing R-loops across the gene body. On another hand, R-loops and/or RNA:DNA hybrids accumulate in cis to the DSB, due to stalled RNA PolII generating short, abortive, RNAs which thread back in the DNA duplex, or/and potentially de novo PolII transcription from DNA end. Senataxin is further recruited to remove RNA:DNA hybrids at the vicinity of the break induced in active loci. Senataxin and/or R-loop removal, regulate γH2AX establishment, promote Rad51 loading and minimize the occurrence of translocation by a mechanism that still need to be investigated
    Rna Seq Library Preparation, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc rna seq rnaseq libraries
    Senataxin counteracts the formation of translocations. a Rejoining of distant DSBs were detected by PCR, following DSB induction and repair (+4OHT + IAA 2 h) at breaks recently shown to undergo clustering 31 . DNA sequencing confirmed the nature of the amplified products. b MIS12::TRIM37 and LINC00271::LYRM2 rejoining frequencies were analyzed before or after 4OHT + IAA treatment, by quantitative PCR in AID DIvA cells <t>transfected</t> with control or SETX directed siRNA. Mean and s.e.m. of five biological replicates are shown. P values are indicated (one sample t- test). c MIS12::TRIM37 rejoining frequency was analyzed in control or SETX-depleted AID DIvA cells pretreated or not with DRB prior to 4OHT addition as indicated. Mean and s.e.m. of three biological replicates are shown. P value is indicated (paired t -test). d Model: R-loops form as the <t>RNA</t> Polymerase II progresses across the gene. The induction of a DSB elicits ATM activity which triggers RNA polymerase II stalling at the vicinity of the DSB, hence decreasing R-loops across the gene body. On another hand, R-loops and/or RNA:DNA hybrids accumulate in cis to the DSB, due to stalled RNA PolII generating short, abortive, RNAs which thread back in the DNA duplex, or/and potentially de novo PolII transcription from DNA end. Senataxin is further recruited to remove RNA:DNA hybrids at the vicinity of the break induced in active loci. Senataxin and/or R-loop removal, regulate γH2AX establishment, promote Rad51 loading and minimize the occurrence of translocation by a mechanism that still need to be investigated
    Rna Seq Rnaseq Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc rna seq library construction
    Recurrent LACTB2 - NCOA2 fusion in colorectal cancer (CRC). ( a ) Structural variations (SVs) in the tumor tissue of a CRC case were illustrated as a Circos plot with red and blue lines indicating inter-chromosomal and intra-chromosomal SVs, respectively. ( b ) The <t>DNA</t> and <t>RNA</t> structures of the LACTB2 - NCOA2 fusion were illustrated. RT–PCR (M: size marker; N: normal cDNA; T: CRC cDNA) and Sanger sequencing confirmed the tumor-specific occurrence of LACTB2 - NCOA2 fusion. ( c ) The LACTB2 - NCOA2 fusion transcript with the same breakpoints was present in 6 out of 99 (6.1%) CRC cDNA samples as confirmed by RT–PCR and Sanger sequencing (chromatogram).
    Rna Seq Library Construction, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 1123 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Illumina Inc rna seq library kits
    The levels of H3K4me3, MLL1, MLL2, and subset of H3K4me3-enriched genes are elevated in group I and group II <t>GBM.</t> (A) Scheme displays the control regions and MRI scanned group I and group II GBM. (B) The levels of H3K4me3 were analyzed by western blot. Total histone 3 (H3) were used as loading control. (C) A heatmap for expression of genes in MLL complex (log2 scale) by quantitative RT-PCR for human GBM specimens. (D) Analysis of MLL1 and MLL2 protein levels and H3K4me3 abundance in GBM and control specimens by western blot. γ-tubulin and unmodified H3 and H4 were used as loading controls. (E) A heatmap for expression of selected 49 genes by quantitative RT-PCR for human GBM specimens. Inset shows color scale indicating differences in expression level. The white color with symmetry to 0 defines no difference at expression level between GBM and the controls. The red color scales increased expression level of genes in GBM compared to control and the blue color scales decreased expression in GBM relative to control. The dendrogram was computed by hierarchical clustering with Euclidean distance metric and complete linkage. (F) Venn diagram displays the overlap among genes enriched with H3K4me3 identified from ChIP-Seq of SVZ cells (NSCs and NBs), expressed in SVZ cells identified from <t>RNA-Seq</t> of baboon SVZ cells as noted “magenta” portion (n = 1913), and substantially increased in SVZ-associated GBM cases identified from RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”. (G) Venn diagram displays the overlap among genes which are not detectable in baboon SVZ cells by RNA-Seq as noted “green” portion (n = 750), but are enriched with H3K4me3 identified from ChIP-Seq of baboon SVZ cells (NSCs and NBs), and are substantially increased in SVZ-associated GBM cases by RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”.
    Rna Seq Library Kits, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa prepx rna seq library kit
    The levels of H3K4me3, MLL1, MLL2, and subset of H3K4me3-enriched genes are elevated in group I and group II <t>GBM.</t> (A) Scheme displays the control regions and MRI scanned group I and group II GBM. (B) The levels of H3K4me3 were analyzed by western blot. Total histone 3 (H3) were used as loading control. (C) A heatmap for expression of genes in MLL complex (log2 scale) by quantitative RT-PCR for human GBM specimens. (D) Analysis of MLL1 and MLL2 protein levels and H3K4me3 abundance in GBM and control specimens by western blot. γ-tubulin and unmodified H3 and H4 were used as loading controls. (E) A heatmap for expression of selected 49 genes by quantitative RT-PCR for human GBM specimens. Inset shows color scale indicating differences in expression level. The white color with symmetry to 0 defines no difference at expression level between GBM and the controls. The red color scales increased expression level of genes in GBM compared to control and the blue color scales decreased expression in GBM relative to control. The dendrogram was computed by hierarchical clustering with Euclidean distance metric and complete linkage. (F) Venn diagram displays the overlap among genes enriched with H3K4me3 identified from ChIP-Seq of SVZ cells (NSCs and NBs), expressed in SVZ cells identified from <t>RNA-Seq</t> of baboon SVZ cells as noted “magenta” portion (n = 1913), and substantially increased in SVZ-associated GBM cases identified from RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”. (G) Venn diagram displays the overlap among genes which are not detectable in baboon SVZ cells by RNA-Seq as noted “green” portion (n = 750), but are enriched with H3K4me3 identified from ChIP-Seq of baboon SVZ cells (NSCs and NBs), and are substantially increased in SVZ-associated GBM cases by RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”.
    Prepx Rna Seq Library Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher rna seq library
    The levels of H3K4me3, MLL1, MLL2, and subset of H3K4me3-enriched genes are elevated in group I and group II <t>GBM.</t> (A) Scheme displays the control regions and MRI scanned group I and group II GBM. (B) The levels of H3K4me3 were analyzed by western blot. Total histone 3 (H3) were used as loading control. (C) A heatmap for expression of genes in MLL complex (log2 scale) by quantitative RT-PCR for human GBM specimens. (D) Analysis of MLL1 and MLL2 protein levels and H3K4me3 abundance in GBM and control specimens by western blot. γ-tubulin and unmodified H3 and H4 were used as loading controls. (E) A heatmap for expression of selected 49 genes by quantitative RT-PCR for human GBM specimens. Inset shows color scale indicating differences in expression level. The white color with symmetry to 0 defines no difference at expression level between GBM and the controls. The red color scales increased expression level of genes in GBM compared to control and the blue color scales decreased expression in GBM relative to control. The dendrogram was computed by hierarchical clustering with Euclidean distance metric and complete linkage. (F) Venn diagram displays the overlap among genes enriched with H3K4me3 identified from ChIP-Seq of SVZ cells (NSCs and NBs), expressed in SVZ cells identified from <t>RNA-Seq</t> of baboon SVZ cells as noted “magenta” portion (n = 1913), and substantially increased in SVZ-associated GBM cases identified from RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”. (G) Venn diagram displays the overlap among genes which are not detectable in baboon SVZ cells by RNA-Seq as noted “green” portion (n = 750), but are enriched with H3K4me3 identified from ChIP-Seq of baboon SVZ cells (NSCs and NBs), and are substantially increased in SVZ-associated GBM cases by RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”.
    Rna Seq Library, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 174 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    New England Biolabs rna seq library
    The levels of H3K4me3, MLL1, MLL2, and subset of H3K4me3-enriched genes are elevated in group I and group II <t>GBM.</t> (A) Scheme displays the control regions and MRI scanned group I and group II GBM. (B) The levels of H3K4me3 were analyzed by western blot. Total histone 3 (H3) were used as loading control. (C) A heatmap for expression of genes in MLL complex (log2 scale) by quantitative RT-PCR for human GBM specimens. (D) Analysis of MLL1 and MLL2 protein levels and H3K4me3 abundance in GBM and control specimens by western blot. γ-tubulin and unmodified H3 and H4 were used as loading controls. (E) A heatmap for expression of selected 49 genes by quantitative RT-PCR for human GBM specimens. Inset shows color scale indicating differences in expression level. The white color with symmetry to 0 defines no difference at expression level between GBM and the controls. The red color scales increased expression level of genes in GBM compared to control and the blue color scales decreased expression in GBM relative to control. The dendrogram was computed by hierarchical clustering with Euclidean distance metric and complete linkage. (F) Venn diagram displays the overlap among genes enriched with H3K4me3 identified from ChIP-Seq of SVZ cells (NSCs and NBs), expressed in SVZ cells identified from <t>RNA-Seq</t> of baboon SVZ cells as noted “magenta” portion (n = 1913), and substantially increased in SVZ-associated GBM cases identified from RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”. (G) Venn diagram displays the overlap among genes which are not detectable in baboon SVZ cells by RNA-Seq as noted “green” portion (n = 750), but are enriched with H3K4me3 identified from ChIP-Seq of baboon SVZ cells (NSCs and NBs), and are substantially increased in SVZ-associated GBM cases by RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”.
    Rna Seq Library, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 179 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc rna seq libraries
    Gene body H3K36me3 level is negatively correlated with age-dependent <t>mRNA</t> expression change in Drosophila heads. ( A ) All genes with mappable H3K36me3 ChIP–chip and <t>RNA-seq</t> reads are plotted in the order of normalized H3K36me3 levels at the young
    Rna Seq Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 14523 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies rna seq library construction
    Gene body H3K36me3 level is negatively correlated with age-dependent <t>mRNA</t> expression change in Drosophila heads. ( A ) All genes with mappable H3K36me3 ChIP–chip and <t>RNA-seq</t> reads are plotted in the order of normalized H3K36me3 levels at the young
    Rna Seq Library Construction, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Pacific Biosciences rna seq library construction
    Gene body H3K36me3 level is negatively correlated with age-dependent <t>mRNA</t> expression change in Drosophila heads. ( A ) All genes with mappable H3K36me3 ChIP–chip and <t>RNA-seq</t> reads are plotted in the order of normalized H3K36me3 levels at the young
    Rna Seq Library Construction, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Gnomegen rna seq library kit
    Gene body H3K36me3 level is negatively correlated with age-dependent <t>mRNA</t> expression change in Drosophila heads. ( A ) All genes with mappable H3K36me3 ChIP–chip and <t>RNA-seq</t> reads are plotted in the order of normalized H3K36me3 levels at the young
    Rna Seq Library Kit, supplied by Gnomegen, used in various techniques. Bioz Stars score: 89/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher exosomal rna seq libraries
    Comparison of sera <t>exosomal</t> <t>RNA</t> using four different RNA extraction methods. (A) Total RNA yield from ultracentrifugation (UC) and ExoQuick (EQ) treated samples using the RNeasy Mini Kit combined with TRIzol LS, the RNeasy Mini Kit alone, conventional RNA precipitation, and AllPrep DNA/RNA Mini Kit. (B) Demonstration of RNA quality measured by OD 260 /OD 280 in EQ and UC treated samples. Data are shown as the mean ± SD from six independent patient samples. *** P
    Exosomal Rna Seq Libraries, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Senataxin counteracts the formation of translocations. a Rejoining of distant DSBs were detected by PCR, following DSB induction and repair (+4OHT + IAA 2 h) at breaks recently shown to undergo clustering 31 . DNA sequencing confirmed the nature of the amplified products. b MIS12::TRIM37 and LINC00271::LYRM2 rejoining frequencies were analyzed before or after 4OHT + IAA treatment, by quantitative PCR in AID DIvA cells transfected with control or SETX directed siRNA. Mean and s.e.m. of five biological replicates are shown. P values are indicated (one sample t- test). c MIS12::TRIM37 rejoining frequency was analyzed in control or SETX-depleted AID DIvA cells pretreated or not with DRB prior to 4OHT addition as indicated. Mean and s.e.m. of three biological replicates are shown. P value is indicated (paired t -test). d Model: R-loops form as the RNA Polymerase II progresses across the gene. The induction of a DSB elicits ATM activity which triggers RNA polymerase II stalling at the vicinity of the DSB, hence decreasing R-loops across the gene body. On another hand, R-loops and/or RNA:DNA hybrids accumulate in cis to the DSB, due to stalled RNA PolII generating short, abortive, RNAs which thread back in the DNA duplex, or/and potentially de novo PolII transcription from DNA end. Senataxin is further recruited to remove RNA:DNA hybrids at the vicinity of the break induced in active loci. Senataxin and/or R-loop removal, regulate γH2AX establishment, promote Rad51 loading and minimize the occurrence of translocation by a mechanism that still need to be investigated

    Journal: Nature Communications

    Article Title: Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

    doi: 10.1038/s41467-018-02894-w

    Figure Lengend Snippet: Senataxin counteracts the formation of translocations. a Rejoining of distant DSBs were detected by PCR, following DSB induction and repair (+4OHT + IAA 2 h) at breaks recently shown to undergo clustering 31 . DNA sequencing confirmed the nature of the amplified products. b MIS12::TRIM37 and LINC00271::LYRM2 rejoining frequencies were analyzed before or after 4OHT + IAA treatment, by quantitative PCR in AID DIvA cells transfected with control or SETX directed siRNA. Mean and s.e.m. of five biological replicates are shown. P values are indicated (one sample t- test). c MIS12::TRIM37 rejoining frequency was analyzed in control or SETX-depleted AID DIvA cells pretreated or not with DRB prior to 4OHT addition as indicated. Mean and s.e.m. of three biological replicates are shown. P value is indicated (paired t -test). d Model: R-loops form as the RNA Polymerase II progresses across the gene. The induction of a DSB elicits ATM activity which triggers RNA polymerase II stalling at the vicinity of the DSB, hence decreasing R-loops across the gene body. On another hand, R-loops and/or RNA:DNA hybrids accumulate in cis to the DSB, due to stalled RNA PolII generating short, abortive, RNAs which thread back in the DNA duplex, or/and potentially de novo PolII transcription from DNA end. Senataxin is further recruited to remove RNA:DNA hybrids at the vicinity of the break induced in active loci. Senataxin and/or R-loop removal, regulate γH2AX establishment, promote Rad51 loading and minimize the occurrence of translocation by a mechanism that still need to be investigated

    Article Snippet: RNA extraction and RNA-seq library preparation For RNA-seq, DIvA cells (transfected with the control siRNA) were lysed using TRI reagent (SIGMA) and spiked-in with ERCC RNA Spike-In Mix (Thermo Fisher Scientific).

    Techniques: Polymerase Chain Reaction, DNA Sequencing, Amplification, Real-time Polymerase Chain Reaction, Transfection, Activity Assay, Translocation Assay

    Recurrent LACTB2 - NCOA2 fusion in colorectal cancer (CRC). ( a ) Structural variations (SVs) in the tumor tissue of a CRC case were illustrated as a Circos plot with red and blue lines indicating inter-chromosomal and intra-chromosomal SVs, respectively. ( b ) The DNA and RNA structures of the LACTB2 - NCOA2 fusion were illustrated. RT–PCR (M: size marker; N: normal cDNA; T: CRC cDNA) and Sanger sequencing confirmed the tumor-specific occurrence of LACTB2 - NCOA2 fusion. ( c ) The LACTB2 - NCOA2 fusion transcript with the same breakpoints was present in 6 out of 99 (6.1%) CRC cDNA samples as confirmed by RT–PCR and Sanger sequencing (chromatogram).

    Journal: Oncogene

    Article Title: Disruption of NCOA2 by recurrent fusion with LACTB2 in colorectal cancer

    doi: 10.1038/onc.2015.72

    Figure Lengend Snippet: Recurrent LACTB2 - NCOA2 fusion in colorectal cancer (CRC). ( a ) Structural variations (SVs) in the tumor tissue of a CRC case were illustrated as a Circos plot with red and blue lines indicating inter-chromosomal and intra-chromosomal SVs, respectively. ( b ) The DNA and RNA structures of the LACTB2 - NCOA2 fusion were illustrated. RT–PCR (M: size marker; N: normal cDNA; T: CRC cDNA) and Sanger sequencing confirmed the tumor-specific occurrence of LACTB2 - NCOA2 fusion. ( c ) The LACTB2 - NCOA2 fusion transcript with the same breakpoints was present in 6 out of 99 (6.1%) CRC cDNA samples as confirmed by RT–PCR and Sanger sequencing (chromatogram).

    Article Snippet: Poly-A-containing mRNA purification, double-stranded cDNA synthesis, end repair, 3' end adenylation, adapter ligation and enrichment of DNA fragments for RNA-Seq library construction were performed using the reagents provided in the Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Marker, Sequencing

    Impact of biological replication on mRNA editing discovery. Distribution (in %) of unbiased mRNA editing events across the 12 classes of substitution according to the number of replicates they are detected in, ranging from N = 1 to N = 3, in white adipose tissue (WAT) and liver. The first two classes (AtoG and TtoC) are associated to ADAR-mediated RNA editing, and the next two (CtoT and GtoA) to APOBEC-meditated RNA editing. At the top-right of each graph, the total number of RNA editing events detected for a given number of replicates is shown. ADAR: Adenosine deaminases acting on RNA. APOBEC: Apolipoprotein B mRNA editing enzyme, catalytic polypetide-like.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3

    doi: 10.1534/g3.115.022251

    Figure Lengend Snippet: Impact of biological replication on mRNA editing discovery. Distribution (in %) of unbiased mRNA editing events across the 12 classes of substitution according to the number of replicates they are detected in, ranging from N = 1 to N = 3, in white adipose tissue (WAT) and liver. The first two classes (AtoG and TtoC) are associated to ADAR-mediated RNA editing, and the next two (CtoT and GtoA) to APOBEC-meditated RNA editing. At the top-right of each graph, the total number of RNA editing events detected for a given number of replicates is shown. ADAR: Adenosine deaminases acting on RNA. APOBEC: Apolipoprotein B mRNA editing enzyme, catalytic polypetide-like.

    Article Snippet: RNA sequencing: Libraries with a mean insert size of 200 bp were prepared according to the manufacturer’s instructions for RNA-seq library preparation, selecting polyadenylated mRNA using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) from each sample.

    Techniques:

    The levels of H3K4me3, MLL1, MLL2, and subset of H3K4me3-enriched genes are elevated in group I and group II GBM. (A) Scheme displays the control regions and MRI scanned group I and group II GBM. (B) The levels of H3K4me3 were analyzed by western blot. Total histone 3 (H3) were used as loading control. (C) A heatmap for expression of genes in MLL complex (log2 scale) by quantitative RT-PCR for human GBM specimens. (D) Analysis of MLL1 and MLL2 protein levels and H3K4me3 abundance in GBM and control specimens by western blot. γ-tubulin and unmodified H3 and H4 were used as loading controls. (E) A heatmap for expression of selected 49 genes by quantitative RT-PCR for human GBM specimens. Inset shows color scale indicating differences in expression level. The white color with symmetry to 0 defines no difference at expression level between GBM and the controls. The red color scales increased expression level of genes in GBM compared to control and the blue color scales decreased expression in GBM relative to control. The dendrogram was computed by hierarchical clustering with Euclidean distance metric and complete linkage. (F) Venn diagram displays the overlap among genes enriched with H3K4me3 identified from ChIP-Seq of SVZ cells (NSCs and NBs), expressed in SVZ cells identified from RNA-Seq of baboon SVZ cells as noted “magenta” portion (n = 1913), and substantially increased in SVZ-associated GBM cases identified from RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”. (G) Venn diagram displays the overlap among genes which are not detectable in baboon SVZ cells by RNA-Seq as noted “green” portion (n = 750), but are enriched with H3K4me3 identified from ChIP-Seq of baboon SVZ cells (NSCs and NBs), and are substantially increased in SVZ-associated GBM cases by RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”.

    Journal: Scientific Reports

    Article Title: Epigenetic Regulation by Chromatin Activation Mark H3K4me3 in Primate Progenitor Cells within Adult Neurogenic Niche

    doi: 10.1038/srep05371

    Figure Lengend Snippet: The levels of H3K4me3, MLL1, MLL2, and subset of H3K4me3-enriched genes are elevated in group I and group II GBM. (A) Scheme displays the control regions and MRI scanned group I and group II GBM. (B) The levels of H3K4me3 were analyzed by western blot. Total histone 3 (H3) were used as loading control. (C) A heatmap for expression of genes in MLL complex (log2 scale) by quantitative RT-PCR for human GBM specimens. (D) Analysis of MLL1 and MLL2 protein levels and H3K4me3 abundance in GBM and control specimens by western blot. γ-tubulin and unmodified H3 and H4 were used as loading controls. (E) A heatmap for expression of selected 49 genes by quantitative RT-PCR for human GBM specimens. Inset shows color scale indicating differences in expression level. The white color with symmetry to 0 defines no difference at expression level between GBM and the controls. The red color scales increased expression level of genes in GBM compared to control and the blue color scales decreased expression in GBM relative to control. The dendrogram was computed by hierarchical clustering with Euclidean distance metric and complete linkage. (F) Venn diagram displays the overlap among genes enriched with H3K4me3 identified from ChIP-Seq of SVZ cells (NSCs and NBs), expressed in SVZ cells identified from RNA-Seq of baboon SVZ cells as noted “magenta” portion (n = 1913), and substantially increased in SVZ-associated GBM cases identified from RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”. (G) Venn diagram displays the overlap among genes which are not detectable in baboon SVZ cells by RNA-Seq as noted “green” portion (n = 750), but are enriched with H3K4me3 identified from ChIP-Seq of baboon SVZ cells (NSCs and NBs), and are substantially increased in SVZ-associated GBM cases by RNA-Seq analyses (yellow- group I GBM; light purple- group II GBM). The GO terms for overrepresented genes among this overlap are shown in the “box”.

    Article Snippet: RNA-Seq analysis Total RNA was extracted from purified baboon SVZ cells and frozen GBM specimens using TRIzol reagent and sequencing libraries were generated with Illumina RNA-Seq library kit.

    Techniques: Magnetic Resonance Imaging, Western Blot, Expressing, Quantitative RT-PCR, Chromatin Immunoprecipitation, RNA Sequencing Assay

    Gene body H3K36me3 level is negatively correlated with age-dependent mRNA expression change in Drosophila heads. ( A ) All genes with mappable H3K36me3 ChIP–chip and RNA-seq reads are plotted in the order of normalized H3K36me3 levels at the young

    Journal: Genes & Development

    Article Title: Trimethylation of Lys36 on H3 restricts gene expression change during aging and impacts life span

    doi: 10.1101/gad.254144.114

    Figure Lengend Snippet: Gene body H3K36me3 level is negatively correlated with age-dependent mRNA expression change in Drosophila heads. ( A ) All genes with mappable H3K36me3 ChIP–chip and RNA-seq reads are plotted in the order of normalized H3K36me3 levels at the young

    Article Snippet: Two-hundred nanograms of mRNA was then used to prepare RNA-seq libraries, which were sequenced on an Illumina HiSeq 2000 at six samples per lane.

    Techniques: Expressing, Chromatin Immunoprecipitation, RNA Sequencing Assay

    Comparison of sera exosomal RNA using four different RNA extraction methods. (A) Total RNA yield from ultracentrifugation (UC) and ExoQuick (EQ) treated samples using the RNeasy Mini Kit combined with TRIzol LS, the RNeasy Mini Kit alone, conventional RNA precipitation, and AllPrep DNA/RNA Mini Kit. (B) Demonstration of RNA quality measured by OD 260 /OD 280 in EQ and UC treated samples. Data are shown as the mean ± SD from six independent patient samples. *** P

    Journal: PLoS ONE

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    doi: 10.1371/journal.pone.0196913

    Figure Lengend Snippet: Comparison of sera exosomal RNA using four different RNA extraction methods. (A) Total RNA yield from ultracentrifugation (UC) and ExoQuick (EQ) treated samples using the RNeasy Mini Kit combined with TRIzol LS, the RNeasy Mini Kit alone, conventional RNA precipitation, and AllPrep DNA/RNA Mini Kit. (B) Demonstration of RNA quality measured by OD 260 /OD 280 in EQ and UC treated samples. Data are shown as the mean ± SD from six independent patient samples. *** P

    Article Snippet: Somewhat surprisingly, our results showed that for exosomal RNA-Seq libraries, Nanodrop quantification correlates higher with RT-qPCR measurements than Bioanalyzer.

    Techniques: RNA Extraction

    Minimal sera volume for exosome detection and RNA extraction. (A) Representative immunoblots for CD63 comparing exosome enrichment using ultracentrifugation (UC) and ExoQuick (EQ) among samples of varying volumes. (B) Scatter dot plots depict total exosomal RNA recovered per sample volume using EQ. (C) Scatter dot plots show RNA quality measured by OD 260 /OD 280 per sample volume. Data are shown as the mean ± standard deviation (SD) from six independent patient samples. P -values were calculated using one-way ANOVA.

    Journal: PLoS ONE

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    doi: 10.1371/journal.pone.0196913

    Figure Lengend Snippet: Minimal sera volume for exosome detection and RNA extraction. (A) Representative immunoblots for CD63 comparing exosome enrichment using ultracentrifugation (UC) and ExoQuick (EQ) among samples of varying volumes. (B) Scatter dot plots depict total exosomal RNA recovered per sample volume using EQ. (C) Scatter dot plots show RNA quality measured by OD 260 /OD 280 per sample volume. Data are shown as the mean ± standard deviation (SD) from six independent patient samples. P -values were calculated using one-way ANOVA.

    Article Snippet: Somewhat surprisingly, our results showed that for exosomal RNA-Seq libraries, Nanodrop quantification correlates higher with RT-qPCR measurements than Bioanalyzer.

    Techniques: RNA Extraction, Western Blot, Standard Deviation

    Exosomal RNAs are stable over two decades. Dot plots of total RNA yield and OD 260 /OD 280 from 105 EQ-treated archival patient samples using the RNeasy Mini Kit combined with TRIzol LS. Storage time for each sample is indicated on the x-axis. The Spearman’s rank correlations for RNA yield versus storing time and OD 260 /OD 280 versus storage time are 0.185 ( P = 0.06) and 0.04 ( P = 0.70), respectively.

    Journal: PLoS ONE

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    doi: 10.1371/journal.pone.0196913

    Figure Lengend Snippet: Exosomal RNAs are stable over two decades. Dot plots of total RNA yield and OD 260 /OD 280 from 105 EQ-treated archival patient samples using the RNeasy Mini Kit combined with TRIzol LS. Storage time for each sample is indicated on the x-axis. The Spearman’s rank correlations for RNA yield versus storing time and OD 260 /OD 280 versus storage time are 0.185 ( P = 0.06) and 0.04 ( P = 0.70), respectively.

    Article Snippet: Somewhat surprisingly, our results showed that for exosomal RNA-Seq libraries, Nanodrop quantification correlates higher with RT-qPCR measurements than Bioanalyzer.

    Techniques:

    Flow chart for evaluation of exosomal RNAs from cell-free sera as biomarkers for human diseases. Graphic summary of the workflow including time allotment for preparation for cell-free serum (steps ①-③), comparison of methods for exosome enrichment (step ④), validation by transmission electron microscopy (TEM) and immunoblotting for CD63 or other exosomal markers (step ⑤), RNA extraction (step ⑥), and preparation of RNA-Seq libraries (step ⑦). 10–100 nanograms RNA can be used for library preparation with the NEBNext Ultra Directional RNA Library Prep Kit. Step ② is an optional centrifugation step that can be included to ensure the most efficient removal of trace amounts of cell debris and shedding microvesicles. A validation step can be performed with RT-qPCR for specific candidate RNA following RNA-Seq analysis (step ⑧).

    Journal: PLoS ONE

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    doi: 10.1371/journal.pone.0196913

    Figure Lengend Snippet: Flow chart for evaluation of exosomal RNAs from cell-free sera as biomarkers for human diseases. Graphic summary of the workflow including time allotment for preparation for cell-free serum (steps ①-③), comparison of methods for exosome enrichment (step ④), validation by transmission electron microscopy (TEM) and immunoblotting for CD63 or other exosomal markers (step ⑤), RNA extraction (step ⑥), and preparation of RNA-Seq libraries (step ⑦). 10–100 nanograms RNA can be used for library preparation with the NEBNext Ultra Directional RNA Library Prep Kit. Step ② is an optional centrifugation step that can be included to ensure the most efficient removal of trace amounts of cell debris and shedding microvesicles. A validation step can be performed with RT-qPCR for specific candidate RNA following RNA-Seq analysis (step ⑧).

    Article Snippet: Somewhat surprisingly, our results showed that for exosomal RNA-Seq libraries, Nanodrop quantification correlates higher with RT-qPCR measurements than Bioanalyzer.

    Techniques: Flow Cytometry, Transmission Assay, Electron Microscopy, Transmission Electron Microscopy, RNA Extraction, RNA Sequencing Assay, Centrifugation, Quantitative RT-PCR

    Exosomal RNA-Seq libraries from archival sera specimens. (A) Bioanalyzer results for 5 independent specimens demonstrate inserted size of exosomal RNAs. (B) Number of mapped reads generated from RNA-Seq libraries for 5 independent specimens with 20 ng exosomal RNAs. RNA-Seq library concentrations were calculated using three different methods: Nanodrop, BioAnalyzer (BioA), and RT-qPCR (qPCR). The Spearman’s rank correlations for Nanodrop versus reads, BioAnalyzer versus reads, and qPCR versus reads are 0.7 ( P = 0.23), 0.6 ( P = 0.35), and 0.7 ( P = 0.23), respectively. (C) Relative abundance of biotypes detected for 5 exosomal RNA-Seq libraries from healthy female subjects. PC = protein coding, PP = processed pseudogene, lincRNA = long intergenic non-coding RNA, UP = unprocessed pseudogene, snRNA = small nuclear RNA, miRNA = microRNA, TEC = to be experimentally confirmed, snoRNA = small nucleolar RNA, TUP = transcribed unprocessed pseudogene.

    Journal: PLoS ONE

    Article Title: Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens

    doi: 10.1371/journal.pone.0196913

    Figure Lengend Snippet: Exosomal RNA-Seq libraries from archival sera specimens. (A) Bioanalyzer results for 5 independent specimens demonstrate inserted size of exosomal RNAs. (B) Number of mapped reads generated from RNA-Seq libraries for 5 independent specimens with 20 ng exosomal RNAs. RNA-Seq library concentrations were calculated using three different methods: Nanodrop, BioAnalyzer (BioA), and RT-qPCR (qPCR). The Spearman’s rank correlations for Nanodrop versus reads, BioAnalyzer versus reads, and qPCR versus reads are 0.7 ( P = 0.23), 0.6 ( P = 0.35), and 0.7 ( P = 0.23), respectively. (C) Relative abundance of biotypes detected for 5 exosomal RNA-Seq libraries from healthy female subjects. PC = protein coding, PP = processed pseudogene, lincRNA = long intergenic non-coding RNA, UP = unprocessed pseudogene, snRNA = small nuclear RNA, miRNA = microRNA, TEC = to be experimentally confirmed, snoRNA = small nucleolar RNA, TUP = transcribed unprocessed pseudogene.

    Article Snippet: Somewhat surprisingly, our results showed that for exosomal RNA-Seq libraries, Nanodrop quantification correlates higher with RT-qPCR measurements than Bioanalyzer.

    Techniques: RNA Sequencing Assay, Generated, Quantitative RT-PCR, Real-time Polymerase Chain Reaction