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  • 99
    Zymo Research rna
    Rna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 531 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rna
    Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 178232 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total rna
    Total Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 471882 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rna extraction
    Rna Extraction, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 40204 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    rna  (Promega)
    99
    Promega rna
    Rna, supplied by Promega, used in various techniques. Bioz Stars score: 99/100, based on 19539 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    TaKaRa total rna
    Total Rna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 46719 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore rna
    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled <t>RNA</t> or <t>siRNA</t> for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P
    Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 5994 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore total rna
    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled <t>RNA</t> or <t>siRNA</t> for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P
    Total Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 26190 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    98
    Thermo Fisher quantitative real time pcr total rna
    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled <t>RNA</t> or <t>siRNA</t> for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P
    Quantitative Real Time Pcr Total Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 16065 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Qiagen qiaamp viral rna mini kit
    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled <t>RNA</t> or <t>siRNA</t> for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P
    Qiaamp Viral Rna Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 23436 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Agilent technologies rna integrity
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Rna Integrity, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 43937 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher total rnas
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Total Rnas, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 23282 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc rna
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Rna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 6613 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher purelink rna mini kit
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Purelink Rna Mini Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 16743 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher high capacity rna to cdna kit
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    High Capacity Rna To Cdna Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 18369 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Qiagen rnalater
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Rnalater, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 13474 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen total rna
    <t>KSHV</t> induces alternative <t>RNA</t> splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR
    Total Rna, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 275349 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies rna 6000 nano kit
    Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient <t>RNA</t> 6000 <t>Nano</t> kit respectively.
    Rna 6000 Nano Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 13207 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Zymo Research total rna
    Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient <t>RNA</t> 6000 <t>Nano</t> kit respectively.
    Total Rna, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 7667 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher total cellular rna
    Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient <t>RNA</t> 6000 <t>Nano</t> kit respectively.
    Total Cellular Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 15858 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    98
    Thermo Fisher t7 rna polymerase
    Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient <t>RNA</t> 6000 <t>Nano</t> kit respectively.
    T7 Rna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 12287 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled RNA or siRNA for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P

    Journal: Scientific Reports

    Article Title: Supra-pharmacological concentration of capsaicin stimulates brown adipogenesis through induction of endoplasmic reticulum stress

    doi: 10.1038/s41598-018-19223-2

    Figure Lengend Snippet: Requirement of ER stress for efficient brown adipogenesis. ( A and B ) HB2 brown preadipocytes were treated with or without 5 mM of 4-PBA or 100 μM of capsaicin or both for 8 days in the presence of insulin (20 nM). ( C and D ) HB2 brown preadipocytes were transfected with scrambled RNA or siRNA for Xbp1. Cells were treated with or without 100 μM of capsaicin in the presence of insulin (20 nM) for 8 days. ( A and C ) Oil Red O staining of cells on day 8 was performed, and the dye intensity was quantified (n = 2). ( B and D ) The expression level of Ucp1 was examined by RT-qPCR analysis. Black bar: vehicle; Hatched bar: capsaicin. The data are presented as the mean ± SE (n = 4). * P

    Article Snippet: At confluence (day -2), cells were transfected with 6 μl of Lipofectamine RNAi Max (Thermo Fisher, Waltham, MA, USA) and 60 pmol of siRNA for Xbp1 or scrambled RNA (MISSION siRNA; Sigma) for 2 days.

    Techniques: Transfection, Staining, Expressing, Quantitative RT-PCR

    KSHV induces alternative RNA splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: KSHV induces alternative RNA splicing in infected LEC. ( A ) Confirmation of KSHV infection in LECs. The cell morphology of mock infection LECs at 2 days (LEC panel) shows a cobble stone appearance, whereas LECs infected by BCBL1-derived rKSHV at 2 days have become elongated and spindle shaped (KLEC panels). The GFP positive cells indicate successful KSHV infection. KSHV infection was further confirmed by RT–PCR of KSHV genes (upper-right panel). LEC and KLEC indicate cDNA from these two samples was used as PCR-template. LEC- and KLEC- mean no-RT control, and the (–) set is a no template control. Three KSHV genes: LANA, vCyclin and vFLIP were all expressed in the KLECs. Immunofluorescent staining of KSHV LANA protein is demonstrated in the lower right panel, which shows a typical nuclear stippling staining pattern. ( B ) PCA plots of both gene and exon levels between KLEC and LEC. The PCA plot, based on the differential expressed genes with a pFDR

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Infection, Derivative Assay, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Staining

    Dedifferentiation-like AS drift in KSHV-infected LECs. ( A ) A gene-level MDS plot using KLEC-LEC differential expressed genes (Affymetrix Human Genome U133 Plus 2.0 array). In this figure, no dedifferentiation could be found. ( B ) An exon-level MDS plot using NI of KSHV-induced AS probe sets. An arrow indicates that the exomes of the infected LECs have moved away from those of control LECs and toward to those of CD34 + endothelial stem/precursor cells. (right) Average linkage distances between sample groups. ( C ) Venn diagrams showing AS events common between KSHV-LEC and CD34 + cells. ( D ) A heat map showing the 33 AS events common between KSHV-LEC and CD34 + cells. The Gene symbols of AS genes are also listed. ( E ) DomainGraph ‘Probeset view’ of EGFR and CASP9. EGFR exon 25 is downregulated upon KSHV infection, and this KSHV-regulated isoform would seem to harbor an altered protein kinase domain. Part of CASP9 exon 4 is downregulated in infected LECs, and this AS will affect the integrity and function of the CARD domain. Green boxes: probe sets with exon exclusion; White boxes: probe sets that do not meet the minimum expression threshold in AltAnalyze; Gray boxes: no alternative expression event detected. (right) Validation of AS events by RT–qPCR. Primer sets for EGFR exon 25 and CASP9 exon 4b were designed for detecting differential expressed exons, whereas primer sets for EGFR exon 26 and CASP9 exon 5 for constantly expressed exons. Total RNA was from primary LECs infected with JSC-1-derived rKSHV.219 viruses. Results are expressed as the mean ± SD. Ratios between AS exons and constant exons are shown. * P

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: Dedifferentiation-like AS drift in KSHV-infected LECs. ( A ) A gene-level MDS plot using KLEC-LEC differential expressed genes (Affymetrix Human Genome U133 Plus 2.0 array). In this figure, no dedifferentiation could be found. ( B ) An exon-level MDS plot using NI of KSHV-induced AS probe sets. An arrow indicates that the exomes of the infected LECs have moved away from those of control LECs and toward to those of CD34 + endothelial stem/precursor cells. (right) Average linkage distances between sample groups. ( C ) Venn diagrams showing AS events common between KSHV-LEC and CD34 + cells. ( D ) A heat map showing the 33 AS events common between KSHV-LEC and CD34 + cells. The Gene symbols of AS genes are also listed. ( E ) DomainGraph ‘Probeset view’ of EGFR and CASP9. EGFR exon 25 is downregulated upon KSHV infection, and this KSHV-regulated isoform would seem to harbor an altered protein kinase domain. Part of CASP9 exon 4 is downregulated in infected LECs, and this AS will affect the integrity and function of the CARD domain. Green boxes: probe sets with exon exclusion; White boxes: probe sets that do not meet the minimum expression threshold in AltAnalyze; Gray boxes: no alternative expression event detected. (right) Validation of AS events by RT–qPCR. Primer sets for EGFR exon 25 and CASP9 exon 4b were designed for detecting differential expressed exons, whereas primer sets for EGFR exon 26 and CASP9 exon 5 for constantly expressed exons. Total RNA was from primary LECs infected with JSC-1-derived rKSHV.219 viruses. Results are expressed as the mean ± SD. Ratios between AS exons and constant exons are shown. * P

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Infection, Expressing, Quantitative RT-PCR, Derivative Assay

    Modification of domain and motif compositions within KSHV-induced isoforms. ( A ) Table of protein domains in genes with AS exons. In total, 17 domains/motifs that are involved in adhesion and oncogenic signaling transduction are affected on KSHV infection. ( B ) Part of the SH3_2 domain is altered in BAIAP2L1 due to the upregulated exon 11. Similarly, part of the DEP domain (Domain found in Dishevelled, Egl-10, and Pleckstrin) in DVL2 is affected on KSHV infection due to the downregulation of exon 12. Probe sets with exon inclusion are in red, whereas those with exon exclusion in green. (right) Validation of AS events by RT–qPCR. Total RNA was from LECs infected with JSC-1-derived rKSHV.

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: Modification of domain and motif compositions within KSHV-induced isoforms. ( A ) Table of protein domains in genes with AS exons. In total, 17 domains/motifs that are involved in adhesion and oncogenic signaling transduction are affected on KSHV infection. ( B ) Part of the SH3_2 domain is altered in BAIAP2L1 due to the upregulated exon 11. Similarly, part of the DEP domain (Domain found in Dishevelled, Egl-10, and Pleckstrin) in DVL2 is affected on KSHV infection due to the downregulation of exon 12. Probe sets with exon inclusion are in red, whereas those with exon exclusion in green. (right) Validation of AS events by RT–qPCR. Total RNA was from LECs infected with JSC-1-derived rKSHV.

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Modification, Transduction, Infection, Quantitative RT-PCR, Derivative Assay

    AS modifies miRNA binding site architecture. ( A ) The miRNA expression profile of KSHV infected LECs. In total, 216 miRNAs that have summarized probe set intensities > 4 on a log 2 scale can be considered to be expressed in the cells. The y -axis scale is the RMA-normalized hybridization signal (log 2 transformed) ( B ) Venn diagram of expressed miRNAs and altered miRNA binding sites identified by AltAnalyze. Overall, 85 miRNA-altered miRNA binding sites can be identified. ( C ) Correlation between differential gene expression and miRNA–miRNA binding sites regulation. (Upper) Genes downregulated in KSHV-LEC, and their miRNA binding sites are in inclusive exons. (Lower) Genes up-regulated in KSHV-LEC, and their miRNA binding sites are in exclusive exons. (Some ‘miR-’ prefixes were omitted for better demonstration.) ( D ) Relative expression levels of genes with miRNA binding site alteration. Potential miRNA binding sites are upregulated in MLPH and CTCL1, and their gene expression levels are significantly down. In contrast, the miRNA binding sites in RAPGEF5 are downregulated, and its gene expression level is up. Total RNA was from LECs infected with JSC-1-derived rKSHV. ( E ) RAPGEF5 is crucial for LEC motility. Primary LECs transduced with shRNA against LacZ or RAPGEF5 were subjected to Transwell cell migration assays (right). The knock-down effect was measured by RT–qPCR (left). Mean expression levels of RAPGEF5 were compared with that of GAPDH control.

    Journal: Nucleic Acids Research

    Article Title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells

    doi: 10.1093/nar/gkr405

    Figure Lengend Snippet: AS modifies miRNA binding site architecture. ( A ) The miRNA expression profile of KSHV infected LECs. In total, 216 miRNAs that have summarized probe set intensities > 4 on a log 2 scale can be considered to be expressed in the cells. The y -axis scale is the RMA-normalized hybridization signal (log 2 transformed) ( B ) Venn diagram of expressed miRNAs and altered miRNA binding sites identified by AltAnalyze. Overall, 85 miRNA-altered miRNA binding sites can be identified. ( C ) Correlation between differential gene expression and miRNA–miRNA binding sites regulation. (Upper) Genes downregulated in KSHV-LEC, and their miRNA binding sites are in inclusive exons. (Lower) Genes up-regulated in KSHV-LEC, and their miRNA binding sites are in exclusive exons. (Some ‘miR-’ prefixes were omitted for better demonstration.) ( D ) Relative expression levels of genes with miRNA binding site alteration. Potential miRNA binding sites are upregulated in MLPH and CTCL1, and their gene expression levels are significantly down. In contrast, the miRNA binding sites in RAPGEF5 are downregulated, and its gene expression level is up. Total RNA was from LECs infected with JSC-1-derived rKSHV. ( E ) RAPGEF5 is crucial for LEC motility. Primary LECs transduced with shRNA against LacZ or RAPGEF5 were subjected to Transwell cell migration assays (right). The knock-down effect was measured by RT–qPCR (left). Mean expression levels of RAPGEF5 were compared with that of GAPDH control.

    Article Snippet: Microarray hybridization Total RNA from KSHV infected LECs or mock infections with biological replicates were checked for RNA integrity by Bioanalyzer (Agilent, Santa Clara, CA, USA).

    Techniques: Binding Assay, Expressing, Infection, Hybridization, Transformation Assay, Derivative Assay, Transduction, shRNA, Migration, Quantitative RT-PCR

    Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.

    Journal: RNA Biology

    Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

    doi: 10.1080/15476286.2018.1451723

    Figure Lengend Snippet: Over-drying time does not affect quantity of small RNA in mirRICH method. (A) 15% PAGE (Polyacrylamide gel electrophoresis) and (B) 15% UREA denaturing gels electrophoresis of the RNA samples are prepared from two different breast cancer cells, MDA-MB-231 and MCF7 cells with either TRIzol with 1hr drying or 24hr drying, mirRICH with 1hr drying or 24hr drying. The 100-bp marker is indicated as ladder. (C) Peak images of experiment samples of MDA-MB-231 and MCF7 were obtained by Aglient RNA 6000 Nano kit respectively.

    Article Snippet: Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent.

    Techniques: Polyacrylamide Gel Electrophoresis, Electrophoresis, Multiple Displacement Amplification, Marker

    Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.

    Journal: RNA Biology

    Article Title: mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets

    doi: 10.1080/15476286.2018.1451723

    Figure Lengend Snippet: Comparison of the quantity and the quality of small RNAs isolated by TRIzol, mirRICH and mirVana. Equal number of two different breast cancer cells, MDA-MB-231 and MCF7 cells were prepared and extracted with three different methods: TRIzol, mirRICH, and mirVana. Peak images of small RNA samples were obtained by Aglient RNA 6000 Nano kit (A) and small RNA analysis kit (B) respectively. (C) 15% PAGE (Polyacrylamide gel electrophoresis) and (D) 15% UREA denaturing gels electrophoresis of the RNA samples from two different breast cancer cells, MDA-MB-231 and MCF7 are prepared by three different methods, TRIzol (T), mirRICH (M) and mirVana (K). The 100-bp marker is indicated as ladder.

    Article Snippet: Agilent RNA 6000 Nano kit and small RNA analysis kit was purchased from Agilent.

    Techniques: Isolation, Multiple Displacement Amplification, Polyacrylamide Gel Electrophoresis, Electrophoresis, Marker