polymerase chain reaction pcr kits  (Thermo Fisher)


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    Structured Review

    Thermo Fisher polymerase chain reaction pcr kits
    Polymerase Chain Reaction Pcr Kits, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/polymerase chain reaction pcr kits/product/Thermo Fisher
    Average 89 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    polymerase chain reaction pcr kits - by Bioz Stars, 2020-03
    89/100 stars

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    Related Articles

    Nucleic Acid Electrophoresis:

    Article Title: Beneficial Effects of Fractions of Nardostachys jatamansi on Lipopolysaccharide-Induced Inflammatory Response
    Article Snippet: Prestained sodium dodecyl sulfate-polyacrylamide gel electrophoresis markers were obtained from Bio-Rad (Hercules, CA, USA). .. Trizol reagent and polymerase chain reaction (PCR) kits were purchased from Invitrogen Corporation (Carlsbad, CA, USA).

    Immunohistochemistry:

    Article Title: Impact of immunosuppressive agents on the expression of indoleamine 2,3-dioxygenase, heme oxygenase-1 and interleukin-7 in mesangial cells
    Article Snippet: The cDNA synthesis and polymerase chain reaction (PCR) kits were purchased from Thermo Fisher Scientific (Waltham, MA, USA). .. The immunohistochemistry detection kits used for analyzing the expression of IDO, HO-1 and IL-7 were purchased from Dako (Glostrup, Denmark) and Beijing Zhongshan Golden Bridge Biological Technology Co., Ltd.

    Article Title: Inhibitory effects and mechanism of 5-fluorouracil combined with celecoxib on human gastric cancer xenografts in nude mice
    Article Snippet: Immunohistochemistry kits (SP-9000) were purchased from Zhongshan Golden Bridge Biotechnology Co., Ltd. (Beijing, China). .. TRIzol reagent was from Invitrogen Life Technologies, and the reverse transcription (RT) and polymerase chain reaction (PCR) kits were purchased from Fermentas (Thermo Fisher Scientific).

    Isolation:

    Article Title: Impact of immunosuppressive agents on the expression of indoleamine 2,3-dioxygenase, heme oxygenase-1 and interleukin-7 in mesangial cells
    Article Snippet: The Total RNA Isolation kit was purchased from Invitrogen Life Technologies (Carlsbad, CA, USA). .. The cDNA synthesis and polymerase chain reaction (PCR) kits were purchased from Thermo Fisher Scientific (Waltham, MA, USA).

    Avidin-Biotin Assay:

    Article Title: Protective Effects of Lithospermum erythrorhizon Against Cerulein-Induced Acute Pancreatitis
    Article Snippet: Reagents Avidin-peroxidase, cerulein, Tris–HCl, NaCl, hexadecyltrimethylammoniumbromide, and tetramethylbenzidine (TMB) were purchased from Sigma-Aldrich (St. Louis, Mo). .. TRIzol reagent and polymerase chain reaction (PCR) kits were purchased from Invitrogen Corporation (Carlsbad, Calif).

    Mouse Assay:

    Article Title: Inhibitory effects and mechanism of 5-fluorouracil combined with celecoxib on human gastric cancer xenografts in nude mice
    Article Snippet: TRIzol reagent was from Invitrogen Life Technologies, and the reverse transcription (RT) and polymerase chain reaction (PCR) kits were purchased from Fermentas (Thermo Fisher Scientific). .. The 28 male nude mice (BALB/c nu/nu; age, 5–6 weeks) were purchased from Beijing Weitong Lihua Laboratory Animal Technology Co., Ltd. (Beijing, China).

    Enzyme-linked Immunosorbent Assay:

    Article Title: Beneficial Effects of Fractions of Nardostachys jatamansi on Lipopolysaccharide-Induced Inflammatory Response
    Article Snippet: Enzyme-linked immunosorbent assay (ELISA) antibodies for detection of mouse IL-1β , IL-6, and TNF-α were purchased from R & D Systems (Minneapolis, MN, USA). .. Trizol reagent and polymerase chain reaction (PCR) kits were purchased from Invitrogen Corporation (Carlsbad, CA, USA).

    Article Title: Epidemiology and diagnosis of feline panleukopenia virus in Egypt: Clinical and molecular diagnosis in cats
    Article Snippet: The reverse transcription and polymerase chain reaction (PCR) kits were obtained from Fermentas (Glen Burnie, MD, USA). .. For ELISA analysis, direct ELISA kits were purchased from Sigma (St. Louis, MO, USA).

    Protein Extraction:

    Article Title: Inhibitory effects and mechanism of 5-fluorouracil combined with celecoxib on human gastric cancer xenografts in nude mice
    Article Snippet: TRIzol reagent was from Invitrogen Life Technologies, and the reverse transcription (RT) and polymerase chain reaction (PCR) kits were purchased from Fermentas (Thermo Fisher Scientific). .. The protein extraction kit was from Biyuntian Co. (Jiangsu, China).

    Expressing:

    Article Title: Impact of immunosuppressive agents on the expression of indoleamine 2,3-dioxygenase, heme oxygenase-1 and interleukin-7 in mesangial cells
    Article Snippet: The cDNA synthesis and polymerase chain reaction (PCR) kits were purchased from Thermo Fisher Scientific (Waltham, MA, USA). .. The primary and secondary antibodies used for western blot analysis for detecting the protein expression levels of IDO, HO-1 and IL-7 were purchased from Santa Cruz Biotechnology, Inc. (Austin, TX, USA) and Beijing Zhongshan Golden Bridge Biological Technology Co., Ltd. (Beijing, China), respectively.

    Polymerase Chain Reaction:

    Article Title: Impact of immunosuppressive agents on the expression of indoleamine 2,3-dioxygenase, heme oxygenase-1 and interleukin-7 in mesangial cells
    Article Snippet: .. The cDNA synthesis and polymerase chain reaction (PCR) kits were purchased from Thermo Fisher Scientific (Waltham, MA, USA). .. The primary and secondary antibodies used for western blot analysis for detecting the protein expression levels of IDO, HO-1 and IL-7 were purchased from Santa Cruz Biotechnology, Inc. (Austin, TX, USA) and Beijing Zhongshan Golden Bridge Biological Technology Co., Ltd. (Beijing, China), respectively.

    Article Title: Inhibitory effects and mechanism of 5-fluorouracil combined with celecoxib on human gastric cancer xenografts in nude mice
    Article Snippet: .. TRIzol reagent was from Invitrogen Life Technologies, and the reverse transcription (RT) and polymerase chain reaction (PCR) kits were purchased from Fermentas (Thermo Fisher Scientific). .. The protein extraction kit was from Biyuntian Co. (Jiangsu, China).

    Article Title: Identification and characterization of chemical components in the bioactive fractions of Cynomorium coccineum that possess anticancer activity
    Article Snippet: .. RNA extract kits, RNA RT and polymerase chain reaction (PCR) kits were obtained from Thermo Fisher. .. Immunoblotting was performed using the Enhanced Chemiluminescence (ECL) western blot detection kit (Millipore).

    Article Title: Epidemiology and diagnosis of feline panleukopenia virus in Egypt: Clinical and molecular diagnosis in cats
    Article Snippet: .. The reverse transcription and polymerase chain reaction (PCR) kits were obtained from Fermentas (Glen Burnie, MD, USA). .. For ELISA analysis, direct ELISA kits were purchased from Sigma (St. Louis, MO, USA).

    Article Title: Protective Effects of Lithospermum erythrorhizon Against Cerulein-Induced Acute Pancreatitis
    Article Snippet: .. TRIzol reagent and polymerase chain reaction (PCR) kits were purchased from Invitrogen Corporation (Carlsbad, Calif). .. IκBα, and β-actin antibody were purchased from Santa Cruz Biotechnology (Santa Cruz, Calif).

    Western Blot:

    Article Title: Impact of immunosuppressive agents on the expression of indoleamine 2,3-dioxygenase, heme oxygenase-1 and interleukin-7 in mesangial cells
    Article Snippet: The cDNA synthesis and polymerase chain reaction (PCR) kits were purchased from Thermo Fisher Scientific (Waltham, MA, USA). .. The primary and secondary antibodies used for western blot analysis for detecting the protein expression levels of IDO, HO-1 and IL-7 were purchased from Santa Cruz Biotechnology, Inc. (Austin, TX, USA) and Beijing Zhongshan Golden Bridge Biological Technology Co., Ltd. (Beijing, China), respectively.

    Article Title: Inhibitory effects and mechanism of 5-fluorouracil combined with celecoxib on human gastric cancer xenografts in nude mice
    Article Snippet: TRIzol reagent was from Invitrogen Life Technologies, and the reverse transcription (RT) and polymerase chain reaction (PCR) kits were purchased from Fermentas (Thermo Fisher Scientific). .. The western blot enhanced chemiluminescence kit was from Thermo Fisher Scientific.

    Article Title: Identification and characterization of chemical components in the bioactive fractions of Cynomorium coccineum that possess anticancer activity
    Article Snippet: RNA extract kits, RNA RT and polymerase chain reaction (PCR) kits were obtained from Thermo Fisher. .. Immunoblotting was performed using the Enhanced Chemiluminescence (ECL) western blot detection kit (Millipore).

    Purification:

    Article Title: Identification and characterization of chemical components in the bioactive fractions of Cynomorium coccineum that possess anticancer activity
    Article Snippet: Deionized water was purified by the Millipore-Q water purification system (USA). .. RNA extract kits, RNA RT and polymerase chain reaction (PCR) kits were obtained from Thermo Fisher.

    Direct ELISA:

    Article Title: Epidemiology and diagnosis of feline panleukopenia virus in Egypt: Clinical and molecular diagnosis in cats
    Article Snippet: The reverse transcription and polymerase chain reaction (PCR) kits were obtained from Fermentas (Glen Burnie, MD, USA). .. For ELISA analysis, direct ELISA kits were purchased from Sigma (St. Louis, MO, USA).

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  • 99
    Thermo Fisher qrt pcr kit
    Discovery of an IFN-inducible subclass of ERVs. ( a ) Immunoblot of pTBK1, TBK1, IKKε, pIRF3, pERK, ERK, pAKT, AKT and tubulin levels in H69 and H69M cells after 24 or 72 h culture. ( b ) Log-2 fold change cytokine/chemokine differences between H69M/H69 CM. ( c ) H E and pTBK1 IHC of a patient-derived SCLC brain metastasis. Scale bar indicates 20 μm. ( d ) Isotype control versus PD-L1 or CD44 surface expression on H69 and H69M cells ± 200 ng/mL 24 h IFNγ stimulation (representative of n=3 biological replicates). ( e ) Immunoblot of pTBK1, TBK1, pERK, ERK, pAKT, AKT and β-actin levels in H69, H69M, H69M-PD-L1 low , and H69M-PD-L1 high cells. ( f ) Log-2 fold change cytokine/chemokines differences between H69M-PD-L1 high or H69M-PD-L1 low /H69 CM. ( g ) <t>qRT-PCR</t> of ERVs in H69M-PD-L1 high normalized to H69M-PD-L1 low of previously published ERVs. Error bars are mean ± s.e.m of n=3 biological replicates. TRIM22 promoter and antisense orientation of MLT1C49 in the 3′UTR are represented below the qRT-PCR graph. ( h ) qRT-PCR of CXCL10 and CCL2 in H69M PD-L1 low cells transfected with pLX-307-GFP control or pLX_307-MLT1C49 construct for 72h. Mean ± s.e.m of n=3 biological replicates shown. ( i ) qRT-PCR of CXCL10 and CCL2 in H69M PD-L1 high cells transfected with scrambled negative control siRNA or siRNAs specific for MLT1C49. Mean ± s.e.m of n=3 biological replicates shown. ( j ) Overlap of 3′UTR antisense ERVs with H69M upregulated genes (log-2 fold change relative to H69 > 2) and table showing the fold change in expression of these genes/ERVs in H69M-PD-L1 high normalized to H69M-PD-L1 low cells. ( k ) Immunoblot of STING, MAVS, pTBK1, TBK1, pIRF3, IRF3, E-Cadherin, Vimentin and β-actin levels in H69M cells after CRISPR mediated deletion of MAVS and/or STING. ( l ) Log-2 fold change cytokine/chemokine differences in CM from H69M cells after CRISPR mediated deletion of MAVS and/or STING compared to sgCTRL (Scramble). ( m ) CXCL10 Luminex absolute levels (pg/mL) in Scramble, STING KO, MAVS KO and double KO (dKO) H69M cells. Mean ± s.e.m of n=2 biological replicates shown. *p
    Qrt Pcr Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qrt pcr kit/product/Thermo Fisher
    Average 99 stars, based on 43 article reviews
    Price from $9.99 to $1999.99
    qrt pcr kit - by Bioz Stars, 2020-03
    99/100 stars
      Buy from Supplier

    85
    Thermo Fisher triacylglyceride assay kit
    Residual Bscl2 − / − EWAT and Bscl2 +/+ EWAT exhibit differential lipid profiles. A) Inactivation of Bscl2 in mice causes massive loss of epididymal white adipose tissue (EWAT). B) Thin layer chromatography (TLC) analysis of total lipids extracted from EWAT of male non-fasting Bscl2 +/+ and Bscl2 −/− mice. M: TLC standards. CE: cholesterol ester; TG: <t>triacylglyceride;</t> FFA: free fatty acid, CHO: cholesterol; DG: diacylglyceride; PL: phospholipid. Total lipids from equal amounts of tissue for each genotype were loaded. B) Enzymatic analysis of EWAT triacylglycerides (TG). Results were presented as µg TG per mg tissue. C) Total EWAT TG contents based on total EWAT weights. n = 6-7 each. **: p
    Triacylglyceride Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/triacylglyceride assay kit/product/Thermo Fisher
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    triacylglyceride assay kit - by Bioz Stars, 2020-03
    85/100 stars
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    85
    Thermo Fisher slk uninfected cells
    ER stress induces KSHV lytic replication in BCBL1 cells. (A) Immunoblotting of RAD21, PARP and actin in <t>BJAB,</t> <t>SLK-BAC16</t> and BCBL1 cells exposed to 5mM DTT or 75ug/ml Puromycin (Puro) for 6 hours. (B) RT-qPCR for latent transcript LANA, lytic transcripts ORF50 and PAN, and RAD21 transcript relative to cellular actin in SLK-BAC16 and BCBL1 cells treated with DMSO, 5mM DTT or 75ug/ml Puromycin (Puro) for 6 hours. The data are expressed as fold change of the treated versus untreated (DMSO) cells. (C) Schematic representation of drug treatments in BCBL1 cells. Cells were treated with a 6-hour pulse of DMSO or 5mM DTT or 75ug/ml Puromycin (Puro) and then cultured in fresh media lacking drugs for the remaining 24 hours or 96 hours. (D) At 6 and 24 hours after drug treatment as described in (C), the level of viral DNA was evaluated by real-time qPCR for ORF50 DNA relative to cellular actin. The data are expressed as fold change of the treated versus untreated (DMSO) cells. (E) Virion DNA was isolated from cell supernatants at 96 h post-treatment and wash-out and assayed by qPCR for ORF50 DNA. Sodium butyrate (SB) treated cell supernatant was used as positive control. The data are expressed as fold change of the treated versus untreated (DMSO) cells.
    Slk Uninfected Cells, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/slk uninfected cells/product/Thermo Fisher
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    slk uninfected cells - by Bioz Stars, 2020-03
    85/100 stars
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    99
    Thermo Fisher pierce co immunoprecipitation kit
    c-Jun transcriptionally promotes miR-5188 expression to form a positive regulatory loop. (A) Venn diagram analysis was used to screen c-Jun-regulated downstream effectors among the top putative targets based on the Cistrome Data Browser. (B) ChIP-seq binding peaks were searched by the Cistrome Data Browser. (C) Bioinformatics analysis was utilized to predict c-Jun-binding sites within the promoter of miR-5188. (D) QPCR was used to examine pre-miR-5188 and mature miR-5188 levels in c-Jun-silenced HCC cells and control cells (n=3 independent experiments, Student's t-test). (E) Chromatin <t>immunoprecipitation</t> (comparison of all groups vs. the IgG group) (n=3 independent experiments, one-way ANOVA) was used to identify c-Jun binding to the miR-5188 promoter. (F) Luciferase reporter assays (comparison of all groups vs. the control group) (n=3 independent experiments, one-way ANOVA) were performed to confirm c-Jun binding to the miR-5188 promoter. (G) Protein-DNA interactions between c-Jun and the miR-5188 promoter were determined using electrophoretic mobility shift assays. (H) TOP/FOP luciferase reporter assays were performed to detect Wnt/β-catenin signaling activity (n=3 independent experiments, one-way ANOVA). (I) Immunohistochemical analysis was used to detect c-Jun expression in xenograft tumors derived from Huh7 cells after stable miR-5188 overexpression and control cells (scale bar: 20 μm) (n=5). (J) Chromatin immunoprecipitation analysis assessed c-Jun binding to the miR-5188 promoter in FOXO1-overexpressing HCCLM3 cells, FOXO1-overexpressing HCCLM3 cells with β-catenin overexpression, FOXO1-silenced Huh7 cells, FOXO1-silenced Huh7 cells with β-catenin knockdown, and the corresponding control cells. All data are presented as the mean ± SD. Experiments were repeated three times.
    Pierce Co Immunoprecipitation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pierce co immunoprecipitation kit/product/Thermo Fisher
    Average 99 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    pierce co immunoprecipitation kit - by Bioz Stars, 2020-03
    99/100 stars
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    Image Search Results


    Discovery of an IFN-inducible subclass of ERVs. ( a ) Immunoblot of pTBK1, TBK1, IKKε, pIRF3, pERK, ERK, pAKT, AKT and tubulin levels in H69 and H69M cells after 24 or 72 h culture. ( b ) Log-2 fold change cytokine/chemokine differences between H69M/H69 CM. ( c ) H E and pTBK1 IHC of a patient-derived SCLC brain metastasis. Scale bar indicates 20 μm. ( d ) Isotype control versus PD-L1 or CD44 surface expression on H69 and H69M cells ± 200 ng/mL 24 h IFNγ stimulation (representative of n=3 biological replicates). ( e ) Immunoblot of pTBK1, TBK1, pERK, ERK, pAKT, AKT and β-actin levels in H69, H69M, H69M-PD-L1 low , and H69M-PD-L1 high cells. ( f ) Log-2 fold change cytokine/chemokines differences between H69M-PD-L1 high or H69M-PD-L1 low /H69 CM. ( g ) qRT-PCR of ERVs in H69M-PD-L1 high normalized to H69M-PD-L1 low of previously published ERVs. Error bars are mean ± s.e.m of n=3 biological replicates. TRIM22 promoter and antisense orientation of MLT1C49 in the 3′UTR are represented below the qRT-PCR graph. ( h ) qRT-PCR of CXCL10 and CCL2 in H69M PD-L1 low cells transfected with pLX-307-GFP control or pLX_307-MLT1C49 construct for 72h. Mean ± s.e.m of n=3 biological replicates shown. ( i ) qRT-PCR of CXCL10 and CCL2 in H69M PD-L1 high cells transfected with scrambled negative control siRNA or siRNAs specific for MLT1C49. Mean ± s.e.m of n=3 biological replicates shown. ( j ) Overlap of 3′UTR antisense ERVs with H69M upregulated genes (log-2 fold change relative to H69 > 2) and table showing the fold change in expression of these genes/ERVs in H69M-PD-L1 high normalized to H69M-PD-L1 low cells. ( k ) Immunoblot of STING, MAVS, pTBK1, TBK1, pIRF3, IRF3, E-Cadherin, Vimentin and β-actin levels in H69M cells after CRISPR mediated deletion of MAVS and/or STING. ( l ) Log-2 fold change cytokine/chemokine differences in CM from H69M cells after CRISPR mediated deletion of MAVS and/or STING compared to sgCTRL (Scramble). ( m ) CXCL10 Luminex absolute levels (pg/mL) in Scramble, STING KO, MAVS KO and double KO (dKO) H69M cells. Mean ± s.e.m of n=2 biological replicates shown. *p

    Journal: Nature medicine

    Article Title: Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses

    doi: 10.1038/s41591-018-0116-5

    Figure Lengend Snippet: Discovery of an IFN-inducible subclass of ERVs. ( a ) Immunoblot of pTBK1, TBK1, IKKε, pIRF3, pERK, ERK, pAKT, AKT and tubulin levels in H69 and H69M cells after 24 or 72 h culture. ( b ) Log-2 fold change cytokine/chemokine differences between H69M/H69 CM. ( c ) H E and pTBK1 IHC of a patient-derived SCLC brain metastasis. Scale bar indicates 20 μm. ( d ) Isotype control versus PD-L1 or CD44 surface expression on H69 and H69M cells ± 200 ng/mL 24 h IFNγ stimulation (representative of n=3 biological replicates). ( e ) Immunoblot of pTBK1, TBK1, pERK, ERK, pAKT, AKT and β-actin levels in H69, H69M, H69M-PD-L1 low , and H69M-PD-L1 high cells. ( f ) Log-2 fold change cytokine/chemokines differences between H69M-PD-L1 high or H69M-PD-L1 low /H69 CM. ( g ) qRT-PCR of ERVs in H69M-PD-L1 high normalized to H69M-PD-L1 low of previously published ERVs. Error bars are mean ± s.e.m of n=3 biological replicates. TRIM22 promoter and antisense orientation of MLT1C49 in the 3′UTR are represented below the qRT-PCR graph. ( h ) qRT-PCR of CXCL10 and CCL2 in H69M PD-L1 low cells transfected with pLX-307-GFP control or pLX_307-MLT1C49 construct for 72h. Mean ± s.e.m of n=3 biological replicates shown. ( i ) qRT-PCR of CXCL10 and CCL2 in H69M PD-L1 high cells transfected with scrambled negative control siRNA or siRNAs specific for MLT1C49. Mean ± s.e.m of n=3 biological replicates shown. ( j ) Overlap of 3′UTR antisense ERVs with H69M upregulated genes (log-2 fold change relative to H69 > 2) and table showing the fold change in expression of these genes/ERVs in H69M-PD-L1 high normalized to H69M-PD-L1 low cells. ( k ) Immunoblot of STING, MAVS, pTBK1, TBK1, pIRF3, IRF3, E-Cadherin, Vimentin and β-actin levels in H69M cells after CRISPR mediated deletion of MAVS and/or STING. ( l ) Log-2 fold change cytokine/chemokine differences in CM from H69M cells after CRISPR mediated deletion of MAVS and/or STING compared to sgCTRL (Scramble). ( m ) CXCL10 Luminex absolute levels (pg/mL) in Scramble, STING KO, MAVS KO and double KO (dKO) H69M cells. Mean ± s.e.m of n=2 biological replicates shown. *p

    Article Snippet: After extraction, 1 μg total RNA was used to generate cDNA with the SuperScript III First-Strand Synthesis SuperMix for qRT-PCR kit, which includes both oligo-dT and random primers (Thermo Fisher Scientific, Waltham, MA).

    Techniques: Immunohistochemistry, Derivative Assay, Expressing, Quantitative RT-PCR, Transfection, Construct, Negative Control, CRISPR, Luminex

    Expression of SPARCS-containing genes across cancers. ( a ) ssGSEA of SPARCS-gene containing signature across TCGA (n=3602 tumors) and significantly associated gene sets grouped based on biological annotations. IC = information coefficient. FDR = false discovery rate. ( b ) Intersection of top 1000 genes co-regulated with SPARCS-containing gene signature in TCGA and CCLE datasets. MHC class I pathway genes in top 40 highlighted in red, EMT related genes in blue and immune evasion markers in green. ( c ) Distribution of high versus low SPARCS-containing gene expression by TCGA cancer histology. ( d ) Immunoblot of AXL, MET, Vimentin, STING, MAVS and β-actin levels in cell lines with high, intermediate, or low SPARCS gene signature expression after 72 h culture. ( e ) qRT-PCR of MLT1C49 , CXCL10, PD-L1 and CD44 in SPARCS high and SPARCS low cell lines ± IFNγ 10 min pulse - 24 h chase. p values indicated for comparison of SPARCS high versus SPARCS low groups. Mean ± s.e.m of n=2 biological replicates shown (Two-tailed Mann-Whitney U test). *p

    Journal: Nature medicine

    Article Title: Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses

    doi: 10.1038/s41591-018-0116-5

    Figure Lengend Snippet: Expression of SPARCS-containing genes across cancers. ( a ) ssGSEA of SPARCS-gene containing signature across TCGA (n=3602 tumors) and significantly associated gene sets grouped based on biological annotations. IC = information coefficient. FDR = false discovery rate. ( b ) Intersection of top 1000 genes co-regulated with SPARCS-containing gene signature in TCGA and CCLE datasets. MHC class I pathway genes in top 40 highlighted in red, EMT related genes in blue and immune evasion markers in green. ( c ) Distribution of high versus low SPARCS-containing gene expression by TCGA cancer histology. ( d ) Immunoblot of AXL, MET, Vimentin, STING, MAVS and β-actin levels in cell lines with high, intermediate, or low SPARCS gene signature expression after 72 h culture. ( e ) qRT-PCR of MLT1C49 , CXCL10, PD-L1 and CD44 in SPARCS high and SPARCS low cell lines ± IFNγ 10 min pulse - 24 h chase. p values indicated for comparison of SPARCS high versus SPARCS low groups. Mean ± s.e.m of n=2 biological replicates shown (Two-tailed Mann-Whitney U test). *p

    Article Snippet: After extraction, 1 μg total RNA was used to generate cDNA with the SuperScript III First-Strand Synthesis SuperMix for qRT-PCR kit, which includes both oligo-dT and random primers (Thermo Fisher Scientific, Waltham, MA).

    Techniques: Expressing, Quantitative RT-PCR, Two Tailed Test, MANN-WHITNEY

    Residual Bscl2 − / − EWAT and Bscl2 +/+ EWAT exhibit differential lipid profiles. A) Inactivation of Bscl2 in mice causes massive loss of epididymal white adipose tissue (EWAT). B) Thin layer chromatography (TLC) analysis of total lipids extracted from EWAT of male non-fasting Bscl2 +/+ and Bscl2 −/− mice. M: TLC standards. CE: cholesterol ester; TG: triacylglyceride; FFA: free fatty acid, CHO: cholesterol; DG: diacylglyceride; PL: phospholipid. Total lipids from equal amounts of tissue for each genotype were loaded. B) Enzymatic analysis of EWAT triacylglycerides (TG). Results were presented as µg TG per mg tissue. C) Total EWAT TG contents based on total EWAT weights. n = 6-7 each. **: p

    Journal: PLoS ONE

    Article Title: Altered Lipid Metabolism in Residual White Adipose Tissues of Bscl2 Deficient Mice

    doi: 10.1371/journal.pone.0082526

    Figure Lengend Snippet: Residual Bscl2 − / − EWAT and Bscl2 +/+ EWAT exhibit differential lipid profiles. A) Inactivation of Bscl2 in mice causes massive loss of epididymal white adipose tissue (EWAT). B) Thin layer chromatography (TLC) analysis of total lipids extracted from EWAT of male non-fasting Bscl2 +/+ and Bscl2 −/− mice. M: TLC standards. CE: cholesterol ester; TG: triacylglyceride; FFA: free fatty acid, CHO: cholesterol; DG: diacylglyceride; PL: phospholipid. Total lipids from equal amounts of tissue for each genotype were loaded. B) Enzymatic analysis of EWAT triacylglycerides (TG). Results were presented as µg TG per mg tissue. C) Total EWAT TG contents based on total EWAT weights. n = 6-7 each. **: p

    Article Snippet: Triacylglyceride concentration was measured using a triacylglyceride assay kit (Thermo Scientific) and normalized to tissue weights.

    Techniques: Mouse Assay, Thin Layer Chromatography

    Enhanced expression of key enzymes responsible for elongation, desaturation, and triacylglyceride synthesis but not de novo lipogenesis in isolated Bscl2 − / − adipocytes. qPCR analyses of genes involved in elongation (A), desaturation (B), de novo lipogenesis (C), lipid uptake (D) as well as triacylglyceride synthesis (E). Each sample was pooled from 3 6-week-old nonfasting male wild-type and Bscl2 −/− mice ( n = 4). *: P

    Journal: PLoS ONE

    Article Title: Altered Lipid Metabolism in Residual White Adipose Tissues of Bscl2 Deficient Mice

    doi: 10.1371/journal.pone.0082526

    Figure Lengend Snippet: Enhanced expression of key enzymes responsible for elongation, desaturation, and triacylglyceride synthesis but not de novo lipogenesis in isolated Bscl2 − / − adipocytes. qPCR analyses of genes involved in elongation (A), desaturation (B), de novo lipogenesis (C), lipid uptake (D) as well as triacylglyceride synthesis (E). Each sample was pooled from 3 6-week-old nonfasting male wild-type and Bscl2 −/− mice ( n = 4). *: P

    Article Snippet: Triacylglyceride concentration was measured using a triacylglyceride assay kit (Thermo Scientific) and normalized to tissue weights.

    Techniques: Expressing, Isolation, Real-time Polymerase Chain Reaction, Mouse Assay

    ER stress induces KSHV lytic replication in BCBL1 cells. (A) Immunoblotting of RAD21, PARP and actin in BJAB, SLK-BAC16 and BCBL1 cells exposed to 5mM DTT or 75ug/ml Puromycin (Puro) for 6 hours. (B) RT-qPCR for latent transcript LANA, lytic transcripts ORF50 and PAN, and RAD21 transcript relative to cellular actin in SLK-BAC16 and BCBL1 cells treated with DMSO, 5mM DTT or 75ug/ml Puromycin (Puro) for 6 hours. The data are expressed as fold change of the treated versus untreated (DMSO) cells. (C) Schematic representation of drug treatments in BCBL1 cells. Cells were treated with a 6-hour pulse of DMSO or 5mM DTT or 75ug/ml Puromycin (Puro) and then cultured in fresh media lacking drugs for the remaining 24 hours or 96 hours. (D) At 6 and 24 hours after drug treatment as described in (C), the level of viral DNA was evaluated by real-time qPCR for ORF50 DNA relative to cellular actin. The data are expressed as fold change of the treated versus untreated (DMSO) cells. (E) Virion DNA was isolated from cell supernatants at 96 h post-treatment and wash-out and assayed by qPCR for ORF50 DNA. Sodium butyrate (SB) treated cell supernatant was used as positive control. The data are expressed as fold change of the treated versus untreated (DMSO) cells.

    Journal: PLoS Pathogens

    Article Title: Deregulation of KSHV latency conformation by ER-stress and caspase-dependent RAD21-cleavage

    doi: 10.1371/journal.ppat.1006596

    Figure Lengend Snippet: ER stress induces KSHV lytic replication in BCBL1 cells. (A) Immunoblotting of RAD21, PARP and actin in BJAB, SLK-BAC16 and BCBL1 cells exposed to 5mM DTT or 75ug/ml Puromycin (Puro) for 6 hours. (B) RT-qPCR for latent transcript LANA, lytic transcripts ORF50 and PAN, and RAD21 transcript relative to cellular actin in SLK-BAC16 and BCBL1 cells treated with DMSO, 5mM DTT or 75ug/ml Puromycin (Puro) for 6 hours. The data are expressed as fold change of the treated versus untreated (DMSO) cells. (C) Schematic representation of drug treatments in BCBL1 cells. Cells were treated with a 6-hour pulse of DMSO or 5mM DTT or 75ug/ml Puromycin (Puro) and then cultured in fresh media lacking drugs for the remaining 24 hours or 96 hours. (D) At 6 and 24 hours after drug treatment as described in (C), the level of viral DNA was evaluated by real-time qPCR for ORF50 DNA relative to cellular actin. The data are expressed as fold change of the treated versus untreated (DMSO) cells. (E) Virion DNA was isolated from cell supernatants at 96 h post-treatment and wash-out and assayed by qPCR for ORF50 DNA. Sodium butyrate (SB) treated cell supernatant was used as positive control. The data are expressed as fold change of the treated versus untreated (DMSO) cells.

    Article Snippet: Cells culture and transfection BJAB (uninfected B cell lymphoma) cells (ATCC), SLK (uninfected) cells (NIH AIDS reagent program), KSHV positive PEL cells (BCBL1, BC3) (gift of Prof. Yan Yuan, UPENN), and double positive KSHV and EBV infected PEL cells (JSC-1, BC1) (gift of Prof. Yan Yuan, UPENN) were grown in RPMI medium (Gibco/ThermoFisher) containing 10% heat-inactivated fetal bovine serum (Hyclone, Cat. No. SH30396.03, Lot No. AB10092300) and the antibiotics penicillin and streptomycin (50 U/ml).

    Techniques: Quantitative RT-PCR, Cell Culture, Real-time Polymerase Chain Reaction, Isolation, Positive Control

    c-Jun transcriptionally promotes miR-5188 expression to form a positive regulatory loop. (A) Venn diagram analysis was used to screen c-Jun-regulated downstream effectors among the top putative targets based on the Cistrome Data Browser. (B) ChIP-seq binding peaks were searched by the Cistrome Data Browser. (C) Bioinformatics analysis was utilized to predict c-Jun-binding sites within the promoter of miR-5188. (D) QPCR was used to examine pre-miR-5188 and mature miR-5188 levels in c-Jun-silenced HCC cells and control cells (n=3 independent experiments, Student's t-test). (E) Chromatin immunoprecipitation (comparison of all groups vs. the IgG group) (n=3 independent experiments, one-way ANOVA) was used to identify c-Jun binding to the miR-5188 promoter. (F) Luciferase reporter assays (comparison of all groups vs. the control group) (n=3 independent experiments, one-way ANOVA) were performed to confirm c-Jun binding to the miR-5188 promoter. (G) Protein-DNA interactions between c-Jun and the miR-5188 promoter were determined using electrophoretic mobility shift assays. (H) TOP/FOP luciferase reporter assays were performed to detect Wnt/β-catenin signaling activity (n=3 independent experiments, one-way ANOVA). (I) Immunohistochemical analysis was used to detect c-Jun expression in xenograft tumors derived from Huh7 cells after stable miR-5188 overexpression and control cells (scale bar: 20 μm) (n=5). (J) Chromatin immunoprecipitation analysis assessed c-Jun binding to the miR-5188 promoter in FOXO1-overexpressing HCCLM3 cells, FOXO1-overexpressing HCCLM3 cells with β-catenin overexpression, FOXO1-silenced Huh7 cells, FOXO1-silenced Huh7 cells with β-catenin knockdown, and the corresponding control cells. All data are presented as the mean ± SD. Experiments were repeated three times.

    Journal: Theranostics

    Article Title: HBX-induced miR-5188 impairs FOXO1 to stimulate β-catenin nuclear translocation and promotes tumor stemness in hepatocellular carcinoma

    doi: 10.7150/thno.37717

    Figure Lengend Snippet: c-Jun transcriptionally promotes miR-5188 expression to form a positive regulatory loop. (A) Venn diagram analysis was used to screen c-Jun-regulated downstream effectors among the top putative targets based on the Cistrome Data Browser. (B) ChIP-seq binding peaks were searched by the Cistrome Data Browser. (C) Bioinformatics analysis was utilized to predict c-Jun-binding sites within the promoter of miR-5188. (D) QPCR was used to examine pre-miR-5188 and mature miR-5188 levels in c-Jun-silenced HCC cells and control cells (n=3 independent experiments, Student's t-test). (E) Chromatin immunoprecipitation (comparison of all groups vs. the IgG group) (n=3 independent experiments, one-way ANOVA) was used to identify c-Jun binding to the miR-5188 promoter. (F) Luciferase reporter assays (comparison of all groups vs. the control group) (n=3 independent experiments, one-way ANOVA) were performed to confirm c-Jun binding to the miR-5188 promoter. (G) Protein-DNA interactions between c-Jun and the miR-5188 promoter were determined using electrophoretic mobility shift assays. (H) TOP/FOP luciferase reporter assays were performed to detect Wnt/β-catenin signaling activity (n=3 independent experiments, one-way ANOVA). (I) Immunohistochemical analysis was used to detect c-Jun expression in xenograft tumors derived from Huh7 cells after stable miR-5188 overexpression and control cells (scale bar: 20 μm) (n=5). (J) Chromatin immunoprecipitation analysis assessed c-Jun binding to the miR-5188 promoter in FOXO1-overexpressing HCCLM3 cells, FOXO1-overexpressing HCCLM3 cells with β-catenin overexpression, FOXO1-silenced Huh7 cells, FOXO1-silenced Huh7 cells with β-catenin knockdown, and the corresponding control cells. All data are presented as the mean ± SD. Experiments were repeated three times.

    Article Snippet: Coimmunoprecipitation (Co-IP) Co-IP was performed using a Pierce Co-Immunoprecipitation kit (Thermo Scientific, Waltham, MA, USA) according to the manufacturer's instructions.

    Techniques: Expressing, Chromatin Immunoprecipitation, Binding Assay, Real-time Polymerase Chain Reaction, Luciferase, Electrophoretic Mobility Shift Assay, Activity Assay, Immunohistochemistry, Derivative Assay, Over Expression

    The hepatitis B X protein augments miR-5188-mediated tumor stemness, metastasis, proliferation, chemoresistance and Wnt/β-catenin/c-Jun signaling in HCC. (A) QPCR analysis examined miR-5188 expression in HBX-overexpressing HCC cells, HBX-overexpressing HCC cells with c-Jun knockdown and the corresponding control cells (one-way ANOVA). (B) Chromatin immunoprecipitation was used to validate c-Jun binding to the transcriptional regulatory region of miR-5188 in miR-5188-depleted Huh7 cells, HBX-overexpressing Huh7 cells, HBX-overexpressing Huh7 cells with miR-5188 depletion, miR-5188-overexpressing HCCLM3 cells, HBX-depleted HCCLM3 cells, HBX-depleted HCCLM3 cells with miR-5188 overexpression, and the corresponding control cells. EdU incorporation assays (scale bar: 10 μm) (C), flow cytometry analysis (D) , Transwell assays (scale bar: 10 μm) (E) and anticancer drug sensitivity tests (F) were used to detect stemness, migration, invasion and drug chemoresistance in HBX-overexpressing Huh7 cells, HBX-overexpressing Huh7 cells with miR-5188 knockdown, HBX-silenced HCCLM3 cells, HBX-silenced HCCLM3 cells with miR-5188 overexpression, and the corresponding control cells (one-way ANOVA). (G) Western blot analysis was performed to assess stemness, metastasis, proliferation, chemoresistance, and Wnt/β-catenin signaling-associated protein expression levels in HBX-overexpressing Huh7 cells, HBX-overexpressing Huh7 cells with miR-5188 knockdown, HBX-silenced HCCLM3 cells, HBX-silenced HCCLM3 cells with miR-5188 overexpression, and the corresponding control cells. Comparison of all groups vs. the control group by one-way ANOVA, n=3 independent experiments. All data are presented as the mean ± SD. Experiments were repeated three times.

    Journal: Theranostics

    Article Title: HBX-induced miR-5188 impairs FOXO1 to stimulate β-catenin nuclear translocation and promotes tumor stemness in hepatocellular carcinoma

    doi: 10.7150/thno.37717

    Figure Lengend Snippet: The hepatitis B X protein augments miR-5188-mediated tumor stemness, metastasis, proliferation, chemoresistance and Wnt/β-catenin/c-Jun signaling in HCC. (A) QPCR analysis examined miR-5188 expression in HBX-overexpressing HCC cells, HBX-overexpressing HCC cells with c-Jun knockdown and the corresponding control cells (one-way ANOVA). (B) Chromatin immunoprecipitation was used to validate c-Jun binding to the transcriptional regulatory region of miR-5188 in miR-5188-depleted Huh7 cells, HBX-overexpressing Huh7 cells, HBX-overexpressing Huh7 cells with miR-5188 depletion, miR-5188-overexpressing HCCLM3 cells, HBX-depleted HCCLM3 cells, HBX-depleted HCCLM3 cells with miR-5188 overexpression, and the corresponding control cells. EdU incorporation assays (scale bar: 10 μm) (C), flow cytometry analysis (D) , Transwell assays (scale bar: 10 μm) (E) and anticancer drug sensitivity tests (F) were used to detect stemness, migration, invasion and drug chemoresistance in HBX-overexpressing Huh7 cells, HBX-overexpressing Huh7 cells with miR-5188 knockdown, HBX-silenced HCCLM3 cells, HBX-silenced HCCLM3 cells with miR-5188 overexpression, and the corresponding control cells (one-way ANOVA). (G) Western blot analysis was performed to assess stemness, metastasis, proliferation, chemoresistance, and Wnt/β-catenin signaling-associated protein expression levels in HBX-overexpressing Huh7 cells, HBX-overexpressing Huh7 cells with miR-5188 knockdown, HBX-silenced HCCLM3 cells, HBX-silenced HCCLM3 cells with miR-5188 overexpression, and the corresponding control cells. Comparison of all groups vs. the control group by one-way ANOVA, n=3 independent experiments. All data are presented as the mean ± SD. Experiments were repeated three times.

    Article Snippet: Coimmunoprecipitation (Co-IP) Co-IP was performed using a Pierce Co-Immunoprecipitation kit (Thermo Scientific, Waltham, MA, USA) according to the manufacturer's instructions.

    Techniques: Real-time Polymerase Chain Reaction, Expressing, Chromatin Immunoprecipitation, Binding Assay, Over Expression, Flow Cytometry, Cytometry, Migration, Western Blot