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  • 99
    Thermo Fisher pierce ip lysis buffer
    PP1α/β was encapsidated into pgRNA and DNA-containing nucleocapsids. AML12 and its derived cell lines supporting tet-off inducible accumulation of empty capsids (AML12HBVcore and AML12HBVpolR105A), pgRNA-containing (AML12HBVpolY63F) and both pgRNA- and DNA-containing (AML12HBV_DE11) nucleocapsids were cultured in the absence of tet for 2 days. The cells were lysed with <t>IP</t> <t>lysis</t> <t>buffer.</t> IP assays were performed with an antibody against HBV Cp, PP1β or control IgG. HBV Cp, PP1α and/or β in input cell lysates and immunocomplexes of IP were detected by Western blot assays with the corresponding antibodies.
    Pierce Ip Lysis Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1210 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore ip buffer
    PP1α/β was encapsidated into pgRNA and DNA-containing nucleocapsids. AML12 and its derived cell lines supporting tet-off inducible accumulation of empty capsids (AML12HBVcore and AML12HBVpolR105A), pgRNA-containing (AML12HBVpolY63F) and both pgRNA- and DNA-containing (AML12HBV_DE11) nucleocapsids were cultured in the absence of tet for 2 days. The cells were lysed with <t>IP</t> <t>lysis</t> <t>buffer.</t> IP assays were performed with an antibody against HBV Cp, PP1β or control IgG. HBV Cp, PP1α and/or β in input cell lysates and immunocomplexes of IP were detected by Western blot assays with the corresponding antibodies.
    Ip Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 3862 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ip lysis buffer
    PP1α/β was encapsidated into pgRNA and DNA-containing nucleocapsids. AML12 and its derived cell lines supporting tet-off inducible accumulation of empty capsids (AML12HBVcore and AML12HBVpolR105A), pgRNA-containing (AML12HBVpolY63F) and both pgRNA- and DNA-containing (AML12HBV_DE11) nucleocapsids were cultured in the absence of tet for 2 days. The cells were lysed with <t>IP</t> <t>lysis</t> <t>buffer.</t> IP assays were performed with an antibody against HBV Cp, PP1β or control IgG. HBV Cp, PP1α and/or β in input cell lysates and immunocomplexes of IP were detected by Western blot assays with the corresponding antibodies.
    Ip Lysis Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 2822 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Cell Signaling Technology Inc simplechip enzymatic chromatin ip kit
    β-Catenin/TCF/Lef-1 binds to and activates the promoter of miR-183-96-182 cluster gene. ( A ) Schematic illustration of the promoter region of the miR-183-96-182 cluster gene showing the locations of the core promoter and putative TBEs. The first nucleotide of miR-96 was set as 1. ( B ) ChIP assay experiments were performed using a <t>SimpleChIP®</t> Enzymatic Chromatin IP Kit and a rabbit mAb against β-Catenin. Five binding sites for β-Catenin/TCF/Lef-1 complex were confirmed in AGS cells. An extra site downstream of the putative core promoter was confirmed in HeLa cells. ( C ) A renilla luciferase construct was generated by subcloning the upstream TBEs containing a DNA fragment into a luciferase vector. Cotransfection of a construct encoding β-Catenin together with the luciferase vector into AGS cells increased the renilla luciferase activity while cotransfection of a construct encoding GSK3β had the opposite effect (compared with EV, * P
    Simplechip Enzymatic Chromatin Ip Kit, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 99/100, based on 2802 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc truseq dna sample preparation kit
    β-Catenin/TCF/Lef-1 binds to and activates the promoter of miR-183-96-182 cluster gene. ( A ) Schematic illustration of the promoter region of the miR-183-96-182 cluster gene showing the locations of the core promoter and putative TBEs. The first nucleotide of miR-96 was set as 1. ( B ) ChIP assay experiments were performed using a <t>SimpleChIP®</t> Enzymatic Chromatin IP Kit and a rabbit mAb against β-Catenin. Five binding sites for β-Catenin/TCF/Lef-1 complex were confirmed in AGS cells. An extra site downstream of the putative core promoter was confirmed in HeLa cells. ( C ) A renilla luciferase construct was generated by subcloning the upstream TBEs containing a DNA fragment into a luciferase vector. Cotransfection of a construct encoding β-Catenin together with the luciferase vector into AGS cells increased the renilla luciferase activity while cotransfection of a construct encoding GSK3β had the opposite effect (compared with EV, * P
    Truseq Dna Sample Preparation Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 2305 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    scanalytics inc ip lab software
    β-Catenin/TCF/Lef-1 binds to and activates the promoter of miR-183-96-182 cluster gene. ( A ) Schematic illustration of the promoter region of the miR-183-96-182 cluster gene showing the locations of the core promoter and putative TBEs. The first nucleotide of miR-96 was set as 1. ( B ) ChIP assay experiments were performed using a <t>SimpleChIP®</t> Enzymatic Chromatin IP Kit and a rabbit mAb against β-Catenin. Five binding sites for β-Catenin/TCF/Lef-1 complex were confirmed in AGS cells. An extra site downstream of the putative core promoter was confirmed in HeLa cells. ( C ) A renilla luciferase construct was generated by subcloning the upstream TBEs containing a DNA fragment into a luciferase vector. Cotransfection of a construct encoding β-Catenin together with the luciferase vector into AGS cells increased the renilla luciferase activity while cotransfection of a construct encoding GSK3β had the opposite effect (compared with EV, * P
    Ip Lab Software, supplied by scanalytics inc, used in various techniques. Bioz Stars score: 92/100, based on 966 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher classic ip kit
    β-Catenin/TCF/Lef-1 binds to and activates the promoter of miR-183-96-182 cluster gene. ( A ) Schematic illustration of the promoter region of the miR-183-96-182 cluster gene showing the locations of the core promoter and putative TBEs. The first nucleotide of miR-96 was set as 1. ( B ) ChIP assay experiments were performed using a <t>SimpleChIP®</t> Enzymatic Chromatin IP Kit and a rabbit mAb against β-Catenin. Five binding sites for β-Catenin/TCF/Lef-1 complex were confirmed in AGS cells. An extra site downstream of the putative core promoter was confirmed in HeLa cells. ( C ) A renilla luciferase construct was generated by subcloning the upstream TBEs containing a DNA fragment into a luciferase vector. Cotransfection of a construct encoding β-Catenin together with the luciferase vector into AGS cells increased the renilla luciferase activity while cotransfection of a construct encoding GSK3β had the opposite effect (compared with EV, * P
    Classic Ip Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 764 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Rigaku data collection rigaku r axis rapid ip diffractometer absorption correction
    β-Catenin/TCF/Lef-1 binds to and activates the promoter of miR-183-96-182 cluster gene. ( A ) Schematic illustration of the promoter region of the miR-183-96-182 cluster gene showing the locations of the core promoter and putative TBEs. The first nucleotide of miR-96 was set as 1. ( B ) ChIP assay experiments were performed using a <t>SimpleChIP®</t> Enzymatic Chromatin IP Kit and a rabbit mAb against β-Catenin. Five binding sites for β-Catenin/TCF/Lef-1 complex were confirmed in AGS cells. An extra site downstream of the putative core promoter was confirmed in HeLa cells. ( C ) A renilla luciferase construct was generated by subcloning the upstream TBEs containing a DNA fragment into a luciferase vector. Cotransfection of a construct encoding β-Catenin together with the luciferase vector into AGS cells increased the renilla luciferase activity while cotransfection of a construct encoding GSK3β had the opposite effect (compared with EV, * P
    Data Collection Rigaku R Axis Rapid Ip Diffractometer Absorption Correction, supplied by Rigaku, used in various techniques. Bioz Stars score: 91/100, based on 202 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher immunoprecipitation buffer
    The de novo autism splice site mutation causes exon skipping in BTRC isoforms and reduces their translational efficiency. (A) The exon structure of three splicing isoforms of the BTRC gene showing positions of the cloned abridged introns and the splice site mutation; numbers denote base pairs (bp). (B) Minigene assays demonstrate exon 4 skipping as a result of the splice site mutation. The assays show the RT-PCR results performed using total RNA from HeLa cells transfected with BTRC minigene constructs; numbers denote base pairs. (C) Splicing assays with the full-length constructs carrying abridged introns confirm exon skipping observed in the minigene assays. (D) Immunoblotting (IB) from the whole cell lysates of HeLa cells transfected with different BTRC minigene constructs and an empty vector, as indicated. Membranes were probed to observe BTRC overexpression, and to investigate expression of p-β-catenin, Cul1 and SKP1. β-actin was used as loading control. <t>Immunoprecipitation</t> was performed with the antibody recognizing V5-tag and proteins were detected by immunoblotting (IB) with the p-β-catenin, Cul1, SKP1 and V5 antibodies. The splice site mutation causes reduced translational efficiency of both BTRC_1Mut and BTRC_2Mut mutant isoforms as compared to their wild type counterparts. Schematic diagram of Skp1-Cul1-BTRC ubiquitin protein ligase complex is shown at the bottom. (E) Quantification of protein pull-downs with V5-IP using ImageJ software. The band intensity values were normalized to WT expression levels. Error bars represent 95% confidence intervals (CI) based on 3 independent experiments. On average, 40% reduction of BTRC protein expression is observed as a result of a mutation. Consequently, the reduction of the corresponding BTRC binding partners (p-β-catenin, Cul1, and SKP1) is also observed. (F) Expression profiles of brain-expressed BTRC isoforms show higher expression of ASD-impacted BTRC-001 and BTRC-002. Numbers denote base pairs (a, b, c panels) or kDa (d). P-values: * - P
    Immunoprecipitation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 602 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Santa Cruz Biotechnology co immunoprecipitation ip
    TMEM16A was associated with cyclophilin D (CypD) in the mitochondria. (A) Endogenous expression of TMEM16A in the mitochondria was detected in BASMCs by immunoblotting with TMEM16A antibody ( n = 6; cyto, mem and mito are cytoplasm, membrane and mitochondria for short). (B) The endogenous TMEM16A expression in mitochondria was detected in BASMCs by immunogold staining with gold‐labelled TMEM16A antibody (see arrows, n = 6). (C–F) Co‐IP showed that cyclophilin D, but not ANT or VDAC, immunoprecipitated with TMEM16A in BASMCs ( n = 5). IP, <t>immunoprecipitation;</t> IB, immunoblot. (G) H 2 O 2 increased the association between TMEM16A and cyclophilin D, which was attenuated by preincubation with CsA (5 μmol·L −1 ) 30 min before H 2 O 2 treatment ( n = 5, * P
    Co Immunoprecipitation Ip, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 91/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Beyotime ip lysis buffer
    TMEM16A was associated with cyclophilin D (CypD) in the mitochondria. (A) Endogenous expression of TMEM16A in the mitochondria was detected in BASMCs by immunoblotting with TMEM16A antibody ( n = 6; cyto, mem and mito are cytoplasm, membrane and mitochondria for short). (B) The endogenous TMEM16A expression in mitochondria was detected in BASMCs by immunogold staining with gold‐labelled TMEM16A antibody (see arrows, n = 6). (C–F) Co‐IP showed that cyclophilin D, but not ANT or VDAC, immunoprecipitated with TMEM16A in BASMCs ( n = 5). IP, <t>immunoprecipitation;</t> IB, immunoblot. (G) H 2 O 2 increased the association between TMEM16A and cyclophilin D, which was attenuated by preincubation with CsA (5 μmol·L −1 ) 30 min before H 2 O 2 treatment ( n = 5, * P
    Ip Lysis Buffer, supplied by Beyotime, used in various techniques. Bioz Stars score: 94/100, based on 921 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc truseq chip sample prep kit
    TMEM16A was associated with cyclophilin D (CypD) in the mitochondria. (A) Endogenous expression of TMEM16A in the mitochondria was detected in BASMCs by immunoblotting with TMEM16A antibody ( n = 6; cyto, mem and mito are cytoplasm, membrane and mitochondria for short). (B) The endogenous TMEM16A expression in mitochondria was detected in BASMCs by immunogold staining with gold‐labelled TMEM16A antibody (see arrows, n = 6). (C–F) Co‐IP showed that cyclophilin D, but not ANT or VDAC, immunoprecipitated with TMEM16A in BASMCs ( n = 5). IP, <t>immunoprecipitation;</t> IB, immunoblot. (G) H 2 O 2 increased the association between TMEM16A and cyclophilin D, which was attenuated by preincubation with CsA (5 μmol·L −1 ) 30 min before H 2 O 2 treatment ( n = 5, * P
    Truseq Chip Sample Prep Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 850 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher crosslink immunoprecipitation kit
    ASPL-C converts p97 hexamers into stable p97:ASPL-C heterooligomers. ( a ) <t>Co-immunoprecipitation</t> of a p97:ASPL protein complex from human brain homogenate using an anti-ASPL antibody. Anti-FLAG antibody and beads alone were used as negative controls. ( b ) Schematic representation of fragments and full-length ASPL and p97. Conserved protein domains are depicted: ubiquitin-like domain (UBL); ubiquitin regulatory-X domain (UBX); N-terminal protein binding domains (N a and N b ); ATPase domains (D1 and D2). ( c ) Blue-native gel stained with Coomassie Brilliant Blue, demonstrating the remodelling of p97 hexamers by ASPL-C in a concentration-dependent manner. p97 (10 μg) and ASPL-C (0.3, 0.6, 1.8, 3, 6 and 12 μg) were briefly mixed and incubated on ice for 5 min; then protein complexes were analysed by BN-PAGE. A 1:1 molar ratio of p97 monomers and ASPL-C was sufficient to promote the formation of p97:ASPL-C heterooligomers. ( d ) Negatively stained electron micrographs of purified p97 in the presence and absence of ASPL-C; scale bar 50 nm.
    Crosslink Immunoprecipitation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 515 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher crosslink ip kit
    ASPL-C converts p97 hexamers into stable p97:ASPL-C heterooligomers. ( a ) <t>Co-immunoprecipitation</t> of a p97:ASPL protein complex from human brain homogenate using an anti-ASPL antibody. Anti-FLAG antibody and beads alone were used as negative controls. ( b ) Schematic representation of fragments and full-length ASPL and p97. Conserved protein domains are depicted: ubiquitin-like domain (UBL); ubiquitin regulatory-X domain (UBX); N-terminal protein binding domains (N a and N b ); ATPase domains (D1 and D2). ( c ) Blue-native gel stained with Coomassie Brilliant Blue, demonstrating the remodelling of p97 hexamers by ASPL-C in a concentration-dependent manner. p97 (10 μg) and ASPL-C (0.3, 0.6, 1.8, 3, 6 and 12 μg) were briefly mixed and incubated on ice for 5 min; then protein complexes were analysed by BN-PAGE. A 1:1 molar ratio of p97 monomers and ASPL-C was sufficient to promote the formation of p97:ASPL-C heterooligomers. ( d ) Negatively stained electron micrographs of purified p97 in the presence and absence of ASPL-C; scale bar 50 nm.
    Crosslink Ip Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 422 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher pierce c myc tag ip co ip kit
    ASPL-C converts p97 hexamers into stable p97:ASPL-C heterooligomers. ( a ) <t>Co-immunoprecipitation</t> of a p97:ASPL protein complex from human brain homogenate using an anti-ASPL antibody. Anti-FLAG antibody and beads alone were used as negative controls. ( b ) Schematic representation of fragments and full-length ASPL and p97. Conserved protein domains are depicted: ubiquitin-like domain (UBL); ubiquitin regulatory-X domain (UBX); N-terminal protein binding domains (N a and N b ); ATPase domains (D1 and D2). ( c ) Blue-native gel stained with Coomassie Brilliant Blue, demonstrating the remodelling of p97 hexamers by ASPL-C in a concentration-dependent manner. p97 (10 μg) and ASPL-C (0.3, 0.6, 1.8, 3, 6 and 12 μg) were briefly mixed and incubated on ice for 5 min; then protein complexes were analysed by BN-PAGE. A 1:1 molar ratio of p97 monomers and ASPL-C was sufficient to promote the formation of p97:ASPL-C heterooligomers. ( d ) Negatively stained electron micrographs of purified p97 in the presence and absence of ASPL-C; scale bar 50 nm.
    Pierce C Myc Tag Ip Co Ip Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher pierce co ip kit
    ASPL-C converts p97 hexamers into stable p97:ASPL-C heterooligomers. ( a ) <t>Co-immunoprecipitation</t> of a p97:ASPL protein complex from human brain homogenate using an anti-ASPL antibody. Anti-FLAG antibody and beads alone were used as negative controls. ( b ) Schematic representation of fragments and full-length ASPL and p97. Conserved protein domains are depicted: ubiquitin-like domain (UBL); ubiquitin regulatory-X domain (UBX); N-terminal protein binding domains (N a and N b ); ATPase domains (D1 and D2). ( c ) Blue-native gel stained with Coomassie Brilliant Blue, demonstrating the remodelling of p97 hexamers by ASPL-C in a concentration-dependent manner. p97 (10 μg) and ASPL-C (0.3, 0.6, 1.8, 3, 6 and 12 μg) were briefly mixed and incubated on ice for 5 min; then protein complexes were analysed by BN-PAGE. A 1:1 molar ratio of p97 monomers and ASPL-C was sufficient to promote the formation of p97:ASPL-C heterooligomers. ( d ) Negatively stained electron micrographs of purified p97 in the presence and absence of ASPL-C; scale bar 50 nm.
    Pierce Co Ip Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 536 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher direct ip kit
    ASPL-C converts p97 hexamers into stable p97:ASPL-C heterooligomers. ( a ) <t>Co-immunoprecipitation</t> of a p97:ASPL protein complex from human brain homogenate using an anti-ASPL antibody. Anti-FLAG antibody and beads alone were used as negative controls. ( b ) Schematic representation of fragments and full-length ASPL and p97. Conserved protein domains are depicted: ubiquitin-like domain (UBL); ubiquitin regulatory-X domain (UBX); N-terminal protein binding domains (N a and N b ); ATPase domains (D1 and D2). ( c ) Blue-native gel stained with Coomassie Brilliant Blue, demonstrating the remodelling of p97 hexamers by ASPL-C in a concentration-dependent manner. p97 (10 μg) and ASPL-C (0.3, 0.6, 1.8, 3, 6 and 12 μg) were briefly mixed and incubated on ice for 5 min; then protein complexes were analysed by BN-PAGE. A 1:1 molar ratio of p97 monomers and ASPL-C was sufficient to promote the formation of p97:ASPL-C heterooligomers. ( d ) Negatively stained electron micrographs of purified p97 in the presence and absence of ASPL-C; scale bar 50 nm.
    Direct Ip Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 407 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher crosslink magnetic ip co ip kit
    DEPP is located in mitochondria and peroxisomes. a) SH-EP/tetEGFP and SH-EP/tetEYFP-DEPP cells were treated with 200 ng/ml doxy for 24 hours and subjected to subcellular fractionation. The protein levels of DEPP, GFP and catalase in the cytosolic and the nuclear fraction were determined by immunoblot. Alpha-Tubulin (cytosolic) and Lamin (nuclear) were used to control the purity of the fractions (left panel). The peroxisomal fraction of SH-EP/tetEYFP-DEPP cells treated with 200 ng/ml doxy for 24 hours was separated using a peroxisome isolation <t>kit</t> (PEROX1, Sigma). DEPP protein expression was determined by immunoblot. Catalase (peroxisomes) and CoxIV (mitochondria) were used to control the purity of the peroxisomal fraction (right panel). b) SH-EP/tetEYFP-DEPP cells were grown on eight-well chambered cover glasses, treated with 200 ng/ml doxy for 24 hours and analyzed by live confocal microscopy. Mitochondria were stained using the specific mitochondrial probe MitoTrackerRed/CMXRos (30 nM). Peroxisomal staining was performed with a CellLight® Peroxisomes-RFP fusion construct. c) SH-EP/tetDEPP cells treated with 200 ng/ml doxy for 24 hours were subjected to CoIP analysis with a Pierce <t>Crosslink</t> <t>Magnetic</t> <t>IP/Co-IP</t> kit to investigate whether the DEPP protein co-immunopurifies with PEX7-cross-linked beads. The expression of PEX7 and DEPP was determined by immunoblot. Alpha-Tubulin served as loading control.
    Crosslink Magnetic Ip Co Ip Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 351 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    PP1α/β was encapsidated into pgRNA and DNA-containing nucleocapsids. AML12 and its derived cell lines supporting tet-off inducible accumulation of empty capsids (AML12HBVcore and AML12HBVpolR105A), pgRNA-containing (AML12HBVpolY63F) and both pgRNA- and DNA-containing (AML12HBV_DE11) nucleocapsids were cultured in the absence of tet for 2 days. The cells were lysed with IP lysis buffer. IP assays were performed with an antibody against HBV Cp, PP1β or control IgG. HBV Cp, PP1α and/or β in input cell lysates and immunocomplexes of IP were detected by Western blot assays with the corresponding antibodies.

    Journal: PLoS Pathogens

    Article Title: Protein phosphatase 1 catalyzes HBV core protein dephosphorylation and is co-packaged with viral pregenomic RNA into nucleocapsids

    doi: 10.1371/journal.ppat.1008669

    Figure Lengend Snippet: PP1α/β was encapsidated into pgRNA and DNA-containing nucleocapsids. AML12 and its derived cell lines supporting tet-off inducible accumulation of empty capsids (AML12HBVcore and AML12HBVpolR105A), pgRNA-containing (AML12HBVpolY63F) and both pgRNA- and DNA-containing (AML12HBV_DE11) nucleocapsids were cultured in the absence of tet for 2 days. The cells were lysed with IP lysis buffer. IP assays were performed with an antibody against HBV Cp, PP1β or control IgG. HBV Cp, PP1α and/or β in input cell lysates and immunocomplexes of IP were detected by Western blot assays with the corresponding antibodies.

    Article Snippet: Immunoprecipitation (IP) assayCells were lysed with IP lysis buffer (Thermo Fisher, 87788) and the lysates were cleared by centrifugation at 12,000 rpm for 10 min at 4°C.

    Techniques: Derivative Assay, Cell Culture, Lysis, Western Blot

    β-Catenin/TCF/Lef-1 binds to and activates the promoter of miR-183-96-182 cluster gene. ( A ) Schematic illustration of the promoter region of the miR-183-96-182 cluster gene showing the locations of the core promoter and putative TBEs. The first nucleotide of miR-96 was set as 1. ( B ) ChIP assay experiments were performed using a SimpleChIP® Enzymatic Chromatin IP Kit and a rabbit mAb against β-Catenin. Five binding sites for β-Catenin/TCF/Lef-1 complex were confirmed in AGS cells. An extra site downstream of the putative core promoter was confirmed in HeLa cells. ( C ) A renilla luciferase construct was generated by subcloning the upstream TBEs containing a DNA fragment into a luciferase vector. Cotransfection of a construct encoding β-Catenin together with the luciferase vector into AGS cells increased the renilla luciferase activity while cotransfection of a construct encoding GSK3β had the opposite effect (compared with EV, * P

    Journal: Nucleic Acids Research

    Article Title: Glycogen synthase kinase 3 beta inhibits microRNA-183-96-182 cluster via the ?-Catenin/TCF/LEF-1 pathway in gastric cancer cells

    doi: 10.1093/nar/gkt1275

    Figure Lengend Snippet: β-Catenin/TCF/Lef-1 binds to and activates the promoter of miR-183-96-182 cluster gene. ( A ) Schematic illustration of the promoter region of the miR-183-96-182 cluster gene showing the locations of the core promoter and putative TBEs. The first nucleotide of miR-96 was set as 1. ( B ) ChIP assay experiments were performed using a SimpleChIP® Enzymatic Chromatin IP Kit and a rabbit mAb against β-Catenin. Five binding sites for β-Catenin/TCF/Lef-1 complex were confirmed in AGS cells. An extra site downstream of the putative core promoter was confirmed in HeLa cells. ( C ) A renilla luciferase construct was generated by subcloning the upstream TBEs containing a DNA fragment into a luciferase vector. Cotransfection of a construct encoding β-Catenin together with the luciferase vector into AGS cells increased the renilla luciferase activity while cotransfection of a construct encoding GSK3β had the opposite effect (compared with EV, * P

    Article Snippet: Chromatin immunoprecipitation assay Chromatin immunoprecipitation (ChIP) assays were performed using a SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) from Cell Signal Technology following the manufacturer’s protocol.

    Techniques: Chromatin Immunoprecipitation, Binding Assay, Luciferase, Construct, Generated, Subcloning, Plasmid Preparation, Cotransfection, Activity Assay

    Chromatin immunoprecipitation (ChIP) and DNA sequencing analysis of EBOV trVLP nucleic acids. Extracts from HEK 293T cells infected with trVLPs were processed and pulled down using a Chromatin IP Kit with antibodies recognizing candidate host proteins. Purified nucleic acids were amplified by qPCR, and products were sequenced by the Sanger chain termination method. Genotypes were attributed and compared with the Zaire ebolavirus sequence (GenBank No. KJ660348.2) using BioEdit software. Samples from HSP90AB1, ANXA5, ARFGAP1, FLT4, GRP78, HSPA1A, MEK2, NTRK1, and MAPK11 are consistent with sequences from EBOV, while HSPA8 and YWHAZ are not. Isotype negative controls were included.

    Journal: Frontiers in Microbiology

    Article Title: Chaperones, Membrane Trafficking and Signal Transduction Proteins Regulate Zaire Ebola Virus trVLPs and Interact With trVLP Elements

    doi: 10.3389/fmicb.2018.02724

    Figure Lengend Snippet: Chromatin immunoprecipitation (ChIP) and DNA sequencing analysis of EBOV trVLP nucleic acids. Extracts from HEK 293T cells infected with trVLPs were processed and pulled down using a Chromatin IP Kit with antibodies recognizing candidate host proteins. Purified nucleic acids were amplified by qPCR, and products were sequenced by the Sanger chain termination method. Genotypes were attributed and compared with the Zaire ebolavirus sequence (GenBank No. KJ660348.2) using BioEdit software. Samples from HSP90AB1, ANXA5, ARFGAP1, FLT4, GRP78, HSPA1A, MEK2, NTRK1, and MAPK11 are consistent with sequences from EBOV, while HSPA8 and YWHAZ are not. Isotype negative controls were included.

    Article Snippet: Whole-cell extracts were then prepared using a Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology; Cat# 9003) following the manufacturer’s instructions with appropriate antibodies recognizing host proteins, and normal mouse or rabbit IgGs served as isotype controls.

    Techniques: Chromatin Immunoprecipitation, DNA Sequencing, Infection, Purification, Amplification, Real-time Polymerase Chain Reaction, Sequencing, Software

    The de novo autism splice site mutation causes exon skipping in BTRC isoforms and reduces their translational efficiency. (A) The exon structure of three splicing isoforms of the BTRC gene showing positions of the cloned abridged introns and the splice site mutation; numbers denote base pairs (bp). (B) Minigene assays demonstrate exon 4 skipping as a result of the splice site mutation. The assays show the RT-PCR results performed using total RNA from HeLa cells transfected with BTRC minigene constructs; numbers denote base pairs. (C) Splicing assays with the full-length constructs carrying abridged introns confirm exon skipping observed in the minigene assays. (D) Immunoblotting (IB) from the whole cell lysates of HeLa cells transfected with different BTRC minigene constructs and an empty vector, as indicated. Membranes were probed to observe BTRC overexpression, and to investigate expression of p-β-catenin, Cul1 and SKP1. β-actin was used as loading control. Immunoprecipitation was performed with the antibody recognizing V5-tag and proteins were detected by immunoblotting (IB) with the p-β-catenin, Cul1, SKP1 and V5 antibodies. The splice site mutation causes reduced translational efficiency of both BTRC_1Mut and BTRC_2Mut mutant isoforms as compared to their wild type counterparts. Schematic diagram of Skp1-Cul1-BTRC ubiquitin protein ligase complex is shown at the bottom. (E) Quantification of protein pull-downs with V5-IP using ImageJ software. The band intensity values were normalized to WT expression levels. Error bars represent 95% confidence intervals (CI) based on 3 independent experiments. On average, 40% reduction of BTRC protein expression is observed as a result of a mutation. Consequently, the reduction of the corresponding BTRC binding partners (p-β-catenin, Cul1, and SKP1) is also observed. (F) Expression profiles of brain-expressed BTRC isoforms show higher expression of ASD-impacted BTRC-001 and BTRC-002. Numbers denote base pairs (a, b, c panels) or kDa (d). P-values: * - P

    Journal: bioRxiv

    Article Title: Isoform transcriptome of developing human brain provides new insights into autism risk variants

    doi: 10.1101/2020.06.27.175489

    Figure Lengend Snippet: The de novo autism splice site mutation causes exon skipping in BTRC isoforms and reduces their translational efficiency. (A) The exon structure of three splicing isoforms of the BTRC gene showing positions of the cloned abridged introns and the splice site mutation; numbers denote base pairs (bp). (B) Minigene assays demonstrate exon 4 skipping as a result of the splice site mutation. The assays show the RT-PCR results performed using total RNA from HeLa cells transfected with BTRC minigene constructs; numbers denote base pairs. (C) Splicing assays with the full-length constructs carrying abridged introns confirm exon skipping observed in the minigene assays. (D) Immunoblotting (IB) from the whole cell lysates of HeLa cells transfected with different BTRC minigene constructs and an empty vector, as indicated. Membranes were probed to observe BTRC overexpression, and to investigate expression of p-β-catenin, Cul1 and SKP1. β-actin was used as loading control. Immunoprecipitation was performed with the antibody recognizing V5-tag and proteins were detected by immunoblotting (IB) with the p-β-catenin, Cul1, SKP1 and V5 antibodies. The splice site mutation causes reduced translational efficiency of both BTRC_1Mut and BTRC_2Mut mutant isoforms as compared to their wild type counterparts. Schematic diagram of Skp1-Cul1-BTRC ubiquitin protein ligase complex is shown at the bottom. (E) Quantification of protein pull-downs with V5-IP using ImageJ software. The band intensity values were normalized to WT expression levels. Error bars represent 95% confidence intervals (CI) based on 3 independent experiments. On average, 40% reduction of BTRC protein expression is observed as a result of a mutation. Consequently, the reduction of the corresponding BTRC binding partners (p-β-catenin, Cul1, and SKP1) is also observed. (F) Expression profiles of brain-expressed BTRC isoforms show higher expression of ASD-impacted BTRC-001 and BTRC-002. Numbers denote base pairs (a, b, c panels) or kDa (d). P-values: * - P

    Article Snippet: Then, 3 mg of total protein was diluted with immunoprecipitation buffer to achieve a concentration of 3 mg/ml.

    Techniques: Mutagenesis, Clone Assay, Reverse Transcription Polymerase Chain Reaction, Transfection, Construct, Plasmid Preparation, Over Expression, Expressing, Immunoprecipitation, Software, Binding Assay

    TMEM16A was associated with cyclophilin D (CypD) in the mitochondria. (A) Endogenous expression of TMEM16A in the mitochondria was detected in BASMCs by immunoblotting with TMEM16A antibody ( n = 6; cyto, mem and mito are cytoplasm, membrane and mitochondria for short). (B) The endogenous TMEM16A expression in mitochondria was detected in BASMCs by immunogold staining with gold‐labelled TMEM16A antibody (see arrows, n = 6). (C–F) Co‐IP showed that cyclophilin D, but not ANT or VDAC, immunoprecipitated with TMEM16A in BASMCs ( n = 5). IP, immunoprecipitation; IB, immunoblot. (G) H 2 O 2 increased the association between TMEM16A and cyclophilin D, which was attenuated by preincubation with CsA (5 μmol·L −1 ) 30 min before H 2 O 2 treatment ( n = 5, * P

    Journal: British Journal of Pharmacology

    Article Title: Transmembrane member 16A participates in hydrogen peroxide‐induced apoptosis by facilitating mitochondria‐dependent pathway in vascular smooth muscle cells

    doi: 10.1111/bph.14432

    Figure Lengend Snippet: TMEM16A was associated with cyclophilin D (CypD) in the mitochondria. (A) Endogenous expression of TMEM16A in the mitochondria was detected in BASMCs by immunoblotting with TMEM16A antibody ( n = 6; cyto, mem and mito are cytoplasm, membrane and mitochondria for short). (B) The endogenous TMEM16A expression in mitochondria was detected in BASMCs by immunogold staining with gold‐labelled TMEM16A antibody (see arrows, n = 6). (C–F) Co‐IP showed that cyclophilin D, but not ANT or VDAC, immunoprecipitated with TMEM16A in BASMCs ( n = 5). IP, immunoprecipitation; IB, immunoblot. (G) H 2 O 2 increased the association between TMEM16A and cyclophilin D, which was attenuated by preincubation with CsA (5 μmol·L −1 ) 30 min before H 2 O 2 treatment ( n = 5, * P

    Article Snippet: Co‐immunoprecipitation (IP) and Western blotting were performed as described previously (Ma et al (VDAC; Santa Cruz) antibodies overnight at 4°C.

    Techniques: Expressing, Staining, Co-Immunoprecipitation Assay, Immunoprecipitation

    ASPL-C converts p97 hexamers into stable p97:ASPL-C heterooligomers. ( a ) Co-immunoprecipitation of a p97:ASPL protein complex from human brain homogenate using an anti-ASPL antibody. Anti-FLAG antibody and beads alone were used as negative controls. ( b ) Schematic representation of fragments and full-length ASPL and p97. Conserved protein domains are depicted: ubiquitin-like domain (UBL); ubiquitin regulatory-X domain (UBX); N-terminal protein binding domains (N a and N b ); ATPase domains (D1 and D2). ( c ) Blue-native gel stained with Coomassie Brilliant Blue, demonstrating the remodelling of p97 hexamers by ASPL-C in a concentration-dependent manner. p97 (10 μg) and ASPL-C (0.3, 0.6, 1.8, 3, 6 and 12 μg) were briefly mixed and incubated on ice for 5 min; then protein complexes were analysed by BN-PAGE. A 1:1 molar ratio of p97 monomers and ASPL-C was sufficient to promote the formation of p97:ASPL-C heterooligomers. ( d ) Negatively stained electron micrographs of purified p97 in the presence and absence of ASPL-C; scale bar 50 nm.

    Journal: Nature Communications

    Article Title: Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers

    doi: 10.1038/ncomms13047

    Figure Lengend Snippet: ASPL-C converts p97 hexamers into stable p97:ASPL-C heterooligomers. ( a ) Co-immunoprecipitation of a p97:ASPL protein complex from human brain homogenate using an anti-ASPL antibody. Anti-FLAG antibody and beads alone were used as negative controls. ( b ) Schematic representation of fragments and full-length ASPL and p97. Conserved protein domains are depicted: ubiquitin-like domain (UBL); ubiquitin regulatory-X domain (UBX); N-terminal protein binding domains (N a and N b ); ATPase domains (D1 and D2). ( c ) Blue-native gel stained with Coomassie Brilliant Blue, demonstrating the remodelling of p97 hexamers by ASPL-C in a concentration-dependent manner. p97 (10 μg) and ASPL-C (0.3, 0.6, 1.8, 3, 6 and 12 μg) were briefly mixed and incubated on ice for 5 min; then protein complexes were analysed by BN-PAGE. A 1:1 molar ratio of p97 monomers and ASPL-C was sufficient to promote the formation of p97:ASPL-C heterooligomers. ( d ) Negatively stained electron micrographs of purified p97 in the presence and absence of ASPL-C; scale bar 50 nm.

    Article Snippet: Co-IP experiments in reverse direction were carried out using the Pierce Crosslink Immunoprecipitation Kit (cat. 26147) according to manufactures instructions using the anti-p97 antibody (LifeSpan Biosciences, cat. LS-C287469, 1:2,000 dilution).

    Techniques: Immunoprecipitation, Protein Binding, Staining, Concentration Assay, Incubation, Polyacrylamide Gel Electrophoresis, Purification

    DEPP is located in mitochondria and peroxisomes. a) SH-EP/tetEGFP and SH-EP/tetEYFP-DEPP cells were treated with 200 ng/ml doxy for 24 hours and subjected to subcellular fractionation. The protein levels of DEPP, GFP and catalase in the cytosolic and the nuclear fraction were determined by immunoblot. Alpha-Tubulin (cytosolic) and Lamin (nuclear) were used to control the purity of the fractions (left panel). The peroxisomal fraction of SH-EP/tetEYFP-DEPP cells treated with 200 ng/ml doxy for 24 hours was separated using a peroxisome isolation kit (PEROX1, Sigma). DEPP protein expression was determined by immunoblot. Catalase (peroxisomes) and CoxIV (mitochondria) were used to control the purity of the peroxisomal fraction (right panel). b) SH-EP/tetEYFP-DEPP cells were grown on eight-well chambered cover glasses, treated with 200 ng/ml doxy for 24 hours and analyzed by live confocal microscopy. Mitochondria were stained using the specific mitochondrial probe MitoTrackerRed/CMXRos (30 nM). Peroxisomal staining was performed with a CellLight® Peroxisomes-RFP fusion construct. c) SH-EP/tetDEPP cells treated with 200 ng/ml doxy for 24 hours were subjected to CoIP analysis with a Pierce Crosslink Magnetic IP/Co-IP kit to investigate whether the DEPP protein co-immunopurifies with PEX7-cross-linked beads. The expression of PEX7 and DEPP was determined by immunoblot. Alpha-Tubulin served as loading control.

    Journal: Molecular Cancer

    Article Title: C10ORF10/DEPP, a transcriptional target of FOXO3, regulates ROS-sensitivity in human neuroblastoma

    doi: 10.1186/1476-4598-13-224

    Figure Lengend Snippet: DEPP is located in mitochondria and peroxisomes. a) SH-EP/tetEGFP and SH-EP/tetEYFP-DEPP cells were treated with 200 ng/ml doxy for 24 hours and subjected to subcellular fractionation. The protein levels of DEPP, GFP and catalase in the cytosolic and the nuclear fraction were determined by immunoblot. Alpha-Tubulin (cytosolic) and Lamin (nuclear) were used to control the purity of the fractions (left panel). The peroxisomal fraction of SH-EP/tetEYFP-DEPP cells treated with 200 ng/ml doxy for 24 hours was separated using a peroxisome isolation kit (PEROX1, Sigma). DEPP protein expression was determined by immunoblot. Catalase (peroxisomes) and CoxIV (mitochondria) were used to control the purity of the peroxisomal fraction (right panel). b) SH-EP/tetEYFP-DEPP cells were grown on eight-well chambered cover glasses, treated with 200 ng/ml doxy for 24 hours and analyzed by live confocal microscopy. Mitochondria were stained using the specific mitochondrial probe MitoTrackerRed/CMXRos (30 nM). Peroxisomal staining was performed with a CellLight® Peroxisomes-RFP fusion construct. c) SH-EP/tetDEPP cells treated with 200 ng/ml doxy for 24 hours were subjected to CoIP analysis with a Pierce Crosslink Magnetic IP/Co-IP kit to investigate whether the DEPP protein co-immunopurifies with PEX7-cross-linked beads. The expression of PEX7 and DEPP was determined by immunoblot. Alpha-Tubulin served as loading control.

    Article Snippet: Co-immunoprecipitation analysis (CoIP) CoIP was performed with a Pierce Crosslink Magnetic IP/Co-IP kit (Pierce, Rockford, USA) according to the instructions of the manufacturer.

    Techniques: Fractionation, Isolation, Expressing, Confocal Microscopy, Staining, Construct, Co-Immunoprecipitation Assay