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14 protocols using sv5 pk1

1

Chromatin Immunoprecipitation of Yeast Scc1

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Details of the yeast strains and experimental setup have been published elsewhere (Ocampo‐Hafalla et al, 2016). Cells were processed for chromatin immunoprecipitation as described (Lengronne et al, 2004). Pk‐tagged Scc1 was immunoprecipitated using anti‐Pk antibodies (AbD Serotec, SV5‐Pk1) from strains grown in the absence of galactose. Chromatin immunoprecipitates were hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R arrays. Enrichment in the immunoprecipitate relative to a whole genome DNA sample is presented. Each bar represents the average of 25 oligonucleotide probes within adjacent 125‐bp windows.
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2

ChIP-qPCR Protocol for Protein Interactions

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ChIP-qPCR was performed as described in Katou et al. (2003) (link) using anti-PK clone SV5-Pk1 (Serotec) and anti-Rpb1-CTD (8WG16; Abcam, ab817) coupled to Dynabeads (Invitrogen; protein A and sheep anti-mouse M280 IgG). For quantitative PCR, background controls were determined using uncoupled Dynabeads, and enrichment was normalized to chromatin input and transcription-negative site. Primers are available on request.
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3

Yeast Protein Extraction and Analysis

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Yeast protein extracts—except for chromatin fractionation—were prepared using the trichloroacetic acid protocol as described (18 (link)). For chromatin fractionation in Figure 5, total, soluble and pellet (chromatin) proteins were isolated as previously detailed for young yeast cells (35 (link)). Yeast proteins were run on an 8% (HA-Pds1, Brn1-Pk9 and Pgk1), 6% (Myc-Top2 and Myc-Ubr1) or 15% (H4 and Pgk1) sodium dodecyl sulfate-polyacrilamyde gel. HA-Pds1, Myc-Top2, Myc-Ubr1, Pgk1, Brn1-Pk9 and H4 were detected with the mouse monoclonal HA.11 (Covance), the mouse monoclonal 9E10 (Covance), the mouse polyclonal 22C5D8 (Invitrogen), the mouse monoclonal SV5-Pk1 (Serotec) and the rabbit polyclonal ab10158 (Abcam) antibodies, respectively. Peroxidase conjugate (Figures 1D, 4B, 4D and 5B) and fluorophore conjugate (Supplementary Figures S1A and S4A) secondary antibodies were used.
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4

Chromatin Crosslinking and ChIA-PET

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Chromatin was fixed with 3% paraformaldehyde followed by further cross-linking with 10 mM dimethyl adipimidate (DMA). Crosslinked chromatin was sheared into 300–500 bp DNA fragments by Bioruptor (Diagenode). Cut14-Pk and Rad21-Myc proteins were immunoprecipitated using mouse monoclonal anti-PK (SV5-Pk1, Serotec) or mouse monoclonal anti-Myc (9E10, Clontech), and protein G-coupled Dynabeads (Life Technologies). Immunoprecipitated chromatin was subjected to the ChIA-PET procedure20 . ChIP DNA was split into an equal amount and separately ligated to either A or B linkers, and mixed ligation products were further subjected to proximity ligation. The ligation product was digested by EcoP15I and purified using streptavidin-coupled magnetic beads (Invitrogen). Illumina sequencing adaptors were added to DNA fragments, which were then subjected to PCR amplification (Phusion PCR Master Mix; New England Biolabs). This PCR was performed in a total of 32 separate tubes for each ChIA-PET library. Assembled PCR products were sequenced on the Illumina HiSeq 2000 platform to obtain 100 bp single end reads.
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5

Chromatin Crosslinking and ChIA-PET

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Chromatin was fixed with 3% paraformaldehyde followed by further cross-linking with 10 mM dimethyl adipimidate (DMA). Crosslinked chromatin was sheared into 300–500 bp DNA fragments by Bioruptor (Diagenode). Cut14-Pk and Rad21-Myc proteins were immunoprecipitated using mouse monoclonal anti-PK (SV5-Pk1, Serotec) or mouse monoclonal anti-Myc (9E10, Clontech), and protein G-coupled Dynabeads (Life Technologies). Immunoprecipitated chromatin was subjected to the ChIA-PET procedure20 . ChIP DNA was split into an equal amount and separately ligated to either A or B linkers, and mixed ligation products were further subjected to proximity ligation. The ligation product was digested by EcoP15I and purified using streptavidin-coupled magnetic beads (Invitrogen). Illumina sequencing adaptors were added to DNA fragments, which were then subjected to PCR amplification (Phusion PCR Master Mix; New England Biolabs). This PCR was performed in a total of 32 separate tubes for each ChIA-PET library. Assembled PCR products were sequenced on the Illumina HiSeq 2000 platform to obtain 100 bp single end reads.
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6

Western Blotting Antibody Validation

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Western blotting was performed using the following antibodies: peroxidase-anti-peroxidase (PAP) (P1291, Sigma, 1:2000); anti-Calmodulin binding protein (CBP) (RCBP-45A-Z, ICLab, 1:500); anti-tubulin (B-5–1–2, Sigma, 1:5000); anti-FLAG (M2, F1804, Sigma, 1:1000); anti-MYC (9E10, Agro-Bio LC; 9E11, ab56, Abcam, 1:1000; or rabbit polyclonal ab9106, Abcam, 1:1000); anti-V5 (SV5-Pk1, AbD Serotec, 1:1000); anti-HA (16B12, Ozyme; rabbit polyclonal, ab9110, Abcam, 1:1000). Protein concentrations were measured by the Bradford method and used to load equal amounts of proteins across samples. Quantification of signal intensity was performed using staining, film exposure or digital acquisition that were within the linear range of detection, as verified by loading serial dilutions of one sample, and analysed using ImageJ.
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7

ChIP Assay for Brn1-Pk Enrichment

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Chromatin immunoprecipitation (ChIP) assays were performed as described (36 (link)) with the anti-Pk antibody SV5-Pk1 (Serotec) for Brn1-Pk9. Oligonucleotide sequences for the real-time PCR amplifications performed on purified DNA before (input; I) or after (immunoprecipitated; IP) immunoprecipitation are shown in Supplementary Table S2. Protein enrichment at each specific region was calculated as the ratio between the IP and the I in the tagged strain relative to the same ratio in the untagged strain. The average and SEM of three independent experiments are shown.
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8

Western Blot Analysis of Igo1 and Whi5

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For Igo1-myc8, 10 μg whole-cell extracts were run on 12% acryl–bisacrylamide (29:1) gels and 8.5% acryl–bisacrylamide (29:1) 25 µM Phos-tag gels (Wako Chemicals GmbH, Germany). For Whi5-PK3, 10 μg whole-cell extracts were run on 12.5% acryl–bisacrylamide (125:1) gels and 8.5% acryl–bisacrylamide (29:1) 5 µM Phos-tag gels. Proteins were transferred to nitrocellulose membranes (Protran; Amersham, GE Healthcare, Germany) using wet blotting and revealed using standard immuno-blotting and ECL procedures. Western blot quantifications were performed from images acquired with the multi-application gel imaging system PXi 4 (Syngene, A Division of Synoptics Ltd, UK), using ImageJ. Primary antibodies were mouse monoclonal anti-myc (1:1000 from ascites for Igo1-myc8), rabbit polyclonal anti-swi6 (1:100,000) and mouse monoclonal anti-PK (1:5,000; clone SV5-Pk1; Bio-Rad Antibodies, France).
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9

Immunoblotting with Epitope Tags

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The primary antibodies used in this study were rabbit anti-myc (ab9106, abcam), mouse anti-flag (2368, Cell Signaling), mouse anti-V5 (SV5-Pk1, Bio-Rad) and rabbit anti-HA (C29F4, Cell signaling). The secondary antibodies used in this study were goat anti-rabbit IgG (H+L), HRP conjugate (65-6120, Life Technologies) and goat anti-mouse IgG (H+L), HRP conjugate (32430, Life Technologies).
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10

Analysis of GPR55 Expression in HEK293FT Cells

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HEK293FT cells were seeded at a density of ~7 × 105 cells/well in a 6-well plate with DMEM containing 2% FBS. After overnight culture, cells were transfected with pcDNA3.2-GPR55-V5 using PEI MAX and Opti-MEM for 24 h, followed by incubation with curcumin for 3 h. The cells were washed with PBS(−) and sonicated in lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100, 2.5 mM sodium pyrophosphate, 1 mM β-glycerophosphate, 1 mM sodium orthovanadate, 10 μg/mL leupeptin, 1 μg/mL aprotinin, 1 mM phenylmethylsulfonyl fluoride). After centrifugation (20,000 × g for 10 min), the supernatant was analyzed by western blotting with monoclonal anti-V5 (SV5-Pk1, Bio-Rad, Hercules, CA, USA, RRID:AB_322378) or monoclonal anti-β-actin antibody (2D4H5, Proteintech, Rosemont, IL, USA, RRID:AB_2687938). After reaction to horseradish peroxidase-conjugated secondary antibody (Bio-Rad, RRID:AB_11125547), the immunoreactive bands were developed with Immobilon Western Chemiluminescent HRP substrate (Millipore, Bedford, MA, USA) and were detected with LAS4000 imager (GE Healthcare, Piscataway, NJ, USA). Band intensities were determined using ImageJ software version 1.53k (NIH, Bethesda, MD, USA). All blots were processed in parallel and derived from the same experiment.
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