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6 protocols using igg mouse

1

Antibody Reagents for YAP/LATS Signaling

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The following antibodies were used in our study: HA (Covance, MMS-101P), Flag (Sigma, F1804), Myc (Santa Cruz, sc-40), Myc (ascite), IgG Mouse (Santa Cruz, sc-2025), CIT (Santa Cruz, sc-390437), and YAP (Novus H00010431-M01) for immunostaining and immunoprecipitation; Yap (Cell Signaling 4912 s) for western blotting; pYAP S127 (Cell Signaling, 4911 s), LATS1 (Benthyl, A300-477A), LATS2 (Cell Signaling, 5888 s), β-actin (Sigma, A5361), pLATS 1079 (Cell Signaling, 8654), pLATS 909 (Cell Signaling, 9157 s), MST1 (Cell Signaling, 3682), MST2 (Cell Signaling, 3952 s), and BrdU (BD555627).
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2

Antibody Characterization for Cell Biology

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The InlP polyclonal antibody was obtained after injection of an immunogenic peptide (amino acids 365 to 379, LDVSYNHNYATGGVC) in rabbits and subsequent affinity purification. The InlC polyclonal antibody is described in27 (link). The other primary antibodies are polyclonal antibodies against RBM5 (Sigma, HPA017335 for IF and Bethyl, A302-228A for IP), PML (Abcam, sc-966), anticoilin (Proteintech, 10967-1-AP), anti-nucleolin (Santa cruz, sc-13057) and monoclonal antibodies against tubulin (hybridoma E7), SC35 (AbCam, ab11826), FLAG-M2 (Sigma-Aldrich, F1804), Myc (9E10, Santa Cruz Biotechnology, sc-40), HA (6E2, Cell Signaling technology #2367), V5 (R960-2, Invitrogen). The immunoprecipitation control antibodies are IgG mouse (Santa-Cruz, sc-2025) and IgG rabbit (Santa-Cruz sc-2027). The secondary antibodies are coupled to Alexa-488 (Life technologies) or Cy3 or Cy5 (Jackson ImmunoResearch). DAPI and Hoechst are from Roche Applied Sciences and Thermo Fisher Scientific, respectively. Lipofectamine LTX Max is from Invitrogen.
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3

Immunoprecipitation of SAFB Protein

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Native whole-cell extracts prepared using 0.5× NLB were incubated with ProtG Dynabeads (Life Technologies, no. 10004D) coupled to 1 μg of either SAFB antibody (‘Antibodies’) or IgG (mouse; Santa Cruz, no. sc-2025) in a cold room for 150 min. Beads were washed twice in 0.5× NLB for 5 min then once with NDB. RNase-treated samples were resuspended in 90 µl of NDB to which 10 µl of RNaseA + T1 mix (Thermo Scientific, no EN0551) was added. Samples were then incubated at 20 °C for 15 min and washed twice with 0.5× NLB. Elution from the beads was performed in 1× protein-loading dye by incubation for 5 min at 95 °C with shaking. Interaction partners were detected using the antibodies against proteins shown in Extended Data Fig. 7 (‘Antibodies’).
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4

Chromatin Immunoprecipitation (ChIP) Protocol

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ChIP assays were performed as described [33 (link),34 (link)]. Briefly, 2.5 million cells were crosslinked with 37% w/v formaldehyde, quenched with 2.5M glycine, washed 3 times with ice cold PBS, and sonicated in a Bioruptor (Diagenode). The following primary antibodies were utilized for incubation of crosslinked chromatin overnight: HDAC1 (Abcam #31263, 3μg), HDAC2 (Abcam #12169, 3μg) pan-H4ac (Upstate #06–866, 5μg), H3K9Ac (Abcam #12179, 5μg), H3K9me3 (Abcam #8898, 5μg), SIN3A (Abcam #3479, 5μg) and as a negative control IgG Rabbit (Cell Signaling Technologies #2729S, 3 or 5μg), IgG Rabbit (Santa Cruz #2027, 3 or 5μg), or IgG Mouse (Santa Cruz #2025, 3 or 5μg,). Protein A/G magnetic beads (Pierce #88802) were added at 50 μL per ChIP sample. ChIP-qPCR primers were designed using Primer3 web tool and are listed in S5 Table.
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5

Antibody Characterization for Cell Biology

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The following are other antibodies used in this study: anti-actin-HRP (horseradish peroxidase) (Santa Cruz, sc-47778), mouse anti-PCNA (Abcam, ab29), rabbit anti-XPO1-C-terminal (Santa Cruz, sc-5595), mouse anti-XPO1-N-terminal (Santa Cruz, sc-136220), mouse anti-Coilin (Sigma C-1862), mouse anti-XPO5 (Abcam ab57491), mouse anti-XPOT (Abcam ab49933), rabbit anti-H3 (Abcam ab1791), mouse anti-GEMIN5 (Santa Cruz, sc-136200), mouse anti-SMN1 (Abcam, ab5831), goat anti-LaminB (Santa Cruz, sc-6216), mouse anti-CSE1L (Santa Cruz sc-135855), rabbit anti-Dyskerin (Santa Cruz sc-48794), rabbit anti-PHAX (Bethyl, A303–916A), goat anti-PHAX (M-19) (Santa Cruz, sc-11704), mouse anti-UBF1 (Santa Cruz sc-13125), mouse anti-nucleolin (Enzo, ADI-KAM-CP100) mouse anti-TRF2 (Imgenex, IG124A), mouse anti-XPO5 (Abcam ab57491), mouse anti-NFKB (Santa Cruz sc-372), mouse anti-RANBP2 (Santa Cruz, sc-74518), mouse anti-Fibrillarin (Abcam, ab4566), mouse anti-FLAG M2 (Sigma), IgG mouse (Santa Cruz sc-2025), mouse anti-Coilin (Sigma, C1862), rabbit anti-TCAB1 (Novus, NB100–68252); IgG rabbit (Abcam ab37415). All Alexa-conjugated secondary antibodies were purchased from Life Technologies.
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6

Immunoprecipitation Assay for Protein Interactions

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For immunoprecipitation (IP) assays, cells were lysed in IP buffer with protease-phosphatase inhibitors (20 mM Tris–HCl pH 8, 137 mM NaCl, 1% NP-40 and 2 mM EDTA) at 4°C for 30 min under constant rotation. Lysates were cleared by centrifugation at 12 000 rpm for 20 min at 4°C. Protein concentration was determined and 800–1000 μg of proteins were pre-cleared with 25 μl of Dynabeads G (Invitrogen) for 2 h under constant rotation at 4°C. In parallel, 5 μg of primary antibody and the corresponding control IgG were incubated with 20 μl of Dynabeads G for 2 h under constant rotation at room temperature. Finally, the Dynabeads with the antibodies were washed three times with citrate phosphate pH5 buffer with 0,01% Tween-20 and incubated with the pre-cleared samples overnight at 4°C under constant rotation. The day after, samples were washed three times with PBS (Gibco-Life Technology, Waltham, MA, USA) with proteases and phosphatases inhibitors and boiled in Laemmli buffer at 95°C for 5 min. Pelleted beads were separated using a magnetic separation rack and the supernatants were used for subsequent Western blot analysis. Antibodies used were: SLU7 (BD Bioscience, Franklin Lakes, NJ, USA 612604; 5 μg), DNMT1 (Abcam, ab13537; 5 μg), IgG mouse (Santa Cruz, SC2025; 5 μg).
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