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7 protocols using tead1

1

ChIP-seq analysis of transcription factors

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ChIP was carried out as described previously 25 (link), 57 (link) with the following antibodies: goat IgG (Santa Cruz Biotechnology, sc-2028), Sox10 (R&D, AF2864), and Tead1 (BD Biosciences, 610923). Primers used included the following:
Tekt3 +7.8kb (Forward: aataccagcagatccggaagac, Reverse: ttgactcgttctcccaggtttt),
Itga6 −22.8kb (Forward: tgcttctgataagccccaac, Reverse: aagtcccagacacgtccttg),
Itga6 −20.6kb (Forward: tggaggcagaaggagaaaaa, Reverse: aggggcctgttaggaacact),
Itga6 −16.2kb (Forward: gacttgagctgtctgcatgg, Reverse: tggactgactaggcttccaca),
Itga6 −8.5kb (Forward: aaaagccaaacaaacccaga, Reverse: ggctagggcaagctaaggat),
Itga6 −7.8kb (Forward: tgcttttggtcatgtggttg, Reverse: accactggctagctcagcat),
Itga6 −165bp (Forward: tcgataaaacgccggagagt, Reverse: gtagctagcagccgctcaat),
Dag1 +3kb (Forward: atgaacccctcttcctgacc, Reverse: ccttgctgagactgtgctca),
Dag1 −36kb (Forward: ggatggaagactgaaaggcc, Reverse: ccctttccctctggtgtgag).
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2

ChIP Assay for Histone Modifications

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ChIP assays were performed using the ChIP-IT® Express Kit (Active Motif). 10 μg of sonificated chromatin extract was incubated with antibodies against H3K27me3, H3K27ac, H3K9me3, H3K4me1, H3K4me3 (no. 39155, 39297, 39161, 39135, 39915 all from Active Motif), PU.1, Smad3 (no. 2266, 9523 both from Cell Signaling Technology, Danvers, USA) and TEAD1 (no. 610923 from BD Biosciences) or normal rabbit or mouse IgG antibody (no. sc-2027 X, sc-2025, both from Santa Cruz Biotechnology). Purification was performed using the Chromatin IP DNA Purification Kit (Active Motif) and bound sequences were determined by quantitative real-time PCR using primers listed in supplementary table.
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3

Western Blot Analysis of Cellular Proteins

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Total proteins were isolated using complete Lysis-M buffer (Roche). The protein concentration was measured using the ND-1000 method (Thermo Fisher Scientific). Equal amounts of protein lysates were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred using the iBot® Blotting System (Invitrogen). The membranes were blocked for 1 h at room temperature with a buffer containing 2% bovine serum albumin in Tris-buffered saline with 0.1% Tween-20. The membranes were incubated overnight in the diluted antibodies and blocked with secondary immunoglobulin G (IgG) antibody for 1 h. Specific proteins were detected using the ECL prime western blotting detection reagent (Amersham Biosciences, Buckinghamshire, UK). The monoclonal/polyclonal antibodies, including PARP, MDR1, YAP1 (= YAP, YAP65), p-YAP, TAZ, β-actin, Lamin A/C (Cell Signaling Technology), MOB1B (= MOB4A, Abgent), and TEAD1 (BD Biosciences, city, US state, country), were used. Nuclear and cytoplasmic fractions were prepared using the NE-PER Nuclear and Cytoplasmic Extraction reagents based on the manufacturer’s instruction (Thermo Fisher Scientific).
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4

ChIP Assay for Histone Modifications

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ChIP assays were performed using the ChIP-IT® Express Kit (Active Motif). 10 μg of sonificated chromatin extract was incubated with antibodies against H3K27me3, H3K27ac, H3K9me3, H3K4me1, H3K4me3 (no. 39155, 39297, 39161, 39135, 39915 all from Active Motif), PU.1, Smad3 (no. 2266, 9523 both from Cell Signaling Technology, Danvers, USA) and TEAD1 (no. 610923 from BD Biosciences) or normal rabbit or mouse IgG antibody (no. sc-2027 X, sc-2025, both from Santa Cruz Biotechnology). Purification was performed using the Chromatin IP DNA Purification Kit (Active Motif) and bound sequences were determined by quantitative real-time PCR using primers listed in supplementary table.
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5

Comprehensive Western Blotting Assay Protocol

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Western blotting was performed as described.5 (link) Briefly, cell protein samples were prepared in ice-cold lysis buffer (100 mmol/L TrisHCl pH7.4, 10 mmol/L NaCl, 1 mmol/L EDTA, 1 mmol/L EGTA, 10% glycerol, 0.5% deoxycholate, 1% Triton X-100, 0.1% SDS, 20 mmol/L Na4P2O7, 2 mmol/L Na3VO4, 1 mmol/L NaF, 1 mmol/L PMSF) supplemented with 1X protease inhibitor and phosphatase inhibitor (Roche) when necessary. Equal amount of protein samples were loaded and fractionated by SDS-PAGE, then transferred to 0.45 μm pore-size nitrocellulose membranes (Millipore). Membranes were blocked in 5% non-fat milk-TBS (w/v), then incubated with indicated primary antibodies. The following antibodies were used: TEAD1 (BD, #610922), Myc tag (Cell signaling, #2276), VGLL4 (Novus Biologicals, #NBP1–81543), MENIN (Abcam, # ab92443) and GAPDH. The blots were imaged using Licor Odyssey Clx and quantified by Image Studio ver 5.2 software.
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6

Comprehensive Western Blotting Assay Protocol

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Western blotting was performed as described.5 (link) Briefly, cell protein samples were prepared in ice-cold lysis buffer (100 mmol/L TrisHCl pH7.4, 10 mmol/L NaCl, 1 mmol/L EDTA, 1 mmol/L EGTA, 10% glycerol, 0.5% deoxycholate, 1% Triton X-100, 0.1% SDS, 20 mmol/L Na4P2O7, 2 mmol/L Na3VO4, 1 mmol/L NaF, 1 mmol/L PMSF) supplemented with 1X protease inhibitor and phosphatase inhibitor (Roche) when necessary. Equal amount of protein samples were loaded and fractionated by SDS-PAGE, then transferred to 0.45 μm pore-size nitrocellulose membranes (Millipore). Membranes were blocked in 5% non-fat milk-TBS (w/v), then incubated with indicated primary antibodies. The following antibodies were used: TEAD1 (BD, #610922), Myc tag (Cell signaling, #2276), VGLL4 (Novus Biologicals, #NBP1–81543), MENIN (Abcam, # ab92443) and GAPDH. The blots were imaged using Licor Odyssey Clx and quantified by Image Studio ver 5.2 software.
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7

ChIP-seq analysis of transcription factors

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ChIP was carried out as described previously 25 (link), 57 (link) with the following antibodies: goat IgG (Santa Cruz Biotechnology, sc-2028), Sox10 (R&D, AF2864), and Tead1 (BD Biosciences, 610923). Primers used included the following:
Tekt3 +7.8kb (Forward: aataccagcagatccggaagac, Reverse: ttgactcgttctcccaggtttt),
Itga6 −22.8kb (Forward: tgcttctgataagccccaac, Reverse: aagtcccagacacgtccttg),
Itga6 −20.6kb (Forward: tggaggcagaaggagaaaaa, Reverse: aggggcctgttaggaacact),
Itga6 −16.2kb (Forward: gacttgagctgtctgcatgg, Reverse: tggactgactaggcttccaca),
Itga6 −8.5kb (Forward: aaaagccaaacaaacccaga, Reverse: ggctagggcaagctaaggat),
Itga6 −7.8kb (Forward: tgcttttggtcatgtggttg, Reverse: accactggctagctcagcat),
Itga6 −165bp (Forward: tcgataaaacgccggagagt, Reverse: gtagctagcagccgctcaat),
Dag1 +3kb (Forward: atgaacccctcttcctgacc, Reverse: ccttgctgagactgtgctca),
Dag1 −36kb (Forward: ggatggaagactgaaaggcc, Reverse: ccctttccctctggtgtgag).
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