250 sonicator

Chromatin immunoprecipitation (ChIP) assays were performed essentially as described before (Fan et al., 2019 (link); Kong et al., 2019a (link),b (link); Li et al., 2019a (link), b (link), c (link), d (link), e (link), f (link); Liu et al., 2019a (link); Lu et al., 2019 (link); Shao et al., 2019 (link); Weng et al., 2019 (link); Yang et al., 2019a,b (link)). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mM NaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) supplemented with protease inhibitor tablet and PMSF. DNA was fragmented into ∼200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with anti-BRG1 (Santa Cruz, sc-10768), or pre-immune IgG. For re-ChIP, immune complexes were eluted with the elution buffer (1% SDS, 100 mM NaCO₃), diluted with the re-ChIP buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris pH 8.1), and subject to immunoprecipitation with a second antibody of interest.

Chromatin immunoprecipitation (ChIP) assays were performed essentially as described before (Li et al., 2019b , f , 2020a (link), b , c (link); Shao et al., 2019 (link); Weng et al., 2019 (link); Chen et al., 2020a ; Wu X. et al., 2020 (link); Hong et al., 2021 (link)). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mM NaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, and 0.5% deoxycholate) supplemented with protease inhibitor tablet and PMSF. DNA was fragmented into ∼200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with anti-BRG1 (Santa Cruz, sc-10768), anti-Sp1 (Abcam, ab227383), or pre-immune IgG. Precipitated genomic DNA was amplified by real-time PCR with the following primers: SCAP proximal promoter, 5′-ATACTTCCCTCCGGTGTCCAC-3′ and 5′-ACCTCTCACCTCCACCTTTAC-3′; SCAP distal promoter, 5′-AAATGCGAGGACATGTACAATAC-3′ and 5′-ATTTAAAAGCTAAGTTGAC-3′. A total of 10% of the starting material is also included as the input. Data are then normalized to the input and expressed as % recovery relative the input as previously described (Chen et al., 2020b (link), c (link)). All experiments were performed in triplicate wells and repeated three times.

Chromatin immunoprecipitation (ChIP) assays were performed essentially as described before (Coarfa et al., 2020 (link); Hu et al., 2020 (link); Jehanno et al., 2020 (link); Maity et al., 2020 (link); Mallik et al., 2020 (link); Moon et al., 2020 (link); Shen et al., 2020 (link); Wang et al.,2020a,b (link); Zhang et al., 2020 (link); Zhao et al., 2020 (link); Marti et al., 2021 (link); Peng et al., 2021 (link); Rashid et al., 2021 (link)). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mM NaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) supplemented with protease inhibitor tablet and PMSF. DNA was fragmented into ∼200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with anti-Brg1 (Abcam, Ab110641), anti-hypoxia-inducible factor 1 alpha (HIF-1α) (Cell Signaling Techology, 14179), or pre-immune IgG. Precipitated DNA was amplified with the following primers: primer #1: 5′-ATATTACCAATCAGCGGCGAGC-3′ and 5′-ACTGCTATAGGGGGCGC-3′; primer #2, 5′-AAAAGCATGT GCCATTATGC-3′ and 5′-ATTCCTGGCTTTGTGGATGC-3′.

Chromatin immunoprecipitation (ChIP) assays were performed essentially as described before (Mao et al., 2020b (link); Yang et al., 2020a (link),b (link)). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mM NaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) supplemented with protease inhibitor tablet and PMSF. DNA was fragmented into ∼200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with anti-BRG1 (5 μg/reaction, Santa Cruz, sc-10768) or pre-immune IgG. Precipitated genomic DNA was amplified by real-time PCR. A total of 10% of the starting material is also included as the input. Data are then normalized to the input and expressed as% recovery relative the input as previously described (Chen et al., 2020b (link),c (link)). All experiments were performed in triplicate wells and repeated three times.

ChIP assays were performed essentially as described before^{22 ,26 (link),33 –44} . In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mM NaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) supplemented with protease inhibitor tablet and PMSF. DNA was fragmented into ~200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with anti-BRG1 (Santa Cruz, sc-10768), anti-Sp1 (Abcam, ab13370), anti-SRF (Cell Signaling Technology, 5147), (Santa Cruz, sc-585), anti-SLUG (Cell Signaling Technology, 9585), anti-ZEB1 (Cell Signaling Technology, 3396), anti-SNAIL (Cell Signaling Technology, 3879), anti-acetyl H3 (Millipore, 06-599), anti-acetyl H4 (Millipore, 06-598), anti-histone H3 (Millipore, 06-755), or pre-immune IgG. For re-ChIP, immune complexes were eluted with the elution buffer (1% SDS, 100 mM NaCO₃), diluted with the re-ChIP buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris pH 8.1), and subject to immunoprecipitation with a second antibody of interest.

Chromatin immunoprecipitation (ChIP) assays were performed essentially as described before (Chen et al., 2020a (link), b (link), c (link); Dong et al., 2020 (link); Fan et al., 2020 (link); Li et al., 2020a (link), b (link), c (link); Lv et al., 2020 (link); Mao et al., 2020 (link); Sun et al., 2020 (link); Wu et al., 2020 (link); Yang et al., 2020 (link)). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mMNaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) supplemented with protease inhibitor tablet and PMSF. DNA was fragmented into ∼200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with anti-BRG1 (Santa Cruz, sc-10768), anti-NF-κB (Santa Cruz, sc-372), anti-Sp1 (Abcam, ab227383), or pre-immune IgG.

Chromatin Immunoprecipitation (ChIP) assays were performed essentially as described before [47 (link), 48 (link)]. In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mM NaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) supplemented with protease inhibitor tablet and PMSF. DNA was fragmented into ~200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with 5μg of anti-BRG1 (Abcam, Ab110641), anti-NF-κB/p65 (Cell Signaling Tech, 8242), or pre-immune IgG. Precipitated DNA was amplified with the following primers: primer #1, 5ʹ-AAATGTACCAAGTCCCTCC-3ʹ and 5ʹ-ATGAGCAGCAGCCACAGAAG-3ʹ; primer #2, 5ʹ-ATCCTGAATTCAGGTTCTAC-3ʹ and 5ʹ-ATTCTGAGGAGTTGAC-3ʹ.