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32 protocols using ab500

1

Chromatin Immunoprecipitation of Acetylated Lysine

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MEFs and NRVMs were treated overnight with 200 nM apicidin. The cells were subjected to ChIP assay using a commercially available Kit (Abcam ab500). Sheared chromatin was incubated overnight (with rotation, 4°C) with anti-acetyl lysine ChIP grade antibody (Abcam), anti-histone 3 ChIP grade antibody (Abcam) or negative control rabbit IgG. DNA pulldown and purification were performed according to the manufacturer’s protocol (Abcam ab500). DNA samples were subjected to real-time PCR with SYBR green using species-specific primers that span 2,000 base pairs upstream and 500 base pairs downstream of the TSC2 transcription tart site.
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2

Chromatin Immunoprecipitation of HSF1

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A549 and A549-taxolR cells were fixed, nuclei were isolated, and chromatin was sheared by sonication using the ChIP Kit according to the manufacturer’s instructions (ab500; Abcam). The sheared chromatin was immunoprecipitated using HSF1 antibody (ab-52757; Abcam) and IgG (ab500; Abcam). Details regarding the primers used in ChIP-qPCR can be found in Supplementary Table S2. The quantitative PCR conditions were as follows: 10 min at 95 °C, followed by 38 cycles of denaturation (5 s at 95 °C), annealing (10 s at 62 °C), and extension (20 s at 72 °C) with single acquisition of fluorescence at the end of each extension step. ChIP-qPCR was calculated as follows: fold enrichment = 2−((Ct IP)−(Ct mock)). Mean values of three biological replicates were calculated. Statistical analysis was carried out using one-way ANOVA.
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3

ChIP Assay for KLF9 Protein-DNA Interactions

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Chromatin immunoprecipitation (ChIP) assay was conducted using the ChIP kit (ab500, Abcam). First, equal amounts of cells were treated with 1% methanol for 10 min crosslink, washed with phosphate buffer saline, and resuspended in ChIP nuclear lysis buffer. Next, the crosslinked DNA was ultrasonically processed to generate chromatin fragments. After the lysates were clarified by centrifugation, the supernatant was incubated with the antibody against KLF9 (1:1000, 701888, Invitrogen) or immunoglobulin G (IgG; 1:100, ab6757, Abcam) at 4°C overnight. Subsequently, with an equal amount of pre‐clarified chromatins used as input, chromatins were incubated with fully resuspended protein A/G beads. After washing beads, immunocomplex was eluted by heating at 62°C and shaking. The crosslink of protein‐DNA complex was reversed after 2 h incubation. After purification, immunoprecipitated DNA was analyzed by PCR, with information of PCR primers shown in Table 1.
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4

Chromatin Immunoprecipitation (ChIP) Protocol

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For chromatin immunoprecipitation ChIP-kit from Abcam (ab500) was used following the manufacturer’s instruction. Briefly cells were crosslinked with 1% formaldehyde (Sigma) in culture medium for 10 min at room temperature, and chromatin from lysed nuclei was sheared to 200–600 bp fragments using a Branson Sonifier. Chromatin derived from 4 × 106 cells was incubated with indicated antibodies (Supplementary Table 1) overnight at 4 °C. Antibody/antigen complexes were recovered with ProteinA/G beads for 2 h at 4 °C. Quantitative real-time PCR was carried out on a 7900H thermal cycler with custom-made oligonucleotides with PowerUP SYBR green master mix (Thermo Fisher); each sample was analyzed in triplicate. The amount of immunoprecipitated DNA in each sample was determined as the fraction of the input (amplification efficiency (Ct INPUT_Ct ChIP)). Primers are listed in Supplementary Table 4.
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5

ChIP Assay with CAF Cells

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3 × 106 DDR2-expressing and DDR2-depleted CAFs were used for ChIP assay (Abcam ab500) following manufacturer’s protocol. Additional details are in supplemental methods.
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6

ChIP Assay for H4K16Ac Enrichment

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Chromatin immunoprecipitation (ChIP) assays were performed as per the manufacturer's protocol (ab500, Abcam, Cambridge, MA) with minor modifications 29 (link). An antibody against H4K16Ac (Active Motif #61529) was used to pull down the associated DNA. ChIP-DNA were amplified by real-time PCR with primers listed in Table S2, using SYBR® Green PCR Master Mix (Life Technologies, Carlsbad, CA). Results were normalized to input DNA.
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7

AHR Binding Profiling by ChIP

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ChIP studies were performed using an AHR-specific antibody (ab2769; Abcam, Cambridge, MA) and the ChIP kit (ab500; Abcam) according to the manufacturer’s protocol. Cells were fixed and sonicated to produce fragments averaging 500 bp. Following immunoprecipitation with AHR-specific antibody or normal mouse IgG (Santa Cruz Biotechnology, Dallas, TX), DNA was purified and amplified using the following primers: Cyp1b1 primer: 5’-GTTTGGCGCTGGGTTAC-3’ and 5’-AGGTCGGAGCTGACTCTCT-3’ [104 (link)], Sox2 primer: 5’-CTGTGAGAAGGGCGTGAGAG-3’ and 5’- AAACAGCCAGTGCAGGAGTT-3’. The relative DNA amount was calculated using the ΔΔCt method. AHR and IgG control pull-down signal were normalized to input signal.
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8

ChIP-qPCR Assay of YAP1 Targets

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ChIP was performed using a kit from Abcam (catalog # ab500) following the manufacturer’s protocol. Cells were grown to 90% confluence in a 10 cm plate. A total of 1 × 106 cells were used for each reaction. After sonication, YAP1 antibody (Cell Signaling, 14074S) was used for immunoprecipitation overnight with rotation at 4 °C. After DNA purification, quantitative PCR was performed using the following primers:

Human PFKFB3

hPFKFB3_YAP1ChIP_FW: GGGATAACAGCAGCCAGGA

hPFKFB3_YAP1ChIP_RV: CTTCCACGTGGGGAGGAG

Murine Pfkfb3

mPfkfb3_Yap1ChIP_FW: CTGCTCTCGTCCACCCGCAG

mPfkfb3_Yap1ChIP_RV: CTCCTCTCCAGTTCTGTCGG

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9

JLAT10.6 Cells Acetylation Profiling

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JLAT10.6 cells were treated with DMSO or 1 µM of SDL148 for 6 h. ChIP was performed with a ChIP kit from Abcam (ab500) and the anti-acetylated histone H3 antibody (Thermo Scientific). An anti–rabbit IgG (Cell Signaling Technology) was used as an isotype control. Total chromatin (input) and the immunoprecipitated chromatin were used as template, and the HIV-1 LTR was amplified by quantitative PCR using the primers indicated. Actin was used as internal control. We used the HIV-1 LTR primers (f: 5-AGCCCTCAGATG CTACATATAAGCA-3, r: 5-TAG CCAGAGAGCTCCCAGGCTCAG A - 3) and actin primers.
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10

Detecting PEA3 Binding to Rab8A

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To detect whether PEA3 could bind to the promoter of Rab8A, a ChIP assay was conducted according to the ChIP assay kit procedures (ab500, Abcam). Briefly, the treated cells were collected and lysed. Antibody against Rab8A and IgG was applied for immunoprecipitation. PCR amplification of the precipitated DNA was performed.
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