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4 protocols using fast sybr green master mix

1

Chromatin Quantification and Enrichment Analysis

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Chromatin lysates were subjected to column-based DNA clean-up (BioBasic, BS664, Markham, ON, Canada). Pre-IP input lysate from each cell line was used to generate a standard curve by creating 5 samples of 10-fold dilutions with known amounts of chromatin (50-0.005 ng). Two microliters of each sample was mixed with 8 µL of Fast SYBR™ Green Master Mix (Sigma-Aldrich, #4385612, St Louis, MI, USA) and the respective primer pairs, and subsequently run on an ABI ViiA7 qPCR system. Samples were run in triplicates. For downstream analyses, the chromatin amount present per sample was derived from input-generated standard curves and fold enrichment was calculated for SS18-SSX immunoprecipitation against IgG control. Primer sequences designed to target the promoter sequences are listed in Table 3.13 (link),17 (link)
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2

Quantifying Gut Inflammatory Markers

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RNA was isolated from gut mucosal biopsies using a Monarch Total RNA Miniprep Kit [NEB] according to the manufacturer’s protocols. cDNA was generated using LunaScript RT Master Mix Kit [NEB] according to the manufacturer’s protocol. Real-time quantitative PCR [qPCR] was performed using the Fast SYBR Green Master Mix [Sigma] in a QuantStudio 5 Real-Time-PCR-Cycler [Thermofisher Scientific] and the following primer pairs: TNF, Fwd: 5ʹ-GGGCTTATCTGAGGTTTGAG-3ʹ, Rev: 5ʹ-TTCTGCCTACTGCACTTCGA-3ʹ; IL6, Fwd: 5ʹ-TCTGCAATGAGAAAGGAGATGTG-3ʹ, Rev: 5ʹ-AGGTTCAGGTTGTTTTCTGCC-3ʹ; IL8, Fwd: 5ʹ-CTGTGAGGCTGCAGTTCTG-3ʹ, Rev: 5ʹ-GTGATTGAGAGTGGACCCCA-3ʹ. For transcript normalization, housekeeping genes GAPDH [Fwd: 5ʹ-TTCCACGGCACAGTCAAGGC-3ʹ, Rev: 5ʹ-GCGGTTACAGACACAACTCC-3ʹ], β-actin [Fwd: 5ʹ-TCCCTGGAGAAGAGCTACGA-3ʹ, Rev: 5ʹ-GCAGGTCAGGTCCACAAC-3ʹ] and RPS28 [Fwd: 5ʹ-GTTACCAAGGTTCTGGGCAG-3ʹ, Rev: 5ʹ- CAGATATCCAGGACCCAGCC-3ʹ] were selected based on NormFinder and BestKeeper.20 (link),21 (link) One-way ANOVA was performed, followed by Tukey’s test for statistical evaluation using GraphPad Prism 8.
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3

Transcriptomic and Epigenomic Analysis Workflows

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Total RNA from cell lines was extracted using RNeasy plus mini kit (Qiagen). For qRT-PCR analysis, 500 ng of total RNA was reverse transcribed using iScript Reverse Transcription kit (Bio-Rad), and qPCR was performed using Fast SYBR Green Master Mix (Millipore Sigma) and StepOnePlus Real-time PCR system (ThermoFisher Scientific) according the manufacturer’s instructions. Chromatin immunoprecipitation (ChIP) was performed using the Active Motif ChIP kit (Active Motif, Carlsbad, CA, USA) according to the manufacturer's instructions. Briefly, 5 × 107 LS180 cells grown in 15 cm plates were cross-linked with 1% formaldehyde, and cells were lysed and sonicated. Protein–DNA complexes were immunoprecipitated with control IgG or anti-FOXA1 (Santa Cruz) antibody. The IP material was washed and heated at 65°C overnight to reverse the crosslinks. ChIP DNA was column purified (Qiagen) and analyzed by qPCR.
Primer sequences for qRT-PCR and ChIP-qPCR are listed in Supplementary file 3.
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4

Quantitative Gene Expression Analysis

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Total RNA was extracted using TRI reagent (MilliporeSigma) and Direct-zol™ RNA miniprep (Zymo Research Corp.). RNA (1 µg) was then reverse transcribed into cDNA using an RT kit (sensiFAST; Bioline) according to manufacturer's protocol. Fast SYBR Green Master Mix (MilliporeSigma) was used to perform qPCR with a final concentration of 0.25 nM gene-specific primers. The sequences of the primers were as follows: E-cadherin forward: 5′-CCGAGAGCTACACGTTC-3′, reverse: 5′-TCTTCAAAATTCACTCTGCC-3′; fibronectin-1 forward: 5′-CCATAGCTGAGAAGTGTTTTG-3′, reverse 5′-CAAGTACAATCTACCATCATCC-3′; MMP2 forward: 5′-GTGATCTTGACCAGAATACC-3′, reverse: 5′-GCCAATGATCCTGTATGTG-3′; thrombospondin 1 (THBS1) forward: 5′-GTGACTGAAGAGAACAAAGAC-3′, reverse 5′-CAGCTATCAACAGTCCATTC-3′; and zinc-finger E-box-binding homeobox 1 (ZEB-1) forward: 5′-AAAGATGATGAATGCGAGTC-3′, reverse: 5′-TCCATTTTCATCATGACCAC-3′. PCR signals were compared among groups after normalization, with GAPDH forward: 5′-TCGGAGTCAACGGATTTG-3′, reverse: 5′-CAACAATATCCACTTTACCAGAG-3′) used as the internal reference, calculated using the 2−ΔΔCq method (18 (link),34 (link),35 (link)). The thermocycling conditions were as follows: 95 °C for 10 min. Next, they were denatured at 95°C for 15 sec and annealing the primer with DNA template at 60°C for 1 min. These cycles were repeated for 40 times.
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