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7 protocols using snai1

1

Western Blot Analysis of Epithelial-Mesenchymal Transition Markers

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Total protein was extracted from the cells. Approximately 25 μg sample was processed by 12% polyacrylamide gel electrophoresis and then transferred to polyvinylidene fluoride membranes. The membranes were placed in a blocking solution and slowly shaken for 2 h at 37°C. After blocking, the membranes were mixed with primary antibodies to PUMA (ab33906, 1:1000, Abcam, Cambridge, UK), Bax (#33-6400, 1:500, Invitrogen Inc., Carlsbad, CA, USA), Bcl-2 (#MA5-11757, 1:1000, Invitrogen), E-cadherin (GTX100443, 1:500, GeneTex, Inc., Alton Pkwy Irvine, CA, USA), Vimentin (GTX100619, 1:1000, GeneTex), Snai1 (#14-9859-82, 1:500, Invitrogen), N-cadherin (ab70611, 1:2000, Abcam), CDC73 (#PA5-17159, 1:1000, Invitrogen) and GAPDH (ab8245, 1:2000, Abcam) overnight at 4°C. The membranes were then incubated with the secondary antibody to IgG labelled with horseradish peroxidase (ab6721, 1:1000, Abcam) for 2 h at 37°C. Protein signals were visualized using enhanced chemiluminescence. The protein levels were analyzed using ImageJ software. The relative expression of the target protein was obtained by calculating the ratio of optical density (OD) value of the target protein to that of an internal reference.
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2

Protein Extraction and Immunoblotting Assay

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The total protein was collected from HCT116, DLD1, and NCM460 using RIPA lysis buffer, and the protein concentration was measured using the BCA kit (Beyotime Biotechnology Company). After separation by gel electrophoresis, the proteins were transferred to the PVDF membrane and sealed with 5% skimmed milk for 1 h. Then, the proteins were reacted overnight with the primary antibodies (TIMP1, #MA5‐13688, 1:1000; PGF, #MA5‐32855, 1:1000; FSTL3, #PA5‐79285, 1:1000; SNAI1, #MA5‐14801, 1:1000; FOXC1, #PA1‐807, 1:1000; Invitrogen) at 4°C, followed by reaction with the secondary antibody (IgG/HRP, 1:2000, Thermo Fisher Scientific) for 1 h. At last, the visual protein bands were detected with ECL reagent.
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3

Comprehensive Transcriptional Profiling of Angiogenic Pathways

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Total RNA was extracted with Maxwell RSC miRNA Tissue Kit and processed with Maxwell RSC Instrument (Promega). RNAs were quantified with DeNovix spectrophotometer (DeNovix, Wilmington) and reverse transcribed using High-Capacity cDNA reverse transcription kit (Applied Biosystems, Thermofisher Scientific). cDNAs were used to run a real-time PCR using TaqMan probes specific for the following genes: VE-cadherin, ICAM2, TIE1, TEK, FLK1, TGFβ1, TGFBR1, TGFBR2, ACTA2, CTGF, TBX3, SPP1, ACE, Sema7A, Nanog, BMP4, FGFR3, HES5, T, VEGFA, SNAI1, SNAI2, FGFR2, WNT3, WNT4, WNT6, WNT10A, FZD4, FZD6, LRP5, LRP6, β-catenin, TBP (Applied Biosystems. Thermofisher Scientific). Expression data were analyzed with SDS 2.3 software.
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4

Quantifying Stemness and EMT Markers

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Total RNA purification, reverse transcription and qPCR were performed as previously described by [41 (link)]. We used the following probes (Applied biosystems, Foster City, CA, USA): β-Actin (Hs0160665_g1), MYBBP1A (Hs00959671_m1), NANOG (Hs04260366_g1), OCT4 (Hs00999632_g1), SOX2 (Hs01053049_s1), TWIST1 (Hs01675818_s1), CD34 (Hs00990732_m1), CXCR4 (Hs00607978_s1), MYB (Hs00920556_m1), SNAI1 (Hs00195591_m1), VIM (Hs00958111_m1) and SERPINE1 (Hs00167155_m1).
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5

Epithelial-Mesenchymal Transition Markers

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TaqMAN: ZEB1 (Thermo Fisher Scientific, Hs00232783_m1), ZEB2 (Thermo Fisher Scientific, Hs00207691_m1), SNAI1 (Thermo Fisher Scientific, Hs00195591_m1), SNAI2 (Thermo Fisher Scientific, Hs00950344_m1), TWIST1 (Thermo Fisher Scientific, Hs01675818_s1), GAPDH (Thermo Fisher Scientific, 4326317E).
SYBR Green: KRT14 (IDT, Hs.PT.58.4592110), KRT19 (IDT,Hs.PT.58.4188708), MEG3 ex 10-11 (IDT, Hs.PT.58.25190740), GAPDH (IDT, Hs.PT.39a.22214836), KRT5 (IDT, Hs.PT.58.14446018), TP63 (IDT, Hs.PT.58.2966111), CDH3 (IDT, Hs.PT.58.39234242).
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6

RNA Isolation and RT-PCR Protocol

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RNA was isolated from frozen tissues and cell lines using TRIzol Reagent (Invitrogen) and chloroform, and real-time quantitative PCR (RT-PCR) was performed as previously described (21 (link)). CD73 primers and probe sequences, PCR efficiency, and limit of quantification have been previously reported (21 (link)). Taqman primers and probes purchased from Thermo Fisher Scientific include CCND1 Hs00765553; CDH1, Hs01023864; SNAI1, Hs00195591; SNAI2, Hs00950344; ZEB1, Hs00232783; ZEB2, Hs00207691; VIM, Hs009958116. Adenosine receptor primers and probe sets were previously reported and used as described (21 (link)).
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7

Gene Expression Analysis of End1s

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End1s seeded on fibronectin-coated 6-well plates (Corning 354402) and infected as described above were harvested for RNA using TRIzol (Thermo Fisher Scientific 15596026) and the DNA-free DNA removal kit (Thermo Fisher Scientific AM1906), according to manufacturers' protocols. cDNA libraries were subsequently prepared using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific 11766050) according to the manufacturer's protocol. Quantitative real-time PCR was performed on a QuantStudio 3 (Thermo Fisher Scientific) using TaqMan assay kits of the following genes: CTGF (Thermo Fisher Scientific Hs01026927_g1), INHBA (Thermo Fisher Scientific Hs01081598_m1), SNAI1 (Thermo Fisher Scientific Hs00195591_m1), BMP2 (Thermo Fisher Scientific Hs00154192_m1), PELI1 (Thermo Fisher Scientific Hs00900505_m1), ESM1 (Thermo Fisher Scientific Hs00199831_m1), and HPRT (Thermo Fisher Scientific Hs02800695_m1). Statistical analysis was performed in R, using pairwise Student's t-tests and Bonferroni's correction for multiple comparisons; p-values less than 0.05 were considered statistically significant.
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