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8 protocols using ab126745

1

Flow Cytometry Analysis of ADAR1 Expression

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Flow staining was performed in staining media for 30 min on ice in the dark. Cells were blocked using FcR block (Biolegend, San Diego, CA) for 15 minutes before antibody staining with to a final dilution of 1:25. DAPI solution was added before analysis to exclude dead cell debris. Analysis and sorting was performed on BD Aria Fusion, Aria II or Fortessa. Sorted cells were collected into staining media filled FACS tubes or 1.7mL Eppendorf tubes. The LICs are evaluated by the corresponding cell surface markers (Table S1). For intracellular ADAR1 staining, cells were stained with ethidium monoazide (EMA) for 15 min in the dark and then 15 min under light, followed by cell surface staining. After washing in staining buffer, cells were fixed and permeabilizated with an intracellular buffer set (eBioscience, San Diego, CA) and intracellularly stained with an antibody against ADAR1 (Abcam, ab126745) at 1:100 dilution. Secondary antibody of Alexa488 or Alexa647 were used to amplify ADAR1 signals.
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2

Immunohistochemical Determination of ADAR1-p150

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Human breast formalin fixed paraffin embedded tissue array sections (5μm) on positively charged slides were obtained from US Biomax Inc. (Derwood, MD USA, BC081116d). For immunohistochemistry, sections were stained using a Bond RXm autostainer (Leica, Buffalo Grove, IL USA). Briefly, slides were baked at 65°C for 15min and automated software performed dewaxing, rehydration, antigen retrieval, blocking, primary antibody incubation, post primary antibody incubation, detection (DAB), and counterstaining using Bond reagents (Leica). Samples were then removed from the machine, dehydrated through ethanols and xylenes, mounted and cover-slipped. An antibody specifically recognizing ADAR1-p150 (Abcam ab126745) was diluted 1:100 in Antibody Diluent (Leica). Intensity of p150 was scored on a scale of 0 to 3 (range established by samples with the strongest and weakest staining) by increments of 0.5. Any sample scored >1.0 was considered p150-high.
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3

Western Blot Analysis of Protein Expression

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RIPA lysis buffer was used to obtain total proteins (40 μg) from certain cells. Then, the proteins were separated by 8% SDS/PAGE gel and transferred onto PVDF membranes (Millipore, Billerica, MA). After membranes blocking, appropriate dilutions of specific primary antibodies were used to incubate the membranes, and the HRP-conjugated secondary antibodies ensured the blots could be detected by the ECL system (Thermo Fisher Scientific, Rochester, NY). Anti-GAPDH (1: 1000, 6c5) antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Anti-ADAR1 (1: 1000, monoclonal, ab126745) antibody, ITGA2 (1: 1000, ab133557), and anti-ADAR1 (1: 1000, polyclonal, ab88574) antibody were purchased from Abcam (Shanghai, China).
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4

Quantification of ADAR1 Protein Levels

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A total of 5–10 × 106 cells were harvested in RIPA buffer for total protein extraction. Overall, 10–20 μg of each sample were loaded onto 10% polyacrylamide gels for gel electrophoresis. Primary antibodies (polyclonal anti-ADAR1 ab88574 1:500, monoclonal anti-ADAR1 ab126745, 1:1000, and anti-actin ab8227, 1:1000, Abcam) were prepared in blocking buffer. Membranes were incubated overnight at 4 °C with primary antibodies, followed by secondary antibody incubation (anti-rabbit HRP or anti-mouse HRP, 1:5000, Cell Signaling Technology; or anti-chicken HRP, 1:5000, Abcam) in blocking buffer for 1 h at room temperature. Blots were developed using enhanced chemiluminescence (Femto Detection kit, Promega) on a Chemidoc digital imaging machine. Representative images out of three independent Western blots are shown in main and supplementary figures, with uncropped images of key blots provided in Supplementary Fig. 5. Nanofluidic experiments were performed with the Nanopro 1000 instrument (Cell Biosciences). ADAR1 was detected using an ADAR1-specific antibody (ab168809, 1:500 Abcam). A β2-microglubulin-specific antibody (β2M; 1:500 Upstate) was used to normalize the amount of loaded protein.
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5

Immunohistochemical Determination of ADAR1-p150

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Human breast formalin fixed paraffin embedded tissue array sections (5μm) on positively charged slides were obtained from US Biomax Inc. (Derwood, MD USA, BC081116d). For immunohistochemistry, sections were stained using a Bond RXm autostainer (Leica, Buffalo Grove, IL USA). Briefly, slides were baked at 65°C for 15min and automated software performed dewaxing, rehydration, antigen retrieval, blocking, primary antibody incubation, post primary antibody incubation, detection (DAB), and counterstaining using Bond reagents (Leica). Samples were then removed from the machine, dehydrated through ethanols and xylenes, mounted and cover-slipped. An antibody specifically recognizing ADAR1-p150 (Abcam ab126745) was diluted 1:100 in Antibody Diluent (Leica). Intensity of p150 was scored on a scale of 0 to 3 (range established by samples with the strongest and weakest staining) by increments of 0.5. Any sample scored >1.0 was considered p150-high.
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6

Western Blot Analysis of RNA-editing Enzymes

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Cells or frozen tissues were lysed in RIPA buffer and proteins (60 μg) were separated on 10–12% SDS/PAGE gel and then transferred onto PVDF membranes (Millipore, Billerica, MA, USA). After blocking, membranes were incubated with appropriate dilutions of specific primary antibodies followed by incubation with HRP-conjugated secondary antibodies and visualization using ECL system (Thermo Fisher Scientific, Rochester, NY, USA). Anti-β-ACTIN (1 : 1000, c4) and anti-AR (1 : 1000, N20) antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Anti-ADAR1 (1 : 1000, monoclonal, ab126745) antibody, anti-ADAR1 (1 : 1000, polyclonal, ab88574), anti-QKI (1 : 1000, ab126742) were purchased from Abcam (Shanghai, China). Anti-ADAR2 (1 : 500, ENT0119) antibody was purchased from Elabscience Biotechnology (Bethesda, MD, USA).
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7

Flow Cytometric Analysis of ADAR1 Expression

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Flow staining was performed in staining media for 30 min on ice in the dark. Cells were blocked using FcR block (Biolegend, San Diego, CA) for 15 min before antibody staining with to a final dilution of 1:25. DAPI solution was added before analysis to exclude dead cell debris. Analysis and sorting was performed on BD Aria Fusion, Aria II or Fortessa. Sorted cells were collected into staining media filled FACS tubes or 1.7mL Eppendorf tubes. The LICs are evaluated by the corresponding cell surface markers (Table S1). For intracellular ADAR1 staining, cells were stained with ethidium monoazide (EMA) for 15 min in the dark and then 15 min under light, followed by cell surface staining. After washing in staining buffer, cells were fixed and permeabilizated with an intracellular buffer set (eBioscience, San Diego, CA) and intracellularly stained with an antibody against ADAR1 (Abcam, ab126745) at 1:100 dilution. Secondary antibody of Alexa 488 or Alexa 647 were used to amplify ADAR1 signals.
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8

ADAR1 Expression in Gastric Cancer

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Human gastric cancer and adjacent gastric mucosa specimens were collected from 38 patients at Shanghai East hospital. Written informed consent was obtained from all participants and study protocol was approved by the ethics committee of Shanghai East Hospital, Tongji Univeristy School of Medicine. After resection, all the samples were snap-frozen in liquid nitrogen and stored at −80°C prior to RNA extraction. Human gastric cancer tissue microarray (ST2091) containing 208 patients’ sample was purchased from Xian Alenabio Company. Among these patients, 64 were women and 144 were men, with an age range between 17 and 84 years old. ADAR1 expression was assessed by immunohistochemical staining using an anti-ADAR1 antibody (ab126745, Abcam) at a dilution of 1:500. The staining results were classified according to the percentage of positive cells and staining intensity: negative (−), slight positive (+), moderate positive (++), or strong positive (+++). To prevent bias from knowledge of clinical data, scoring of staining intensity was conducted in a blinded manner.
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