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18 protocols using ab16700

1

Isolation of Primary Endometrial Stromal Cells

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Primary endometrial stromal cells from women with adenomyosis were isolated according to a protocol with minor modifications (25 (link)). Briefly, endometrial tissues were homogenized and treated in sequential steps of pancreatin-0.05% trypsin enzymatic solution, collagenase 4 (0.1 U/ml), and DNase I (16 μg/ml) solution in Ca2+/Mg2+-free PBS (Gibco® Thermo Fisher Scientific, Sweden) and incubated for 30 minutes at each step. Enzymatically digested cell suspensions were filtered through a 100 µM cell strainer to remove larger debris while collecting the flowthrough containing both the epithelial and stromal fractions. Later, these cell suspensions were adherent and expanded in vitro for two-three generations, frozen, and stored in liquid nitrogen for the following experiments. The isolated ESC was cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F-12 (Gibco, USA) containing 10% fetal bovine serum (Gibco, USA) and 1% Penicillin-Streptomycin solutions (Gibco, USA). When the cells reached 80-90% confluency, the cells were passaged, and the medium was changed every 2-3 days. Cyto-immunofluorescent staining for vimentin (Abcam, ab16700) and pan-cytokeratin (Abcam, ab86734) was applied for confirmation of stromal cell phenotype.
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2

Protein Expression and Western Blot Analysis

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Proteins were extracted in RIPA buffer supplemented with complete, EDTA-free protease inhibitor cocktail (Roche Diagnostics) and phosphatase inhibitor cocktail 3 (Sigma). Proteins were separated by SDS-PAGE and blotted onto a nitrocellulose membrane. The following antibodies were used: β-actin (dil. 1/5000, A5441, Sigma), phospho-Smad2 (ser465/467) (dil. 1/1000, #3108, Cell Signalling), Smad2 (dil. 1/1000, #3102, Cell Signalling), E-cadherin (dil. 1/10000, BD610181, BD Pharmingen), α-smooth muscle actin (dil. 1/1000, A5228, Sigma) and vimentin (dil. 1/1000, Ab16700, Abcam). Uncropped blots are presented in the Source data file.
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3

Identification of OSCC Cell Lines

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When cells reached about 80% confluence, they were treated with trypsin and removed from the third row of wells to a new 6-well plate. After repeated adherence and culture, the relatively purified OSCC cells were obtained.
The identification of OSCC cells was performed. In short, immunohistochemistry was applied to stain keratin, Vimentin, CSC-related identification, and isolation markers BMI1, ALDH1, and CD44. Slides containing OSCC cells were prepared on the strictly sterilized coverslips. The staining was performed following the manufacturer’s instructions of the streptavidin peroxidase (SP) immunohistochemistry kit, with polyclonal antibodies purchased from Abcam (Cambridge, UK) used as the primary antibodies: keratin (1:1000, ab155478), Vimentin (1:1000, ab16700), BMI1 (1:1000, ab155478), ALDH1 (1:1000, ab155478), and CD44 (1:1000, ab155478). Positive and negative controls were prepared during staining. Known positive cell slides were used as the positive control, while PBS was used to replace the primary antibody as the negative control (NC). The cytoplasm and/or cell membrane showing tan-stained particles was considered positive.
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4

Isolation and Culture of Ligamentum Flavum Cells

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According to our previously described method [4 (link)], LF cells were isolated and cultured from the LF tissues of patients with LSCS or LDH. Briefly, the obtained LF samples were cut into small pieces and digested for 2 h at 37 °C using Dulbecco’s modified Eagle’s medium (DMEM, Gibco) with 0.2% type I collagenase (Gibco), then seeded on to cell culture dish and incubated with DMEM containing 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (Invitrogen). The isolated cells were observed for fibroblast morphology and identified the expression of specific markers [collagen I (1:100, #72026, Cell Signaling Technology) and Vimentin (1:500, ab16700, Abcam)] by immunofluorescence staining. Subsequent experiments were conducted using cells from the third passage to forth passage of LF cells.
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5

Antibody and Staining Protocol for Cellular Imaging

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Rabbit anti-vimentin antibody (ab16700), rabbit anti-tubulin (ab18251), mouse anti-LAMP1 (ab25630) were from (Abcam, Cambridge, UK). Mouse anti-tubulin (T5168, Sigma-Aldrich), rabbit anti-LC3 (0260–100 LC3-2G6, Nanotools, Teningen, Germany), rpS6 (2317) and phosphorylated rpS6 (p-rpS6 S235/236, 4856) were from (New England Biolabs, Herts, UK). Secondary antibodies for immunostaining: anti-rabbit FITC and anti-rabbit TRIC were from (Sigma-Aldrich), anti-rabbit Alexa Fluor 647 (A21246, ThermoFisher, Paisley, UK), anti-rabbit Alexa Fluor 488 (A11034, Invitrogen), anti-mouse Alexa Fluor 568 (A11004, Invitrogen,). Actin staining was performed using Alexa Fluor 594 Phalloidin (A12381, Invitrogen,) or Alexa Fluor 488 Phalloidin (A12379, Invitrogen,). LysoTracker Red (L7528, ThermoFisher) was used to visualise lysosomes in live cell imaging. Secondary antibodies for western immunoblotting: goat anti-rabbit HRP (P0448, Dako, Santa Clara. USA) and goat anti-mouse HRP (P0447, Dako).
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6

Immunofluorescence Analysis of EMT and Fibroblast Markers

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For immunofluorescence analysis, the monocultures and co-culturing cells were seeded on 35 mm2 glass-bottom dishes covered with type-1 rat tail collagen in a growth medium. After 5 days of culturing, the expression of EMT markers and fibroblast-activated proteins was assessed by an immunocytochemical method using antibodies to E-cadherin (ab15148, Abcam, Cambridge, MA, USA), vimentin (ab16700, Abcam, Cambridge, MA, USA), FAP (ab28244, Abcam, Cambridge, MA, USA), αSMA (ab5694, Abcam, Cambridge, MA, USA), EpCam (ab20160, Abcam, Cambridge, MA, USA), and secondary antibodies conjugated with a fluorescent label, either Fluorescein isothiocyanate (FITC; ab6825, Abcam, Cambridge, MA, USA) or Alexa (ab6825, Abcam, Cambridge, MA, USA). Staining was performed according to the antibody manufacturer’s protocols, while the fluorescent dye DAPI was used for staining the nuclei. Fluorescence was recorded using a Leica DMIL fluorescence microscope (Leica, Wetzlar, Germany) equipped with filters: A4 UV BP 360/40 400 BP 470/40 for DAPI, CFP ET YFP ET (Ex: BP 500/20, Em: BP 535/30) for FITC and TX2 green BP 560/40 595 BP 645/75 for Alexa.
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7

Tumor Characterization by Flow Cytometry

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Tumor were harvested from control or treated mice, and digested with collagenase IV (Life Technologies), passed through a 70 µm followed by 40 µm cell strainers (BD Falcon) and washed with PBS. Red blood cells (RBCs) were lysed using RBL (RBC Lysing Buffer, Bio Legend). Single cells suspensions were labelled according to standard procedures. Cells were stained with rabbit anti-Vimentin (1:200, Abcam, ab16700), mouse anti-E-cadherin (1:200, Abcam, ab76055), rabbit anti-Sox9 (1:200, Abcam, ab185966) and mouse anti-Sox2 (1:200, Cell Signaling Technology, L1D6A2).
The gating strategy for viable singlets is shown in Supplementary Figure 3a.
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8

Immunohistochemical Analysis of Vimentin Expression

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Mammary tumors and major organs were fixed in 10% formalin overnight and embedded in paraffin. Sections were cut and stained with hematoxylin and eosin for histologic analysis. Immunohistochemistry was performed as previously described [19 (link)], using a 1:200 dilution of an anti-vimentin antibody (ab16700, Abcam, Toronto, ON, Canada). Tissue sections were scanned using a Motic Easyscan digital slide scanner (Motic, Richmond, BC, Canada). Vimentin-stained sections were analyzed using the positive cell detection feature of the QuPath software v0.4.3 [20 (link)]. This software determines the percentage of vimentin-positive cells within the area of the image.
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9

Immunohistochemical Analysis of EMT Markers

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Specimens were serially sectioned (4 μm), deparaffinized, hydrated, and treated with 3% H
2O
2 to block endogenous peroxidase activity. After antigen retrieval in sodium citrate buffer (pH 9.0), sections were incubated overnight at 4°C with diluted primary antibodies as follows: anti-BRCC3 (ab62075, 2.5 μg/mL; Abcam), anti-ZEB1 (ab81972, 10 μg/mL; Abcam), anti-E-cadherin (ab227639, 1:100; Abcam), or anti-vimentin (ab16700, 1:200; Abcam). Then sections were incubated for 20 min with horseradish peroxidase (HRP)-labelled Goat anti-Rabbit IgG (ab205718, 1:2000; Abcam) or HRP-labeled Donkey anti-Goat IgG (A0181, 1:1000; Beyotime). Finally, sections were developed with DAB for 2 min, counterstained with hematoxylin for 1 min, and examined under a microscope after sealing
[21] (link). PBS was used instead of the primary antibody as a negative control.
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10

Immunofluorescence Imaging of Vimentin and E-cadherin

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Stably transfected cells were fixed in 4% methanol for 5 min, penetrated in 0.1% Triton X-100 (Sangon Biotech), and incubated with anti-Vimentin (1 : 1,000, ab16700, Abcam Inc., Cambridge, MA, USA) and anti-E-cadherin (1 : 100, ab194982, Abcam) at 20°C for 1 h and then with fluorescein isothiocyanate-labeled secondary antibody (1 : 5,000, ab150088, Abcam) at 37°C for 1 h. The slides were then sealed with antifluorescence quenching Vectashield (Vector Laboratories Inc., Burlingame, CA, USA). The nuclei were counterstained with 4′, 6-diamidino-2-phenylindole (Solarbio Science & Technology Co., Ltd., Beijing, China). All cells were examined using a confocal imaging system Zeiss LSM 510 (Zeiss Inc, AG, Oberkochen, Germany).
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