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15 protocols using h9627

1

Transwell Invasion and Migration Assays

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The transwell invasion assay was performed as previously described [39 (link)]. Briefly, cell culture inserts (6.5 mm, Falcon insert, 8-μm pore size; Becton Dickinson, Franklin Lakes, NJ, USA) were pre-coated with Matrigel (#356231, CORNING) diluted 1:20 in serum-free DMEM/F12 medium. Cells were accutased and resuspended in serum-free DMEM/F12 medium in the upper chamber (50,000 cells in 250 μL) and 800 μL of NSC medium containing growth factors was added to the lower chamber. After a 72-h incubation, cells remaining on the upper surface of the filter were removed, and cells that had invaded through the Matrigel to the lower surface were fixed with ethanol, stained with hematoxylin ((H9627, Sigma-Aldrich), and photographed. Data represent the mean of the number of cells counted in five random low-power fields (LPFs).
For transwell migration assays, NIH3T3 cells were cultured in DMEM/F12 media supplemented with 10% (v/v) FBS for 24 h, and the media was then used as conditioned media to attract cells through cell culture inserts precoated with gelatin (G1393, Sigma-Aldrich). After a 48-h incubation, cells that had migrated to the lower surface were fixed with ethanol, stained with hematoxylin (H9627, Sigma-Aldrich), and photographed. Data represent the mean of the number of cells counted in five random high-power fields (HPFs).
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2

Hematoxylin and Eosin Staining

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Formalin-fixed paraffin-embeded sections (4 µm) of whole emrbyos were stained with hematoxylin (Sigma, H9627) for 40 s and with eosin (Sigma-Aldrich, HT110116) for 30 s. The tissue sections were mounted with Permount mounting medium (Fisher Scientific, SP15-100). All procedures were conducted by Molecular Pathology Core, University of Florida. Images were generated with a Zeiss Axio Imager 2 microscope (Carl Zeiss, Inc., Thornwood, NY).
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3

Histological Analysis of Adipose Tissue

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Formalin-fixed paraffin-embeded sections (4 μm) of the spleen, lymph node, and inguinal WAT were stained with hematoxylin (Sigma, H9627) for 40 s and with eosin (Sigma-Aldrich, HT110116) for 30 s. The tissue sections were mounted with Permount mounting medium (Fisher Scientific, SP15–100). All procedures were conducted by Molecular Pathology Core, University of Florida. Images were generated with a Zeiss Axio Imager 2 microscope (Carl Zeiss, Inc, Thornwood, NY). For adipose tissue analysis, adipocytes were counted for four nonoverlapping fields of view for three Dnmt3b+/+ and Dnmt3bCI/CI mice. Cells with single large lipid droplet were considered white adipocytes and cells with multiple small droplets—brown.
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4

Periodic Acid-Schiff Staining of Mouse Testes

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Periodic acid‐Schiff staining was performed as previously reported.30 After organ extraction, fix mouse testes and epididymis in Bouin's fixative solution (PH0976, Phygene, China) for 24 h at room temperature and then put in 70% ethanol, then embed testis and epididymis in paraffin (76242, Sigma–Aldrich, USA). Paraffin‐embedded mouse testis and epididymis tissues were cut into 5 μm thick testis slices and mount on normal glass slides. The slices were deparaffinized in xylene (LM1330‐20–7, LMAI Bio, China), hydrated in gradient alcohol (100%, 95%, 80% and 70%), immersed in iodic acid oxidation solution (77310, Sigma–Aldrich, USA) for 5 min and in Schiff reagent (1.09033, Sigma–Aldrich, USA) for 15 min and counterstained with haematoxylin (H9627, Sigma–Aldrich, USA) for 3 min. Wash slides in running distilled water for 15 min, then dehydrate in alcohol and clear in xylene. The sections were photographed with an optical microscope (Leica, Germany).
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5

Cardiomyocyte Cross-Sectional Area Measurement

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Hearts were removed from the chest cavity and weighed on a Mettler Toledo, AT201 analytical scale. The skeletal muscle of the lower hindlimbs was dissected out, and the length of the left tibia was measured. Heart sections, as described above, were stained with haematoxylin (Sigma‐Aldrich, H9627) and eosin (Sigma‐Aldrich, E4009), and was carried out by the Department of Pathology at the Cincinnati Children's Hospital Medical Center. Sections were examined for sarcolemma staining labelled with wheat germ agglutinin (WGA, Invitrogen), according to manufacturer's instruction. Cardiomyocyte cross‐sectional area was measured using ImageJ Software.4, 8
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6

Histological Analysis of Rat Hippocampus

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The paraffin-embedded hippocampus tissues (collected 9 days after surgery) were dewaxed, rehydrated, and stained with hematoxylin (Sigma, H9627) for 5 min. After washing for 2 min with running water, the slices were incubated with 1% eosin (Sinopharm Group, 71014544) for 5 min and then placed into purified water for 30 s. Subsequently, the sections were placed in graded ethanol for hydration and dimethylbenzene for vitrification. After mounting with neutral balsam, the results were observed and photographed under a microscope (Olympus, IX51).
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7

Histological Characterization of Engineered Bladder

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Regular hematoxylin (H9627, Sigma-Aldrich, Shanghai, China) and eosin (861006, Sigma-Aldrich, Shanghai, China,) (H&E) and Masson’s trichrome (1.00485, Sigma-Aldrich) staining were performed to analyse whether tissue structures such as urothelium layers, muscle bundles, and blood vessels were present in the newly-constructed bladder. Cytokeratin 13 (CK13; sc-53265, Santa Cruz, CA, USA, 1:100) antibodies were used to identify the reconstructed urothelial cells, while α-smooth muscle (SMA; sc-53142, Santa Cruz, CA, USA, 1:100) antibodies were used to identify the smooth muscle cells (SMCs) and blood vessels.
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8

Immunohistochemical Analysis of USP22

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The USP22 immunohistochemical analysis was performed based on previously published methods. 15 Briefly, the tissues were post-fixed with formalin, embedded in paraffin and cut into 4-micrometer sections. Subsequently, the sections were deparaffinized in xylene, rehydrated in ethanol solutions of descending concentration and submerged in ethylenediaminetetraacetic acid (EDTA; pH 8). Antigenicity was retrieved by autoclaving the sections at 121°C for 5 min. After quenching the endogenous peroxidase in 3% H 2 O 2 for 15 min and washing with phosphatebuffered saline (PBS), the sections were incubated with a primary antibody against USP22 (1:200, ab4812; Abcam, Cambridge, UK) overnight at 4°C. A 30-minute peroxidaseconjugated streptavidin incubation and diaminobenzidine incubation were subsequently performed, followed by counterstaining with a commercially available hematoxylin to stain the nuclei (H9627; Sigma-Aldrich, St. Louis, USA).
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9

Histological Analysis of Small Intestine

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After sacrifice, the small intestine was removed and immediately fixed in 10% (w/v) formalin (Sigma Aldrich, HT501128) for 24 h at 4°C. The tissue was then immersed in a series of ethanol solutions of increasing concentrations until 100%. Next, the ethanol was gradually replaced with xylene, which is then replaced by paraffin. Paraffin embedded tissue was cut into 3.5–4.5 μm thin sections using the RM2255 microtome (Leica Biosystems). Paraffin embedded tissue sections were stained for 2–5 min in haematoxylin (Sigma Aldrich, H9627). The cytoplasm was counterstained with 1% (v/v) eosin solution for 2 min (Sigma Aldrich, HT110216). Stained slides were then dehydrated and embedded in Roti-Histo-Kit mounting medium (Carl Roth, 6638.1) and examined with a Zeiss AxioImager.Z1 apotome microscope (Zeiss) and the AxioVision Rel 4.9 software (Zeiss).
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10

Immunohistochemical Analysis of Autophagy Markers

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Mice ovaries were fixed in buffered paraformaldehyde (4%), embedded in paraffin, sectioned to approximately 5 µm, and mounted on glass slides. The ovarian sections were deparafinized in xylene, rehydrated, and retrieved by microwave heating with buffer of citrate ([R&D Systems, 3161500G], 0.05% Tween-20 [Sigma-Aldrich, P1379], pH 6.0) for 0.5 h. Endogenous peroxidase activity was quenched by incubation with 3% H2O2 (Sigma-Aldrich, 216763-100 ml) for 10 min. After blocking in 1% BSA for 1 h, sections were immunostained with rabbit antibodies against MAP1LC3B (Sigma-Aldrich, L7543) or SQSTM1 (Abcam, ab101266), and corresponding secondary antibodies with biotin labeling. The immunoreactive signals were visualized using the 3, 3'-diaminobenzidine chromogen solution (Sigma-Aldrich, D8001). The nuclei were counterstained in hematoxylin (Sigma-Aldrich, H9627) prior to dehydration and coverslip placement.
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