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10 protocols using goat anti rabbit alexa 488

1

Flow Cytometry and IHC for Immune Cell Profiling

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The following fluorochrome-conjugated anti-mouse monoclonal antibodies were used for flow cytometry: α-CD16/32 (cat. 553141), α-CD8 (APC-Cy7, cat. 561967), α -CD45.2 (PerCP-Cy5.5, cat. 561096, PE-CF594, cat. 565390), α-LFA-1 (BV605, cat. 740340), α-CXCR6 (APC, cat. 151105), α-CXCR3 (BV650, cat. 740630), α -CD69 (PE, cat. 561932). Antibodies were purchased from BD Bioscience with the exception of α-CXCR6 (Nordic Biosite). The following non-conjugated antibodies were used for immunohistochemistry and immunofluorescence: α-CD8 (Nordic Biosite, cat. CST-98941S), α-CXCL16 (Nordic Biosite, cat. bs-1441R), biotinylated goat anti-rabbit (BioNordika, cat. VEC-BA-1000-1.5), and Alexa 488 goat anti-rabbit (Abcam, cat. 150081).
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2

Immunofluorescence Analysis of Guanylate Cyclase

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Enucleated eyes were fixed in 10% formalin for 24 h, embedded in paraffin, and sectioned through the equatorial plane at a 4-μm thickness using a HM340E microtome (Walldorf, Germany). Briefly, sections were post-fixed for 5 min in 70% ethanol, and incubated with blocking solution for 90 min in 5% Bovine serum in 0.1 M PBST. Sections were incubated overnight at room temperature with primary antibody (anti guanylate cyclase alpha 1: Abcam, UK) in blocking solution. The next day, sections were washed for 3 times in 0.1 M PBST and incubated with secondary antibody (Alexa 488 goat anti-rabbit: Abcam, UK) and counterstain solution (DAPI: Sigma, USA) for 1 h. Sections were washed 3 times in 0.1 M PBST solution. The sections were analyzed with a fluorescence microscope (TE2000-U; Nikon, Japan).
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3

Multiplex Immunohistochemistry and Immunofluorescence

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Antibodies used were as follows: anti‐CD3 (1:80 for Immunohistochemistry (IHC), Abcam), anti‐CD4 (1:100 for IHC, Zymed Laboratories, Santiago, USA), anti‐CD8 (1:200 for Immunofluorescence (IF) and IHC, Abcam), anti‐CD20 (1:200 for IF and IHC, Abcam), anti‐ki67 (1:100 for IHC, Zymed Laboratories, Santiago, USA) and anti‐CK19 (1:50 for IHC, Zymed Laboratories, Santiago, USA). Alexa 594 goat antimouse (1:200 for IF, Abcam), Alexa 488 goat anti‐rabbit (1:200 for IF, Abcam), DAPI (Southern Biotech) were used in IF. Ultra View Universal Alkaline Phosphatase Red Detection Kit (VENTANA), Ultra View Universal DAB Detection Kit (VENTANA) and Vector SK‐5300 AP Substrate Kit, Vector SK‐5400 BCIP/NBT (Zymed Laboratories) were used for IHC double staining.
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4

Immunofluorescence Staining of Frozen Tumor Sections

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Frozen OCT-embedded D4M.3A primary tumors were cryosectioned into 5 μm thick sections. Immunostaining of the frozen sections was performed using the BOND RX automated IHC stainer (Leica Biosystems, Wetzlar, Germany). Briefly, slides were incubated with goat serum (10% goat serum in PBS X1 + 0.02% Tween-20) for 30 min to block non-specific binding sites. Slides were then incubated with rabbit anti-mouse Ki67 (1:50 dilution, Novus biologicals, Centennial, CO, USA ), rabbit anti-mouse cleaved caspase 3 (1:30 dilution, Cell Signaling, Danvers, MA, USA), rabbit anti-mouse phospho-MEK (1:50 dilution, Cell Signaling, Danvers, MA, USA) and with rabbit anti-mouse phospho-ERK (1:28 dilution, Novus biologicals, Centennial, CO, USA). After1 h incubation, slides were incubated for an additional 1 h with the secondary antibody goat anti-rabbit Alexa-488 (1:350 dilution, Abcam, Cambridge, UK) followed by Hoechst fluorescent dye (1:5000) for additional 10 min for nuclei counterstained. The tissues stained were then fixed and mounted on a glass microscope slide with a glass coverslip using ProLong™ Gold antifade reagent (Invitrogen). Fluorescence images were captured using a fluorescence microscope (Evos FL Auto, Life Technologies) at 40x magnification.
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5

Quantifying c-Fos Expression in Brain Regions

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Following removal, brains were fixed in 10% buffered formalin acetate for 24 h followed by 30% sucrose for 5 d 50 mm sections of ACC, striatum, and BLA were collected and stained for c-Fos. Staining was performed by incubation for 24 h at 4°C in a primary antibody consisting of 1:2000 rabbit polyclonal to c-Fos (Abcam, Cambridge, MA), 3% normal goat serum (Abcam, Cambridge, MA), and 0.5% Triton-X (Sigma, St. Louis, MO) in PBS, followed by four 5-min washes in PBS. Secondary antibody incubations were 2 h at 20 °C in the 0.5% Triton-X/5% normal goat serum/PBS solution with 1:500 goat anti-rabbit Alexa 488 (Abcam, Cambridge, MA) replaced for the primary antibody, followed by four 5-min washes in PBS. Slides were subsequently mounted and cover-slipped with fluoroshield DAPI mounting medium (Abcam, Cambridge, MA). Slices were visualized using a BZ-X710 microscope (Keyence, Itasca, IL), and analyzed with BZ-X Viewer and analysis software. Images for quantification of c-Fos immunoreactivity were taken with a 20× objective with a 724 mm by 543 mm field of view and converted to cells per millimeter squared. For each region, three images were taken from two or three separate slices from both hemispheres at the same approximate AP coordinate (ACC +2.0 mm; VS +2.0 mm; DS 1.6 mm; BLA-3.0 mm), and final cell counts were based on the averages of the three images.
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6

RNA-FISH Assay for RP11-367G18.1 Variant 2

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The RNA‐FISH probes targeting RP11‐367G18.1 variant 2 were designed using a Stellaris Probe Designer and were purchased from LGC Biosearch Technologies (Table S4). Briefly, cells or tissues were fixed with 4% formaldehyde for 15 min at room temperature, washed, and permeabilized as previously described.18 Samples were incubated in a hybridization solution with RNA‐FISH probes. Hybridization was performed for 4 h at 55°C avoiding light. Samples were washed for three times, blocked with 1% BSA for 1 h, and subsequently incubated with anti‐HIF‐1α (1:100 dilution, abcam) or anti‐H4K16Ac (1:250 dilution, abcam) antibody at 4°C overnight. Then, samples were washed and incubated with secondary antibody solution (1:500 dilution; goat anti‐rabbit Alexa488, abcam) containing a 1:10000 dilution of the DAPI stock solution for 1 h at room temperature. Images were acquired using a Leica TCS SP8 STED microscope and analyzed using MetaMorph software version 7.8.0.0 (Universal Imaging) and Leica Application Suite X (LAS X version 3.5.5.19976) software. RP11‐367G18.1 variant 2 in cells were counted from three independent replicates.
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7

SIRT6 Knockout MEF Protocol

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The human embryonic Kidney (HEK)293T cell line was obtained from American Type Culture Collection. SIRT6 knock out (KO) MEFs were obtained as a kind gift from Prof. Haim Cohen, Bar Ilan University. All cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 mM L-Glutamine (all purchased from Biological Industries, Israel) and maintained in a 37 °C incubator with 5% CO2. Primary antibodies against SIRT6, Histone 3, β-actin, H3K9ac, H3K56Ac, GLUT1 and secondary antibodies (goat anti mouse HRP, goat anti rabbit HRP and goat anti rabbit Alexa488) were all purchased from Abcam. Antibody against Flag used for SIRT6-FLAG was purchased from Sigma.
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8

Immunofluorescent Staining of Lung Tissue and Cells

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Immunofluorescent staining was performed on LAM patient lung tissue [18 (link)] or 621-102 TSC2-null cells. Lung tissue slides (10 μm) were deparaffinized using standard protocols for immunohistochemistry. 621-102 Tsc2-null cells were grown on glass coverslips and treated as for the 6-well immunoblot procedure, then fixed with 4% PFA, washed with PBS, and blocked with 1% BSA, 30 min before immunostaining. For antigen retrieval (peIF4E and IgG), slides were boiled 20 min in citrate buffer with 0.05% Tween 20 (pH 6.0) and then blocked for 20 min with 1% BSA. All primary antibodies were used at a 1:250 dilution. The cells were incubated in primary antibodies, namely pS6 (Ser235/236) or α-SMA (Cell Signaling, Danvers, MA, USA) or peIF4E (Ser209) Abcam (76256), for 1 h at RT. Lung tissue slides were incubated in primary antibody, overnight at 4 °C. Secondary antibodies were goat anti-mouse Alexa-594 (Abcam, #150116), goat anti-rabbit Alexa-594 (Abcam, #150080), and goat anti-rabbit Alexa-488 (Abcam, #150077). All secondary antibodies were used at 1:250 dilution. Cell or tissue slides were incubated with appropriate secondary antibody for 1 h at RT, then stained with DAPI (10 mM) (Sigma-Aldrich Gaithersburg, MA, USA) for 10 min, washed, and embedded in 80% glycerol. Samples were analyzed and pictures were taken with a Nikon Eclipse 2000 microscope (Nikon, Melville, NY, USA).
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9

Immunofluorescence Analysis of HCT116 Cells

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HCT116 (5 × 104 cells/well) were seeded on sterilized coverslips contained in six-well plates, which were incubated at 37 °C with 5% CO2 for 24 h. The cancer cells were treated with various conditions, including a control (non-treated cells), conditioned media, and 20 μM H2O2 as a positive control, and incubated at 37 °C with 5% CO2 for 48 h. The treated cells were fixed with 4% paraformaldehyde and washed with PBS. The cells were permeabilized with 0.25% Triton X-100 (Sigma-Aldrich, USA), and then primary antibody (mouse anti-human E-cadherin (1:1000) and rabbit anti-human TrxR-1 (1:1000) (Abcam, USA)) were added. The cells were incubated at 4 °C overnight, and they were then washed with PBS in triplicate. The secondary antibody (goat anti-mouse Alexa488, goat anti-rabbit Alexa488 (1:1000) (Abcam, USA)) was added and incubated for 90 min at room temperature. The protein expression was captured under a fluorescence microscope [22 (link)].
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10

Immunofluorescence Staining of Laminin 5 and Type IV Collagen

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Rabbit polyclonal antibodies (laminin 5 and type IV collagen), mouse monoclonal antibodies (β4 integrin), Phalloidin-iFluor 488 reagent, goat anti-rabbit Alexa 488, and goat anti-mouse Alexa 647 were obtained from Abcam (Tokyo, Japan). Rabbit polyclonal antibodies to plectin were purchased from Novus (Littleton, CO, USA). Human recombinant IL-1β and alpha-minimum essential medium (αMEM) were purchased from Wako (Tokyo, Japan). Fetal calf serum (FCS), penicillin and streptomycin, TrypLE Express, and TRIzol Reagent were purchased from Invitrogen (Carlsbad, CA, USA). The PrimeScript RT reagent kit and SYBR Premix Ex Taq II were purchased from Takara Bio (Tokyo, Japan). Bovine serum albumin (BSA), complete protease inhibitor cocktail, and phenylmethylsulfonyl fluoride were purchased from Sigma Aldrich Japan (Tokyo, Japan). Anti-mouse IgG (whole molecule) peroxidase antibody produced in rabbit, anti-rabbit IgG (whole molecule) peroxidase antibody produced in goat, and ECL Prime Western Blotting Detection Reagents were purchased from GE Healthcare (Buckinghamshire, UK). All chemicals used were of analytical grade.
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