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9 protocols using ab109429

1

Western Blotting and Immunoprecipitation Assay

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For western blotting, total protein was extracted from the cultured cells using RIPA lysis and extraction buffer (Thermo Fisher Scientific) and separated on a 12% SDS–PAGE polyacrylamide gel.
The primary antibodies used in this study were IFITM3 (1:1,000 dilution, ab109429, Abcam), TRAF6 (1:100, sc-8409, Santa Cruz Biotechnology), IRAK1 (1:200, ab238, Abcam), p-ERK (1:800, #4376, Cell Signaling Technology), c-Fos (1:20,#4384, Cell Signaling Technology), c-Myc (1:100, 395R16, Cell Marque), and survivin (1:50, ab76424, Abcam). β-actin served as the internal control.
For the immunoprecipitation (IP) assay, the protein extracts from cultured cells were prepared using IP lysis buffer (50 mM Tris–Cl [pH 7.4], 0.5% NP-40, 150 mM NaCl, 1.5 mM MgCl2, 2 mM DTT, 2 mM EGTA) supplemented with protease/phosphatase inhibitor mixtures (Roche), then centrifuged (12,000 g for 10 minutes at 4℃). The IP assay was performed as previously described [18 (link)].
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2

Comprehensive Stem Cell Marker Analysis

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The following primary antibodies were used in the study including anti-CXCR4 (ab124824, AbCam), anti-TRAIL (AF1121, R&D), anti-c-Kit (AF1356, Novus Biological), anti-CD47 (ab175388, Abcam), anti-Fasl (ab15285, Abcam), anti-PDL1 (NBP1-76769, Novus Biological), anti-CD4 (ab183685, Abcam), anti-SSEA1 (ab16285, Abcam), anti-Oct4 (ab184665, Abcam), anti-Sox2 (MAB2018R-100, R&D), anti-Nanos3 (ab70001, Abcam), anti-Ifitm3 (ab109429, Abcam), anti-Stellar (Invitrogen, PA5-34601), anti-PRDM14 (ab187881, Abcam), anti-Vasa (ab27591, Abcam), anti-DAZL (NB100-2437, Novus biologicals), anti-SMAD2 (ab33875, Abcam).
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3

Western Blotting of Protein Samples

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Protein samples were subjected to SDS-PAGE gels (Bio-Rad), electrophoresed, transferred to Immobilon-P PVDF (Millipore) or Immobilon-FL PVDF membranes (Millipore) and Western blotting (WB). The following primary antibodies were used: PS1-NTF (a kind gift of Merck Research Laboratories); PS1-CTF (MAB5232, Millipore); PS2-CTF (1987–1, Epitomics); nicastrin was generated in our laboratory; Aph-1aL (38–3600, Invitrogen); Pen-2 (ab18189, Abcam); human IFITM3 (anti-Fragilis, ab109429, Abcam); mouse IFITM3 (anti-Fragilis, ab15592, Abcam); APP (22C11, MAB348, Millipore); SPP (317) was generated in our laboratory; cleaved Notch1 (Val1744), Cell Signaling Technology and SM320, generated in our lab); c-myc (9E10, Roche Life Science); N-cadherin (D4R1H, #13116, Cell Signaling Technology); Rab7 (B-3, sc-376362, Santa Cruz Biotechnology); EEA1 (Ab2900, Abcam); β-actin (C4, sc-47778, Santa Cruz Biotechnology); β-tubulin III (T8578, Sigma-Aldrich); tubulin (ab56676, Abcam). HRP-conjugated anti-rabbit and mouse secondary antibodies (NA9340V, NXA931V, GE Healthcare) for ECL substrate (Pierce) and IRDye 800CW goat anti-rabbit IgG (H+L) or anti-mouse IgG (H+L) secondary antibodies (925–32211, 925–32210, LI-COR) for Odyssey CLx Imaging (LI-COR) were used. For quantification, ImageJ and Image Studio Lite (LI-COR) were used, respectively (for source gels see Supplementary Figure 1).
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4

Western Blot Analysis of Protein Expression

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Total protein was extracted from ARPE‐19 cells using lysis (Beyotime, Shanghai, China). Above protein was separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS‐PAGE; Invitrogen, Carlsbad, CA, USA) and transferred onto polyvinylidene fluoride (PVDF) membrane (Invitrogen, USA). Afterwards, the membrane was incubated with primary antibodies against FSTL1 (1/1,000; ab223287; Abcam, USA), CHRDL1 (1/1,000; ab103369; Abcam, USA), IFITM3 (1/1,000; ab109429; Abcam, USA), and GAPDH (1/1,000; ab8245; Abcam, USA), followed by being incubation with horseradish peroxidase (HRP)‐conjugated goat anti‐rabbit IgG secondary antibodies (1/10,000; ab7090; Abcam, USA). The protein bands were visualized using enhanced chemiluminescent (ECL) kit.
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5

Western Blotting of Protein Samples

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Protein samples were subjected to SDS-PAGE gels (Bio-Rad), electrophoresed, transferred to Immobilon-P PVDF (Millipore) or Immobilon-FL PVDF membranes (Millipore) and Western blotting (WB). The following primary antibodies were used: PS1-NTF (a kind gift of Merck Research Laboratories); PS1-CTF (MAB5232, Millipore); PS2-CTF (1987–1, Epitomics); nicastrin was generated in our laboratory; Aph-1aL (38–3600, Invitrogen); Pen-2 (ab18189, Abcam); human IFITM3 (anti-Fragilis, ab109429, Abcam); mouse IFITM3 (anti-Fragilis, ab15592, Abcam); APP (22C11, MAB348, Millipore); SPP (317) was generated in our laboratory; cleaved Notch1 (Val1744), Cell Signaling Technology and SM320, generated in our lab); c-myc (9E10, Roche Life Science); N-cadherin (D4R1H, #13116, Cell Signaling Technology); Rab7 (B-3, sc-376362, Santa Cruz Biotechnology); EEA1 (Ab2900, Abcam); β-actin (C4, sc-47778, Santa Cruz Biotechnology); β-tubulin III (T8578, Sigma-Aldrich); tubulin (ab56676, Abcam). HRP-conjugated anti-rabbit and mouse secondary antibodies (NA9340V, NXA931V, GE Healthcare) for ECL substrate (Pierce) and IRDye 800CW goat anti-rabbit IgG (H+L) or anti-mouse IgG (H+L) secondary antibodies (925–32211, 925–32210, LI-COR) for Odyssey CLx Imaging (LI-COR) were used. For quantification, ImageJ and Image Studio Lite (LI-COR) were used, respectively (for source gels see Supplementary Figure 1).
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6

Western Blot Analysis of Protein Expression

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After 48 h of transfection, cells were washed in cold PBS for three times and then lysed on ice with whole cell lysate for 10 min, with the concentration of the product sequentially determined using the BCA protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA). Subsequently, 30 μg of the total proteins was separated by polyacrylamide gel electrophoresis (PAGE) and then transferred onto polyvinylidene fluoride (PVDF) membranes (Amersham, USA). After being blocked in 5% skim milk at room temperature for 1 h, the membranes were incubated overnight at 4°C with primary antibodies, followed by horseradish peroxidase- (HRP-) labeled secondary antibody goat anti-rabbit IgG H&L (ab6721, 1 : 2000, Abcam, Cambridge, UK) at room temperature for 1 h. Primary antibodies included KLF4 rabbit polyclonal antibody (ab215036, 1 : 1000, Abcam, Cambridge, UK), IFITM3 rabbit polyclonal antibody (ab109429, 1 : 1000, Abcam, Cambridge, UK), and GAPDH rabbit polyclonal antibody (ab9485, 1 : 2500, Abcam, Cambridge, UK). PBST (PBS buffer containing 0.1% Tween-20) was used to wash the membranes after each reaction. An optical luminometer (GE, USA) was employed to visualize the protein bands.
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7

Western Blot Analysis of Cell Signaling Proteins

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All proteins were extracted with radioimmunoprecipitation assay (RIPA) buffer and a protease inhibitor in a 100:1 ratio. Samples were separated by polyacrylamide gel electrophoresis (SDS-PAGE) and transferred into PVDC membrane (Millipore, Massachusetts, USA) for 2h. Then, the membranes were incubated with primary antibody at 4 °C overnight. Tris-HCl solution + Tween-20 (TBST) was used to wash the membranes three times for 10 mins. Subsequently, they were incubated with horseradish peroxidase-conjugated secondary antibody for 1 hr at room temperature. Finally, the blots were detected with enhanced chemiluminescence, and band intensities were measured with Quantity-One software (Bio-Rad, Hercules, CA, USA). The primary antibodies against IFITM3 (ab109429), Bax (ab32503), Bcl2 (ab32124), tubulin (ab15246), GAPDH (ab8245), N-cadherin (ab76011), and E-cadherin (ab40772) were purchased from Abcam. Western blotting was used to calculate the amount of expressed protein.
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8

Comprehensive Gene and Protein Expression Analysis

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All RNA was extracted with TRIzol reagant, then reverse transcribed into cDNA using a reverse transcription kit (Takara, Tokyo, Japan), and then qRT-PCR was run using a PrimeScript RT kit (Takara). All proteins were extracted with RIPA lysate and protease inhibitor in a 100: 1 mixed liquid. The relative expression of each gene was normalized using the expression of housekeeping genes and calculated using the 2 -ΔCt method. The RiboBio-designed primers were TUG1, IFITM3, beta-actin. miR-29a and U6, The primary antibodies,IFITM3 (Ab109429), Bax (ab32503), Bcl2 (ab32124), tubulin (ab15246), MMP19 (ab53146), VEGFA (ab52917), N-cadherin (ab76011) , and E-cadherin (ab40772) , All antibodies were purchased from Abcam. Western blotting was used to calculate the amount of protein expressed.
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9

Multiomics Profiling of RNA and Protein

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Total RNA was extracted with TRIzol reagent, and subsequently reverse transcribed into cDNA using a reverse transcription kit (Takara; Tokyo, Japan). Next, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) was run using a PrimeScript RT kit (Takara). All proteins were extracted with radioimmunoprecipitation assay (RIPA) buffer and a protease inhibitor in a 100:1 ratio. The relative expression of each gene was normalized against the expression of housekeeping genes and calculated using the 2 -ΔCt method. The RiboBiodesigned primers were against TUG1, IFITM3, beta-actin, miR-29a, and U6, The primary antibodies against IFITM3 (Ab109429), Bax (ab32503), Bcl2 (ab32124), tubulin (ab15246), N-cadherin (ab76011) , and E-cadherin (ab40772) were purchased from Abcam. Western blotting was used to calculate the amount of expressed protein.
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