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11 protocols using ab50917

1

Subcutaneous Tumor Xenograft Model

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18 nude mice were purchased from Beijing laboratory animal research center. Three mice were injected subcutaneously with HK1 cells. When the tumor diameter was 5 mm, the tumor was removed and cut into 1–2 mm3 slices, which were further inoculated into the subcutaneous tissues of another 15 mice. The 15 mice were randomly divided into three groups: control group, circRNA CDR1as siRNA group, and miR-7-5p mimic group. Mice in each group were injected with the corresponding reagent every 3 days, and tumor volume was measured. Tumor tissue was removed and weighed after 30 days. The study was approved by the laboratory animal ethics committee of the People’s Hospital of Ganzhou. As described in the literature [22 ], the immunohistochemical staining was performed on the tumor tissue, and the tissue sections were co-incubated with E2F3 antibody (ab50917, 1:100, Abcam).
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2

Western Blot Antibody Reference

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Western blot experiments were performed according to the instruction of our previous studies (19 (link)). The information of antibodies used in this study was given as followings: DDX11 (ab230017, Abcam), E2F1 (#3742, cell signaling technology), E2F2 (#ab138515, Abcam), E2F3 (#ab50917, Abcam), EZH2 (#5246, cell signaling technology), p21 (#2947, cell signaling technology), p53 (#2524, cell signaling technology), phosphorylated Rb (#8147, cell signaling technology), cyclin E (#4136, cell signaling technology), cyclin D1 (#55506, cell signaling technology), MDM2 (#86934, cell signaling technology), β-actin (#3700, cell signaling technology).
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3

miRNA Target Analysis and Validation

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Predicted targets for miRNAs and their target sites were analyzed using TargetScan [31 ], and miRanda [31 ]. For reporter assays, HEK293T cells were transiently transfected with pmirGLO Dual-Luciferase miRNA target expression vectors with wild-type or mutant target sequence together with miRNA mimics/inhibitor and mimics/inhibitor control. Cell extracts were prepared 48 h after transfection, and the ratio of Renilla to firefly luciferase was measured with the Dual-Luciferase Reporter Assay System (Promega Corp, Madison, WI, USA). Anti-E2F3 (ab50917, Abcam), anti-AXL (ab37861, Abcam) and anti-GAPDH (Cell signaling, Danvers, MA, USA) rabbit polyclonal antibodies were used in Western blotting and the protocols was described previously [32 (link)].
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4

HOXB9 Expression Plasmid Construction

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Flag-HOXB9 expression plasmid was constructed by subcloning the HOXB9 full-length complementary DNA (cDNA) fragments into 3× flag vector. All constructs were confirmed by DNA sequencing. The following antibodies were used: HOXB9 (Santa Cruz: sc-398500 and sc-133671) and E2F3 (Abcam: ab50917).
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5

Quantification of E2F3 and Ki-67 in Colorectal Tumors

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The tumors from the nude mice were fixed in 10% paraformaldehyde at 4°C for 12 h, and then dehydrated in different concentrations of ethanol, permeabilized using xylene and embedded in paraffin. The paraffin-embedded tumor tissues were then sliced (0.5 µm), rehydrated, and were stained with HE at 4°C for 10 min and sealed with neutral gum. For IHC assessment of E2F3 and Ki-67 in colorectal tumor tissues from the nude mice, the DAKO Envision system (Dako; Agilent Technologies, Inc.) was used. Briefly, after paraffin-embedded sections of tumor tissues were heated at 60°C, the sections were incubated with primary antibodies against E2F3 (1:200; cat. no. ab50917; Abcam) and Ki-67 (1:1,000; cat. no. ab279653; Abcam) overnight at 4°C. Then, the sections were incubated with biotin-labeled secondary antibodies (1:1,000; cat. no. ab205718; Abcam) at 37°C for 20 min. Under a light microscope, IHC staining scores for E2F3 were obtained by multiplying the intensity (0, negative; 1, low; 2, medium; and 3, high) with the extent of staining (0, 0%; 1, 0-10%; 2, 10-50%; 3, 50-75%; 4, >75%); the final scores were between 0-12. For evaluation of Ki67, the number of positive cells was calculated in three representative areas of high staining.
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6

Quantifying Cellular Protein Expression

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Total protein in cells was extracted with RIPA buffer (KenGEN, China) and quantified with BCA protein concentration kit (P0012S, Beyotime, China). The extracted protein was separated by 10% SDS-PAGE and transferred onto PVDF membrane (IPVH00010, Millipore, USA). After sealing with 5% skim milk for 2 h, the PVDF membrane was washed three times with PBST. Then, the PVDF membrane was incubated with E2F3 antibody (ab50917, 1:2000, Abcam) overnight and washed with PBST for three times. The second antibody was then incubated at room temperature for 1 h. GAPDH (ab9485, 1:2500, Abcam) was used as an internal reference.
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7

Western Blot Analysis of Cell Lysates

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Cells were transfected for 48 h and lysed using RIPA buffer (catalog# 9806S, CST, Danvers, MA, USA). The samples were centrifuged, and proteins in the supernatants were separated by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis with 10% or 12% gels and then transferred to PVDF membranes (Millipore, Billerica, MA, USA). The membranes were blocked by incubation with skim milk(1:5000; Boster, Wuhan, China) and then incubated for 12 h at 4°C with primary antibodies against E2F3 (catalog# ab50917; Abcam, Cambridge, UK), PRDM1 (catalog# ab106766, Abcam), cyclin-dependent kinase 17 (CDK17, catalog# ab159068, Abcam), or β-actin (catalog# ab8227, Abcam). After washing, the membranes were incubated for 2 h at 37°C with anti-rabbit, anti-mouse, or anti-goat IgG secondary antibodies. Electronic chemical Laboratory (ECL) detection kit was used for the signal development (Merck Millipore, Darmstadt, Germany).
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8

Western Blot Analysis of E2F3 and GAPDH

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Total protein was isolated using RIPA buffer (Beyotime, Shanghai, China) and examined using a BCA protein assay kit (Tiangen, Beijing, China). Equal of proteins were subjected to sodium dodecyl sulfonate‐polyacrylamide gel (SDS‐PAGE; Solarbio) and transferred onto polyvinylidene difluoride membranes (Millipore). Next, the samples were blocked with 5% non‐fat milk for 1 hour at room temperature. Afterward, the samples were incubated with primary antibodies: E2F3 (ab50917; Abcam) or GAPDH (ab181602; Abcam) overnight at 4°C and relevant secondary antibody (ab205719; Abcam) for 2 hours at room temperature. Finally, enhanced chemiluminescence reagent (Vazyme, Nanjing, China) was utilized to visualize the proteins.
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9

E2F3 Protein Expression Analysis

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Immunohistochemistry was used to assess cellular expression of E2F3 using a rabbit-anti-E2F3 antibody (abcam ab50917).
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10

Western Blot Analysis of Cellular Proteins

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Cellular protein was extracted using RIPA lysis buffer (Beyotime Biotechnology, Shanghai, China), and protein concentration was determined using a BCA kit (Beyotime Biotechnology, Shanghai, China). After SDS-PAGE, the protein samples were transferred to PVDF membranes and blocked with 5% skimmed milk for 1 h at room temperature. The corresponding primary antibodies were then added to interact with the proteins at 4°C overnight, and then the membrane was rinsed with tris buffered saline with Tween 20 (TBST). Next, the secondary antibodies were added to incubate the membrane for 2 h at room temperature before the membrane was rinsed with TBST again, and then ECL chemiluminescent kit (Millipore, Billerica, MA, USA) was added onto the membrane to develop the bands. The antibodies used in this study, including anti-E2F3 (ab50917, 1:500), anti-Bax (ab32503, 1:500), anti-Bcl-2 (ab185002, 1:500), anti-E-cadherin (ab11512, 1:500), anti-N-cadherin (ab18203, 1:500) and anti-β-actin (ab179467, 1:2000), were all bought from Abcam (Shanghai, China).
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