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8 protocols using dgcr8

1

Immunofluorescent Staining of hnRNPA2B1 and DGCR8

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MM cells were fixed with 4% formaldehyde and permeabilized with 0.3% Triton X-100 in 1 × PBS. After blocking with 2% goat serum, the cells were stained with antibodies against hnRNPA2B1 (Santa Cruz) or DGCR8 (Abcam) at 4°C overnight, followed by incubation with Alexa 594- or Alexa 488-conjugated secondary antibodies (Abclonal) for 30 min at room temperature and the cell nuclei were stained with DAPI and mounted with antifade reagent (Molecular Probes). Immunofluorescent images were acquired with an IX71 confocal microscope system (Olympus).
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2

Protein Expression Analysis in Chondrocytes

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Proteins in endplate chondrocytes were lysed and collected, and the protein concentration was determined by the bicinchoninic acid quantitative method. Denatured protein was separated by sodium dodecyl sulphate‐polyacrylamide gel electrophoresis at 20 g per pore and then transferred onto a nitrocellulose membrane. The membrane was blocked with 5% bovine serum albumin for 1 hour, and primary antibodies against METTL3 (1:1000; Abcam), IL‐1β (1:100, Abcam), cleaved caspase 3 (1:100, Abcam), cleaved caspase 9 (1:100, Abcam), cleaved poly(ADP‐ribose) polymerase (PARP; 1:500, Abcam), ACAN (1:100, Abcam), COL2A1 (1:5000, Abcam), GAPDH (1:5000, Abcam), PIK3R2 (1:5000, Abcam), pAKT (1:5000, Abcam), AKT (1:500, Abcam) or DGCR8 (1:1000, Abcam) were added. The membrane was then incubated at 4°C overnight. The following day, a secondary antibody (1:5000; Cell Signaling Technology, Danvers, MA) was added and the membrane was incubated again for 1 hour at room temperature on a shaker. After washing the membrane three times with Tris‐buffered saline containing Tween 20, images were acquired with a gel imaging system.
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3

Co-immunoprecipitation and Western Blot Analysis

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For co‐immunoprecipitation, cells were lysed using RIPA protein extraction reagent (Beyotime) supplemented with a protease inhibitor cocktail (Roche) and PMSF (Roche). The protein concentration was measured using the Bio‐Rad protein assay kit. The supernatants were collected and incubated with anti‐pStat3, Drosha at 4°C for 12 hours. Protein A Sepharose CL‐4B beads (GE) were incubated with the mixture at 4°C for 2 hours. Then, the beads were washed three times with RIPA buffer. The bound proteins were eluted with SDS‐PAGE loading buffer and used for Western blot. For Western blot assay, approximately 40 μg of protein extract was electrophoresed on a 10% SDS‐polyacrylamide gel electrophoresis (SDS‐PAGE) and then transferred onto 0.22‐μm nitrocellulose membrane (Sigma) and incubated with specific antibodies. The ECL chromogenic substrate was used to visualize the bands. The intensity of the protein bands was quantified by Quantity One software (Bio‐Rad ChemiDoc XRS). GAPDH was used as a control. Antibodies for Jak1, p‐Jak1, Stat3, p‐Stat3, Ago, IL‐6, Drosha, DGCR8 and GAPDH were purchased from Abcam.
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4

RIP-qRT-PCR for RNA-binding proteins

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The Magna RIP RNA-binding protein immunoprecipitation kit (Millipore, Billerica, MA, USA) was used for the RIP experiment. In brief, the OE-RBM15/NC transfected ESCC cells were lysed by RIP lysis buffer, and then the lysates were incubated with antibodies DGCR8 (1:100, Abcam) or IgG (1:100, Abcam) in the suspension of magnetic beads at 4 °C for overnight. The coprecipitated RNAs were extracted with TRIzol reagent (Invitrogen) and then for qRT-PCR analysis.
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5

Protein Immunoprecipitation and Western Blot

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The following antibodies were used for immuno-precipitation and Western Blot experiments, according to the manufacturer's instruction: DGCR8 (Abcam ab90579), EWSR1 (Abcam ab54708), FUS (Bethyl A300–293A), DDX5 (Abcam ab126730), Drosha (Santa Cruz sc-33778), Vinculin (VCL) (Millipore 06–866), PRMT1 (Abcam ab73246), ASYM24 (Millipore), SYM10 (Millipore), Mono-Methyl Arginine (R*GG) (D5A12) (Cell Signaling Technology 8711), LAMIN A/C (sc-6215), Lamin B1 (Abcam ab16048), GAPDH (Abcam ab9484), H3 (Abcam ab1791), H4 (Abcam ab7311), H4R3me2a (Active Motif 39705), TAF15 (Bethyl Laboratories A300–308A), ILF3 (Bethyl A303–615A), ILF2 (sc-271718), DDX17 (sc-130650), HDAC1 (Abcam ab7028) and HA.11 (Biolegend 901513).
MS023 and MS094 compounds were kindly provided by the SGC Toronto—Structural Genomic Consortium (http://www.thesgc.org/scientists/groups/toronto). Compounds were dissolved in DMSO and used at a final concentration of 10 μM for the indicated time intervals.
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6

Immunoprecipitation and Western Blot Analysis

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Cells were lysed using a RIPA lysis buffer containing a protease inhibitor (Beyotime). Next, 3 μg antibody was added to the cell lysate, mixed well and incubated at 4°C overnight. Then, 20 μL protein A/G PLUS‐Agarose beads (Santa Cruz Biotechnology) were added to the mixture and cultured on a spinner at 4°C for 4 h. The bead‐antibody‐protein complex was gently washed three times with pre‐cooled PBS and then boiled for western blotting. PKM2 (1:1000; ProteinTech Group, Inc.) and TRIM9 (1:1000; Abcam) and DGCR8 (1:1000; Abcam).
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7

Unraveling TNBC Proteome: Native PAGE Analysis

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Total protein was isolated from TNBC samples (tumour tissues, paired normal adjacent tissues and cell lines) using RIPA lysis buffer (Beyotime Institute of Biotechnology). Total protein was separated by 10% SDS‐PAGE (25 μg protein per lane), and the protein was transferred with PVDF membrane (MilliporeSigma). Blocking of PVDF membrane was performed with 5% nonfat milk powder (Beyotime). To detect the expression of PKM2 protein in different conformations, the total protein extracted from the sample was not thermal denatured and was denatured using a non‐denatured gel sample loading buffer (Beyotime). Next, protein electrophoresis was performed using native PAGE running buffer (Beyotime). The PVDF membranes were probed at 4°C overnight with antibodies against METTL14 (1:1000; Abcam), PKM2 (ProteinTech Group, Inc.), DGCR8 (1:1000; Abcam), TRIM9 (1:1000; Abcam) and β‐actin (1:5000; Abcam). Finally, protein expression was analysed by chemiluminescence reagents (Hyperfilm ECL).
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8

Immunohistochemical Analysis of Intracranial Tumor Xenografts

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IHC was performed using an immunohistochemical labeling kit (MaxVision Biotechnology, Fuzhou, Fujian, China) as previously described [6 (link)]. Briefly, paraffin-embedded sections of the intracranial tumor implantation specimens of nude mice were labeled with primary antibodies against SPI1 (1:100; Abcam), DGCR8 (1:100; Abcam), TNF-α (1:100; Abcam), nestin (1:100; Abcam) and Ki-67 (1:100; Abcam). The immunohistochemical results were evaluated according to the German immunohistochemical score (GIS) [38 (link)].
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