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5 protocols using ab16048

1

Immunohistochemical Profiling of Cellular Markers

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Human paraffin embedded formalin fixed sections (7 μm) were deparaffinized then subjected to antigen retrieval (20 min in pressure cooker in Trilogy pretreatment buffer, Sigma, 920P-05). Sections were blocked in 10% goat-serum buffer, for 1 h at RT. Primary antibodies for CC1 (1:500, Millipore OP80), LMNA (1:1,000, Abcam, ab226198), LMNB1 (1:1,000, Abcam, ab16048), NG2 (1:500, Sigma, MAB5384-I), were incubated for 4 h at RT. After washes, sections were incubated with Alexa fluor conjugated goat secondary antibodies (1:500) for 1 h at RT. After washes, sections were incubated with DAPI (1:1,000) for 5 min. Primary and secondary antibodies used are listed in the key resources table. Slides were mounted with fluorogold mounting medium and imaged at 20x and/or 40x on Zeiss Axio Vert with Apotome 3.
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2

Epigenetic Profiling of TET Enzymes

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Anti-5hmC rabbit polyclonal (Active Motif, 39791), anti-TET1 (SantaCruz sc-163443), anti-TET2 for western and IHC (Abcam ab94580), anti-TET2 for ChIP-seq (Santa Cruz sc-136926), anti-TET3 (Abnova), anti-Lamin B1 (Abcam ab16048), anti-beta Tubulin (Sigma T0198).
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3

Nuclear Morphology and Protein Levels in SK-N-SH Cells

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The nuclear morphologies of the SK-N-SH cells were visualized by immunostaining with lamin A and lamin B1. The lamin A and vimentin levels in the cells were characterized by immunostaining of lamin A and vimentin. Cells were cultured on nanopillars and incubated overnight before fixation with prewarmed 4% paraformaldehyde (PFA) in PBS (Boster biological technology AR1068) for 15 minutes at room temperature. After washing with PBS three times, the cells were permeabilized in 0.5% Triton X-100 (Sigma) in PBS for 15 minutes, followed by blocking with 5% bovine serum albumin (BSA) (Sigma) in PBS for 1 hour. Subsequently, the samples were incubated with primary antibodies (anti-lamin A, Abcam, ab26300; anti-lamin B1, Abcam, ab16048; anti-vimentin, Sigma, V5255; anti-SNAIL + SLUG, Abcam, ab224731) at 1 : 400 dilution at room temperature for 1 hour or 4 °C overnight. The samples were again washed with PBS for three times and then incubated with secondary antibodies (chicken anti-rabbit IgG Alexa 488, Invitrogen, A21441; anti-mouse IgG Alexa 555, Cell Signaling Technology, 4409s) at 1 : 600 dilution at room temperature for 1 hour. After washing with PBS three times, the samples were stained with DAPI (Sigma), phalloidin (Cytoskeleton, Inc.) or cellmask (Invitrogen) in different experiments.
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4

Immunofluorescence Staining of Retinoblastoma Cells

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Retinoblastoma cells grown in suspension were plated onto poly-D-lysine coated 12-well slides just prior to fixation [48 (link)]. Retinoblastoma cells and R28 cells were fixed with 4% PFA and permeabilized using 0.02% Triton/TBS as described [48 (link)]. Alternatively, cells were fixed and permeabilized with ice-cold methanol followed by acetone at 4°C. Cells were then blocked with 5% NGS in 0.1% BSA/TBS-Tween and incubated overnight at 4°C with primary antibodies in incubating solution containing 1% NGS in 0.1% BSA/PBS-Tween. The antibodies against the following were used: IMPDH1 (Proteintech Cat#22092-1-AP; an antibody raised against the entire IMPDH1 fusion protein), IMPDH2 (Abcam Cat#ab75790), alpha-tubulin (Sigma-Aldrich Cat#T6199), beta-III tubulin (Millipore Cat#MAB1637 and Sigma-Aldrich Cat#T8660), autoantibody It2006 (a kind gift from Edward K. L. Chan), lamin B1 (Abcam Cat#ab16048), detyrosinated tubulin (Millipore Cat#AB3201) and MAP-2 (Abcam Cat#ab32454). Cells were then washed with 0.1% BSA/PBS-Tween and incubated for one hour at 37°C with Alexa fluor® secondary antibodies. Cells were washed with 0.1% BSA/PBS-Tween and mounted with Vectashield Mounting Medium containing DAPI (Vector Laboratories Cat#H-1200) for nuclear staining.
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5

Immunostaining Antibodies and Markers

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The primary antibodies used for immunostaining were goat anti-PDGFRA (1:250, R&D Systems, catalog #AF1062), rabbit anti-PDGFRA (1:250, Abcam, catalog #Ab203491), rabbit anti-OLIG2 (1:500, Abcam, catalog #Ab136253), mouse anti-CC1 (1:100, CalBioChem, catalog #OP80), rabbit anti-IBA1 (1:500, Wako, catalog #019-19741), rabbit anti-LMNB1 (1:1000, Abcam; used with AR, catalog #Ab16048), mouse anti-NEUN (1:500, Millipore, catalog #Ab377), mouse anti-AQP4 (1:100, Abcam, catalog #Ab9512), rabbit anti-KI67 (1:200, Abcam, catalog #Ab16667), rat anti-CD68 (1:400, Abcam, catalog #Ab53444), rabbit anti-MBP (1:250, Abcam, catalog #Ab40390). The secondary antibodies used for immunostaining were Alexa Fluor 488 goat anti-rabbit IgG (1:500, ThermoFisher, catalog #A-11034), Alexa Fluor 555 goat anti-mouse IgG (1:500, ThermoFisher, catalog #A-21422), Alexa Fluor 555 goat anti-rat IgG (1:500, ThermoFisher, catalog #A-21434), Alexa Fluor 488 donkey anti-goat (1:500, ThermoFisher, catalog #A-11055), Alexa Fluor 555 donkey anti-mouse IgG (1:500, ThermoFisher, catalog #A-31570), and Alexa Fluor 647 donkey anti-rabbit (1:500, ThermoFisher, catalog #A-31573).
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