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6 protocols using ab37264

1

Histone Quantification from Cell Extracts

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Chromatin extracts from cell-number normalized samples were prepared with the ChromaFlash Chromatin Extraction Kit according to manufacturer’s instructions (Epigentek). The correspondent to 100 ng DNA of the chromatin extracts were run on SDS-PAGE under reducing conditions and immunoblotted (as described above) with the following antibodies: histone H3.1/H3.2 (ABE154, Millipore), histone H3.3 (09–838, Millipore), histone H3 (61475, Active Motif), histone H4 (ab10158, Abcam), histone H2A (ab18255, Abcam) and histone macro H2A.1 (ab37264, Abcam). Blots for total histone H3 were performed in the same membrane as histone H3.1/H3.2 blots after stripping of the membranes.
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2

Western Blot and Immunofluorescence Antibodies

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For western blot experiments, ChIP grade mH2A1 (Abcam, ab37264), GAPDH (Abcam, ab9484), H2AK119Ub (Millipore, #AB10029) and O-GlcNAc (RL2) (Thermoscientific, MA1-072) antibodies were used at a dilution of 1:1000. For immunofluorescence experiments, O-GlcNAc (RL2) (Thermoscientific, MA1-072), OGT (TI14) (Sigma Aldrich, O6014), RNA polymerase II (phospho S2) (Abcam, ab5095 and ab5408), RNA polymerase II (phospho S2/5) (Cell signaling, #4735), Actin (Abcam, ab1801) and H3K27Me3 (Millipore, #07-449) antibodies were used at a dilution of 1:200, mH2A1 (Cell signaling, #4827) and pan RNA polymerase II (RBP8) (Abcam, ab169924) at a dilution of 1:100.
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3

Immunohistochemical Analysis of Cell Markers

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Staining and image capture were performed on 3μm formalin-fixed and paraffin-embedded sections as described(15 (link),20 (link)). Primary antibodies used included mouse monoclonal antibodies against hemagglutinin tag (HA, MMS-101P, Covance, 1:500), p21 (cat#sc-6246 Santa Cruz, 1:200), gamma-H2AX (cat#05-636 Millipore, 1:500), and pATM (cat#200-301-500 Rockland, 1:200), as well as rabbit polyclonal antibodies against cleaved caspase 3 (CC3, cat#9661S Cell Signaling Technology, 1:200), Ki67 (cat#NCL-Ki67P Novocastra, 1:200), phospho-histone 3 (pH3, cat#06-570 Millipore, 1:200), macroH2A (cat#ab37264 Abcam, 1:150), p16 (cat#sc-1207 Santa Cruz, 1:200), and p53 (cat#NCL-p53-CM5p Novacastra, 1:1000). Cell counting was achieved using Image J software as well as Adobe Photoshop.
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4

Bladder Cancer Tissue Microarray Analysis

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Bladder tissue microarrays, containing 40 cases of bladder cancer tissues with different stages and grades of cancer and 8 cases of normal tissues, were purchased from US Biomax Inc. (Rockville, MD, USA). Paraffin sections were stained with macroH2A1 (ab-37264, Abcam) and Lin28B (ab-71415, Abcam) antibodies at 4 °C overnight. Then, the sections were incubated with secondary antibodies at room temperature for 1 h, followed by incubation with ABC solution (ABC reagent Elite Kit, Vector Laboratories, Burlingame, CA, USA) at room temperature for 1 h. After staining with diaminobenzidine, images were acquired using a Nikon ECLIPSE 80i microscope (Nikon). A scoring for immunohisochemical staining: negative or marginal (<20% of cells), weak (20–50% of cells), moderate (50–80% of cells) and strong (>80% of cells).
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5

CUT&RUN Analysis of macroH2A1 in CAFs

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2 × 105 short-term cultured CAFs before or after 30 min of serum stimulation were processed for CUT&RUN158 (link) for macroH2A1 (antibody ab37264, Abcam, lot number GR278020-1, 1 μg per reaction). Cells were permeabilized with 0.0085% digitonin and incubated with antibody. DNA was cleaved with the CUTANA pAG-MNase (Epicypher). Released DNA was processed using a NEBNext Ultra II Library Preparation kit for Illumina (NEB), including a 14-cycle amplification step. Libraries were sequenced and reads were processed as for ATAC–seq.
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6

Antibody Validation for KDM5 Proteins

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The following antibodies were used in this study: mouse anti-KDM5A (ab78322; Abcam), rabbit anti-KDM5B (A301-813; Bethyl Laboratories, Inc.), rabbit anti-KDM5C (A301-034; Bethyl Laboratories, Inc.), rabbit anti–β-tubulin (ab6046; Abcam), mouse anti-γH2AX (05-636, clone JBW301; Sigma-Aldrich), rabbit anti-GFP (A11122; Invitrogen), rabbit anti-PARP1 (9542; Cell Signaling Technology), mouse anti-PAR (4335-MC-100; Trevigen), rabbit anti–pan-ADP-ribose (MABE1016; Sigma-Aldrich), rabbit anti-MBP (Ab9084; Abcam), mouse anti-Flag (F1804; Sigma-Aldrich), rabbit anti-macroH2A1 (Ab37264; Abcam), rabbit anti-macroH2A1.1 (12455S [D5F6N]; Cell Signaling Technology), mouse anti-macroH2A1.2 (MABE61 [14G7]; Sigma-Aldrich), rabbit IgG (NI01; Calbiochem), mouse IgG (NI03; Calbiochem), and rabbit anti-ZMYND8 (A302-089; Bethyl Laboratories, Inc.).
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