Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional Information |
|---|---|---|---|---|
| Antibody | Rabbit polyclonal anti-Dnmt3a | Santa Cruz Biotechnology | Cat. #: 20703; RRID:AB_2093990 | (1:1000) |
| Antibody | Rabbit polyclonal anti-MeCP2 | Huda Zoghbi lab (in house) | 0535 | (1:10,000) |
| Antibody | Rabbit polyclonal anti-histone H3 | Abcam | Cat. #: 1791; RRID:AB_302613 | (1:20,000) |
| Antibody | goat anti-rabbit-HRP | BioRad | Cat. #: 170–5046;RRID:AB_11125757 | (1:10,000) |
| Antibody | Mouse monoclonal anti-Dnmt3a | Novus | Cat. #: NB120-13888; RRID:AB_789607 | (1:250) |
| Antibody | Rabbit polyclonal anti-Myc | Sigma | Cat. #: C3956; RRID:AB_439680 | (1:200) |
| Antibody | Rabbit monoclonal anti-MeCP2 | Cell Signaling Technology |
Cat. #: 3456; RRID:AB_2143849 | (1:500) |
| Antibody | Chicken polyclonal anti-GFP | Abcam | Cat. #: 13970; RRID:AB_300798 | (1:800) |
| Antibody | Goat anti-mouse Alexa Fluor 555 | Invitrogen | Cat. #: A21127; RRID:AB_141596 | (1:1000) |
| Antibody | Goat polyclonal anti-rabbit Dylight 488 | Bethyl Laboratories | Cat. #: A120-201D2; RRID:AB_10634085 | (1:750) |
| Antibody | Goat anti-chicken Alexa Fluor 488 | Invitrogen | Cat. #: A11039; RRID:AB_142924 | (1:750) |
| Antibody | Donkey anti-rabbit Alexa Fluor 568 | Thermo Fisher Scientific | Cat. #: A10042; RRID:AB_2534017 | (1:1000) |
| Antibody | Mouse monoclonal anti-NeuN | Millipore | Cat. #: MAB377; RRID:AB_2298772 | (1:300) (each batch needs to be empirically tested after labeling with Alexa Fluor 647) |
| Antibody | Rabbit polyclonal anti-GFP 488 | Thermo Fisher Scientific | Cat. #: A-21311; RRID:AB_221477 | (1:1000) |
| Other | cOmplete, EDTA-free Protease Inhibitor Cocktail | Sigma | Cat. #: 5056489001 | |
| Other | Pierce Universal Nuclease for Cell Lysis | Thermo Fisher Scientific | Cat. #: 88701 | |
| Other | Optimal Cutting Temperature medium |
VWR | Cat. #: 25608–930 | |
| Other | VECTASHIELD HardSet Antifade Mounting Medium without DAPI | Vector Laboratories | Cat. #: H-1400 | |
| Other | Cryoseal XYL | Fisher Scientific | Cat. #: 22-050-262 | |
| Other | Aqueous Glutaraldehyde EM Grade, 10% 10 ML |
Electron Microscopy Sciences | Cat. #: 16100 | Dilute fresh |
| Other | Paraformaldehyde | Sigma | Cat. #: P6148 | Make fresh |
| Other | X-Gal | Gold Biotechnologies | Cat. #: X4281C | |
| Other | RNasin Ribonuclease Inhibitors | Promega | Cat. #: N261A | |
| Other | UltraPure BSA (50 mg/mL) | Thermo Fisher Scientific | Cat. # AM2618 | |
| Other | DPBS, no calcium, no magnesium | Invitrogen | Cat. #: 14190144 | |
| Other | UltraPure DEPC-Treated Water (1L) | Invitrogen | Cat. #: 750023 | |
| Commercial assay, kit | GE Healthcare Amersham ECL Prime Western Blotting Detection Reagent | Fisher Scientific | Cat. #: 45010090 | |
| Commercial assay, kit | APEX Alexa Fluor 647 Antibody Labeling Kit | Thermo Fisher Scientific | Cat. #: A10475 | |
| Commercial assay, kit | Single Cell RNA Purification Kit | Norgen Biotek | Cat. #: 51800 | |
| Commercial assay, kit | NuGEN Ovation RNA-Seq v2 | NuGen | protocol p/n 7102, kit p/n 7102–08 | |
| Commercial assay, kit | Rubicon ThruPlex DNA-Seq |
Rubicon Genomics | protocol: QAM-108–002, kit p/n R400428 | |
| Commercial assay, kit |
EZ DNA Methylation-Direct Kit | Zymo | Cat. #: D5021 | |
| Other | Unmethylated lambda DNA spike-in | Promega | Cat. #: D1521 | |
| Strain, Strain background (Mus musculus) | Dnmt3aflox/flox mice | Dr. Margaret Goodell, Baylor College of Medicine (Can be purchased from Riken BRC) | Cat. #: RBRC03731; RRID:IMSR_RBRC03731 | |
| Strain, Strain background (Mus musculus) | Slc32a1-Cre+/+ mice | Jackson Laboratory | Cat. #: 017535; RRID:IMSR_JAX:017535 |
backcrossed to C57Bl/6J |
| Strain, Strain background (Mus musculus) | Mecp2flox/flox and Mecp2flox/y mice | MMRRC | Cat. #: 011918-UCD; RRID:MMRRC_011918-UCD | backcrossed to C57Bl/6J |
| Strain, Strain background (Mus musculus) | R26-CAG-LSL-Sun1-sfGFP-Myc+/+ mice | Dr. M. Margarita Behrens, The Salk Institute for Biological Studies (can be purchased from Jackson Laboratory) | Cat. #: 021039; RRID:IMSR_JAX:021039 | backcrossed to C57Bl/6J |
| Software, algorithm | GraphPad Prism version 6 | GraphPad Software | www.graphpad.com | |
| Other | pClamp10 | Molecular Devices | https://www.moleculardevices.com | |
| Software, algorithm | Minianalysis 6.0.3 | Synaptosoft Inc | http://www.synaptosoft.com/MiniAnalysis/ | |
| Software, algorithm | STAR aligner version 2.5.3a | GitHub | https://github.com/alexdobin/STAR | |
| Software, algorithm | FeatureCount v1.5.3 | Subread | http://subread.sourceforge.net | |
| Software, algorithm | DESeq2 v1.6.2 | Bioconductor | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |