Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Mus musculus) | Dnmt3a | GENCODE | GENCODE:ENSMUSG00000020661 | GENCODE vM10 |
| Genetic reagent (Mus musculus) | Dnmt3a-floxed | PMID:10555141 | Backcrossed to C57BL/6 for at least seven generations | |
| Genetic reagent (Mus musculus) | Nex-Cre; Neurod6-Cre | PMID:17146780 | Jackson Laboratories Backcrossed to C57BL/6J for 10 generations |
|
| Genetic reagent (Mus musculus) | INTACT | PMID:26087164 | (B6.129- Gt(ROSA)26Sor tm5(CAG-Sun1/sfGFP)Nat/MmbeJ) |
|
| Genetic reagent (Mus musculus) | Dnmt3a-KO; Dnmt3a cKO | This paper | See ‘Materials and Methods’, section ‘Generation of the Dnmt3a cKO mice line’ | |
| Antibody | Anti-NeuN (Mouse monoclonal, Clone A60) | Millipore | MAB377 | (1:1000) |
| Antibody | Anti-DNMT3A (Rabbit polyclonal) | Abcam | Ab2850 | (1:250) |
| Antibody | Anti-H3K27me3 (Rabbit polyclonal) | Active Motif | Cat:#39156; RRID:AB_2636821 | (5 µl) |
| Antibody | Anti-H3K27ac (Rabbit polyclonal) | Active Motif | Cat:#39133; RRID:AB_2561016 | (5 µl) |
| Antibody | Anti-H3K4me3 (Rabbit monoclonal) | Millipore Sigma | Cat:#04–745 | (5 µl) |
| Antibody | Anti-IgG (Mouse unknown clonality) | Jackson ImmunoResearch Labs | Cat#015-000-003; RRID:AB_2337188 | (2 µl) |
| Sequence-based reagent | Cytosine-methylated adapters | Illumina | AD001, AD005 | |
| Sequence-based reagent | TruSeq PCR Primer Mix | Illumina | 20015960, 20015961 | |
| Peptide, recombinant protein | T4 DNA ligase | New England Biolabs | M0202L | |
| Commercial assay or kit | Single-Cell RNA Purification Kit | Norgen | Cat:#51800 | |
| Commercial assay or kit | Ovation RNA-Seq System V2 | NuGEN | Cat:#7102–32 | |
| Commercial assay or kit | KAPA LTP Library Preparation Kit | Roche | Cat:#KK8232 | |
| Commercial assay or kit | Qiagen DNeasy Blood and Tissue kit | Qiagen | Cat:#69504 | |
| Commercial assay or kit | EZ methylation Direct kit | Zymo | Cat:#D5021 | |
| Commercial assay or kit | Accel-NGS 2S Plus DNA Library Kit | Swift Biosciences | Cat:#21024 | |
| Chemical compound, drug | Protease inhibitor | Sigma-Aldrich | Cat:#11836153001 | |
| Chemical compound, drug | Phosphatase inhibitor | Pierce | Cat:#A32957 | |
| Chemical compound, drug | Kapa HiFi Hotstart Readymix | Kapa Biosystems | 07958935001-KK2602 | |
| Software, algorithm | Minianalysis | Minianalysis (https://www.synaptosoft.com/MiniAnalysis/) | RRID:SCR_002184 | |
| Software, algorithm | pCLAMP | Molecular Devices (https://www.moleculardevices.com/products/software/pclamp.html) | RRID:SCR_011323 | |
| Software, algorithm | Reconstruct | Synapse Web (https://synapses.clm.utexas.edu/tools/reconstruct/reconstruct.stm) | RRID:SCR_002716 | |
| Software, algorithm | Activity Monitor | MED Associates (https://www.med-associates.com/product/activity-monitor/) | RRID:SCR_014296 | |
| Software, algorithm | ANY-maze | San Diego Instruments (https://sandiegoinstruments.com/product/any-maze/) | RRID:SCR_014289 | |
| Software, algorithm | FastQC | Babraham Bioinformatics (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | RRID:SCR_014583 | v0.11.8 |
| Software, algorithm | Trim Galore | Babraham Bioinformatics (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) | RRID:SCR_011847 | v0.5.0 |
| Software, algorithm | Cutadapt | DOI:10.14806/ej.17.1.200 | RRID:SCR_011841 | v1.16 |
| Software, algorithm | STAR | PMID:23104886 | RRID:SCR_004463 | v2.5.1b |
| Software, algorithm | RSEM | PMID:21816040 | RRID:SCR_013027 | v1.2.30 |
| Software, algorithm | edgeR | PMID:19910308 | RRID:SCR_012802 | v3.24.1 |
| Software, algorithm | SQuIRE | PMID:30624635 | ||
| Software, algorithm | clusterProfiler | PMID:22455463 | RRID:SCR_016884 | v3.10.0 |
| Software, algorithm | GATK | PMID:21478889 | RRID:SCR_001876 | v3.7 |
| Software, algorithm | BWA | PMID:19451168 | RRID:SCR_010910 | v0.7.13-r1126 |
| Software, algorithm | Picard | Broad (https://broadinstitute.github.io/picard/) | RRID:SCR_006525 | V2.10.6 |
| Software, algorithm | BEDTools | PMID:20110278 | RRID:SCR_006646 | v2.27.1 |
| Software, algorithm | methylpy | methylpy (https://github.com/yupenghe/methylpy) | v1.3.2 | |
| Software, algorithm | bowtie2 | PMID:22388286 | RRID:SCR_016368 | v2.3.0 |
| Software, algorithm | MatchIt | DOI:10.18637/jss.v042.i08 | v3.0.2 | |
| Software, algorithm | BART | PMID:29608647 | ||
| Software, algorithm | HOMER | PMID:20513432 | RRID:SCR_010881 | v4.8.3 |
| Software, algorithm | ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline | PMID:22955991 | RRID:SCR_021323 | v1.1.6 |
| Software, algorithm | samtools | PMID:19505943 | RRID:SCR_002105 | v1.2 |
| Software, algorithm | SICER | PMID:19505939 | RRID:SCR_010843 | |
| Software, algorithm | DiffBind | PMID:22217937 | RRID:SCR_012918 | v2.10.0 |
| Software, algorithm | DESeq2 | PMID:25516281 | RRID:SCR_015687 | v1.22.1 |
| Software, algorithm | GREAT | PMID:20436461 | RRID:SCR_005807 | v3.0.0 |
| Software, algorithm | MethylSeekR | PMID:23828043 | RRID:SCR_006513 | v1.22.0 |
| Software, algorithm | regioneR | PMID:26424858 | V1.14.0 | |
| Software, algorithm | R | R Project for Statistical Computing (https://www.r-project.org/) | RRID:SCR_001905 | v3.5.0 |
| Software, algorithm | MATLAB | MathWorks (https://www.mathworks.com/products/matlab.html) | RRID:SCR_001622 | v2017a |
| Software, algorithm | Python | Python Programming Language (https://www.python.org/) | RRID:SCR_008394 | v3.x |