KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| 5-hydroxymethylcytosine(5-hmC); Rabbit polyclonal | Active Motif | Cat#39769; RRID:AB10013602 |
| Phospho-Tau (Ser396) Polyclonal | Thermo Fisher Scientific | Cat#44–752G; RRID:AB_2533745 |
| Tau Monoclonal (T46) | Thermo Fisher Scientific | Cat#13–6400; RRID:AB_2533025 |
| Polyclonal MAP2 | Novus | Cat#NB300–213; RRID:AB_2138178 |
| β-amyloid (D54D2) XP; Rabbit monoclonal | Cell Signaling | Cat#8243S; RRID:AB_2797642 |
| Human SOX2 Affinity Purified Polyclonal | R and D Systems | Cat#AF2018; RRID:AB_355110 |
| Chemicals, peptides, and recombinant proteins | ||
| T4 phage β-glucosyltransferase | New England Biolabs | Cat#M0357L |
| UDP-6-N3-glucose | Jena Biosciences | Cat#CLK-076 |
| AMPure XP beads | Beckman Coulter | A63881 |
| disulfide biotin linker | Click Chemistry Tools | A112–5 |
| Dynabeads MyOne Streptavidin C1 beads | Thermo Fisher Scientific | Cat#65002 |
| Critical commercial assays | ||
| NEBNext Ultra II DNA Library Prep kit for Illumina | New England Biolabs | Cat#E7645L |
| TruSeq RNA Sample Prep V2 kit | New England Biolabs | RS-122–2001 |
| Deposited data | ||
| Raw and analyzed sequencing data | This paper | GSE151818 |
| Raw images | This paper | https://data.mendeley.com/datasets/bxp7jh6yw5/1 |
| PSEN1 mutated neural progenitor cell line | Fetahu et al., 2019 | Table S3 |
| AD postmortem brains | Qin et al., 2020 | Table S3 |
| AD postmortem brains | Zhao et al., 2017 | Table S3 |
| AD postmortem brains | Lardenoije et al., 2019 | Table S3 |
| AD postmortem brains | Gasparoni et al., 2018 | Table S3 |
| AD postmortem brains | Li et al., 2019 | GSE110732 |
| Fetal brain histone modifications | Yan et al., 2016 | Table S3 |
| Epigenome RoadMap Project: fetal brain histone modifications | Kundaje et al., 2015 | http://www.roadmapepigenomics.org/ |
| Enhancer Atlas 2.0 | Gao and Qian, 2020 | http://www.enhanceratlas.org/ |
| Experimental models: Cell lines | ||
| Controls (CTRL): human induced pluripotent stem cells (hiPCS) | Provided by Dr. Gary Bassell (Emory University) | N/A |
| Familial Alzheimer Diseased (FAD): human induced pluripotent stem cells (hiPCS) | Provided by Dr. Chadwick Hales (Emory University) | N/A |
| Alzheimer Diseased (AD) human fibroblasts | Provided by Dr. Selina Wray (UCL Queen Square Institute of Neurology) | N/A |
| Software and algorithms | ||
| National Center for Microscopy and Imaging Research: ImageJ Mosaic Plug-ins | Schneider et al., 2012 |
https://ncmir.ucsd.edu/downloads/montaging_plugins.shtm RRID:SCR_001935 |
| Bowtie v.2.2.6 | Langmead et al., 2009 |
http://bowtie-bio.sourceforge.net/index.shtml RRID:SCR_005476 |
| MACS2 v.2.1.0 | Zhang et al., 2008 |
https://github.com/taoliu/MACS RRID:SCR_013291 |
| ngs.plot v.2.61 | Shen et al., 2014 |
https://code.google.com/p/ngsplot/ RRID:SCR_011795 |
| HOMER v.4.9 | Heinz et al., 2010 | http://homer.ucsd.edu/homer/mer/RRID:SCR_010881 |
| TopHat2 v.1.3.3 | Trapnell et al., 2012 |
https://ccb.jhu.edu/software/tophat/index.shtml RRID:SCR_013035 |
| Cuffdiff v.2.2.1 | Trapnell et al., 2012 | http://cufflinks.cbcb.umd.edu/RRID:SCR_001647 |
| BEDTools | Quinlan and Hall, 2010 |
https://github.com/arq5x/bedtools2 RRID:SCR_006646 |
| SAMTOOLS v.1.9 | Li et al., 2009 |
http://samtools.sourceforge.net/ RRID:SCR_002105 |
| GO Consortium | Ashburner et al., 2000 | http://geneontology.org |
| MuSiC | Wang et al., 2019 | https://github.com/xuranw/MuSiC |
| Genomic Regions Enrichment of Annotations Tool (GREAT) | McLean et al., 2010 | http://great.stanford.edu/public/html/ |