KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| OCT-4 | Cell Signaling Technology | Cat# 2890, RRID:AB_2167725 |
| Nanog | Cell Signaling Technology | Cat# 4893, RRID:AB_10548762 |
| SOX1 | R&D Systems | Cat# AF3369, RRID:AB_2239879 |
| Nestin | Millipore Sigma | Cat# MAB5326, RRID:AB_2251134 |
| PAX6 | R&D Systems | Cat# AF8150, RRID:AB_2827378 |
| H3K9me3 | Abcam | Cat# ab176916, RRID:AB_2797591 |
| HP1a | Cell Signaling Technology | Cat# 2616, RRID:AB_2070987 |
| H3K27me3 | Abcam | Cat# ab6002, RRID:AB_305237 |
| HMGB1 | Thermo Fisher Scientific | Cat# PA1-16926, RRID:AB_2248274 |
| LMNB1 | Abcam | Cat# ab16048, RRID:AB_10107828 |
| p16INK4a | Thermo Fisher Scientific | Cat# MA5-32133, RRID:AB_2809424 |
| KI-67 | Abcam | Cat# ab15580, RRID:AB_443209 |
| Vimentin | Abcam | Cat# ab24525, RRID:AB_778824 |
| GFAP | Millipore | Cat# AB5804, RRID:AB_2109645 |
| BrdU | Cell Signaling Technology | Cat# 5292, RRID:AB_10548898 |
| Alexa-Fluor 488 (Donkey anti-Goat) | Thermo Fisher Scientific | Cat# A-11015, RRID:AB_2534082 |
| Alexa-Fluor 488 (Donkey anti-Rabbit) | Thermo Fisher Scientific | Cat# A-21206, RRID:AB_2535792 |
| Alexa-Fluor 488 (Donkey anti-Mouse) | Thermo Fisher Scientific | Cat# A-21202, RRID:AB_141607 |
| Alexa-Fluor 488 (Donkey anti-Sheep) | Thermo Fisher Scientific | Cat# A-11015, RRID:AB_2534082 |
| Alexa-Fluor 555 (Donkey anti-Goat) | Thermo Fisher Scientific | Cat# A-21432, RRID:AB_2535853 |
| Alexa-Fluor 555 (Donkey anti-Rabbit) | Thermo Fisher Scientific | Cat# A-31572, RRID:AB_162543 |
| Alexa-Fluor 555 (Donkey anti-Mouse) | Thermo Fisher Scientific | Cat# A-31570, RRID:AB_2536180 |
| Alexa-Fluor 555 (Donkey anti-Sheep) | Thermo Fisher Scientific | Cat# A-21099, RRID:AB_2535753 |
| Alexa-Fluor 647 (Donkey anti-Goat) | Thermo Fisher Scientific | Cat# A-21447, RRID:AB_2535864 |
| Alexa-Fluor 647 (Donkey anti-Rabbit) | Thermo Fisher Scientific | Cat# A-31573, RRID:AB_2536183 |
| Alexa-Fluor 647 (Donkey anti-Mouse) | Thermo Fisher Scientific | Cat# A-31571, RRID:AB_162542 |
| Alexa-Fluor 647 (Donkey anti-Sheep) | Thermo Fisher Scientific | Cat# A-21448, RRID:AB_2535865 |
| DAPI | Thermo Fisher Scientific | Cat# D1306, RRID:AB_2629482 |
| Biological Samples | ||
| Iso-E and Iso-T iPSCs (AG05397) | Coriell (Maclean et al., 2012) | Cat# AG05397 |
| Ma-E iPSCs | Cohen, McLean, HMS (Raja et al., 2016) | Cat# CS-0020-01 |
| Ma-T Fibroblast | Coriell | Cat# AG06922 |
| Fe-E iPSCs | WiCell | Cat# WA09 |
| Fe-T Fibroblasts | Coriell | Cat# GM04616 |
| CF1 Mouse embryonic fibroblasts, irradiated | Thermo Fisher Scientific | Cat# A34181 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Fluoromount-G | Electron Microscopy Sciences | Cat# 17984-25 |
| PBS, pH 7.4 | Thermo Fisher Scientific | Cat# 10010049 |
| Triton X-100 | Sigma-Aldrich | Cat# T8787-100ML |
| Paraformaldehyde | Electron Microscopy Sciences | Cat# 15714-S |
| 5-Bromo-2′-deoxyuridine | Sigma-Aldrich | Cat# B5002-5G |
| Corning® Matrigel® hESC-Qualified Matrix | VWR International | Cat# 354277 |
| Corning® Matrigel® Basement Membrane Matrix | VWR International | Cat# 356254 |
| DMEM/F12 Glutamax | Life Technologies | Cat# 10565-042 |
| Knockout Serum Replacement | Life Technologies | Cat# 10828028 |
| MEM non-Essential amino acid solution | Sigma-Aldrich | Cat# M7145 |
| Glutamax | Thermo Fisher Scientific | Cat# 35050-079 |
| recombinant human FGF-basic | PeproTech | Cat# 100-18B |
| 2-mercaptoethanol | Sigma-Aldrich | Cat# M6250 |
| mTeSR1 medium | Stemcell technologies | Cat# 85850 |
| ReLeSR™ | Stemcell Technology | Cat# 05872 |
| AggreWell™800 | Stemcell Technology | Cat# 34811 |
| Neurobasal | Thermo Fisher Scientific | Cat# 21103049 |
| N-2 Supplement | Invitrogen | Cat# 17502-048 |
| B-27 Serum-Free Supplement | Gibco | Cat# 12587010 |
| insulin | Thermo Fisher Scientific | Cat# 41400045 |
| Pen/strep | Gemini Bio-Products | Cat# 400-109 |
| Dorsomorphin | PeproTech | Cat# 8666430 |
| SB431542 | Tocris | Cat# 1614 |
| STEMdiff™ Neural Rosette Selection Reagent | Stemcell technologies | Cat# 05832 |
| Sulfuric acid | Sigma-Aldrich | Cat# 339741-500ML |
| Trichloroacetic acid | BDH | Cat# BDH0310-500G |
| Trypsin | Promega | Cat# V5113 |
| C18 Sep-Pak cartridges | Waters | Cat# 186002318 |
| TrypLE | Thermo Fisher Scientific | Cat# 12605028 |
| Igepal CA-630 (NP-40) | Sigma-Aldrich | Cat# I8896 |
| AMPure beads | Beckman Coulter | Cat# A63880 |
| Critical Commercial Assays | ||
| CytoTune-iPS Sendai Reprogramming kit | Thermofisher scientific | Cat# A16518 |
| Kapa mRNA hyperprep kit for standard RNA libraries | Roche | Cat# KK8540 |
| Nextera DNA Library Prep Kit | Illumina | Cat# FC-121-1030 |
| Qiagen MinElute PCR Purification Kit | Qiagen | Cat# 28006 |
| Arima Hi-C kit | Arima Genomics | N/A |
| Kappa Hyperprep Kit | Roche | Cat# KK8502 |
| Deposited Data | ||
| Hi-C | This paper | GEO: GSE185192 |
| LMNB1 ChIP-seq | This paper | GEO: GSE185192 |
| RNA-seq | This paper | GEO: GSE185192 |
| ATAC-seq | This paper | GEO: GSE185192 |
| Senescence RNA-seq | Casella et al., 2019; Crowe et al., 2016; Alspach et al., 2014; Sati et al., 2020; Zirkel et al., 2018; Borras-Fresneda et al., 2016; | GEO: GSE130727, GSE58910, GSE56293, GSE130306, GSE98448, GSE80207, |
| RNA-seq of iPSC derived from Down syndrome and control individuals | Gonzales et al., 2018 | GSE101942 |
| RNA-seq of iPSC derived neurons, astrocytes and OPCs | Garcia-Leon et al., 2018; Lin et al., 2018; Tcw et al., 2017 | GEO: GSE106984, GSE102956, GSE97904 |
| ChIP-seq of Histone Modifications | Hawkins et al., 2010 | GEO:GSM956008 |
| Experimental Models: Cell Lines | ||
| Iso-E and Iso-T (AG05397) | Coriell Maclean et al., 2012) | Cat# AG05397 |
| Ma-E | Cohen, McLean, HMS (Raja et al., 2016) | Cat# CS-0020-01 |
| Ma-T | Coriell | Cat# AG06922 |
| Fe-E | WiCell | Cat# WA09 |
| Fe-T | Coriell | Cat# GM04616 |
| CF1 Mouse embryonic fibroblasts, irradiated | Thermo Fisher Scientific | Cat# A34181 |
| Software and Algorithms | ||
| Imarisx64 9.2.1 | Bitplane | http://www.bitplane.com/Default.aspx |
| ZEN imaging software | Carl Zeiss | https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html |
| STAR (v.2.6.1a) | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| HTSeq | Anders et al., 2015 | https://htseq.readthedocs.io/en/master/ |
| RUVSeq | Risso et al., 2014 | https://bioconductor.org/packages/release/bioc/html/RUVSeq.html |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| Homer | Heinz et al., 2010 | (http://homer.ucsd.edu/homer/interactions2/index.html |
| MACS2.1.0 | Zhang et al., 2008 | https://github.com/taoliu/MACS |
| R | Chen et al., 2009 | https://www.r-project.org/ |
| Corrplot | Taiyun Wei and Viliam Simko (2017) | https://github.com/taiyun/corrplot |
| Diffbind v1.16.3 | Ross-Innes et al., 2012 | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| Burrows-Wheeler Aligner (BWA) | Li and Durbin, 2009 | http://bio-bwa.sourceforge.net/ |
| Juicer | Rao et al., 2014 | https://github.com/aidenlab/juicer/wiki |
| Graphpad Prism 8 | Graphpad | https://www.graphpad.com/ |
| Distiller | Abdennur and Mirny, 2020 | https://github.com/mirnylab/distiller-nf)) |
| Hi-C explorer | Ramirez et al., 2018 | https://hicexplorer.readthedocs.io/en/latest/content/list-of-tools.html |
| BEDTools | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| deepTools | Ramírez et al., 2016 | https://deeptools.readthedocs.io/en/develop/ |