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. Author manuscript; available in PMC: 2021 Feb 18.
Published in final edited form as: Immunity. 2020 Feb 11;52(2):257–274.e11. doi: 10.1016/j.immuni.2020.01.003

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Anti-mouse CD4 (RM4–4) BioLegend Cat# 116005; RRID:AB_313690
Anti-mouse CD8a (53–6.7) Thermo Cat# 17-0081-82; RRID:AB_469335
Anti-H3K27ac Abcam Cat# ab4729; RRID:AB_2118291
Anti-CTCF Millipore Cat# 07–729; RRID:AB_441965
Anti-SMC1 Bethyl Cat# A300–055A; RRID:AB_2192467
Normal Rabbit IgG CST Cat# #2729; RRID:AB_1031062
Chemicals, Peptides and Recombinant Proteins
7AAD BioLegend Cat# 420403
70uM mesh filters Fisher Cat# 08-771-2
RPMI 1640 medium Invitrogen Cat# 11875085
Fetal Bovine Serum Sigma- Aldrich Cat# F2442
Ethylene glycol bis(succinic acid N hydroxysuccinimideester) (EGS) Thermo Cat# 21565
DMSO Fisher Cat# BP231–1
Formaldehyde solution 16% Thermo Cat# PI28908
Glycine Thermo Cat# 15527013
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001
MboI NEB Cat# R0147
Biotin-14-dATP Invitrogen Cat# 19524–016
dCTP Invitrogen Cat# 18253–013
dTTP Invitrogen Cat# 18255–018
dGTP Invitrogen Cat# 18254–011
Tris HCl, pH 7.5,1M Thermo Cat# 15567027
NaCl, 5M Thermo Cat# AM9759
MgCl2 1M Thermo Cat# AM9530G
IGEPAL CA-630 Sigma Cat# I8896–50ML
EDTA Invitrogen Cat# 15575–038
Protein A Magnetic beads Pierce Cat# 88846
Lithium Chloride, 8M Sigma-Aldrich Cat# L7026
Sodium bicarbonate Sigma-Aldrich Cat#144-55-8
T4 DNA Ligase NEB Cat# M0202L
BSA, 50mg/ml Invitrogen Cat# AM2616
Tween 20 BIO-RAD Cat# 170–6531
DNA Polymerase I, Large (Klenow) Fragment NEB Cat# M0210S
Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32851
Dynabeads MyOne
Streptavidin C-1		 Invitrogen Cat# 65001
Phusion PCR Master Mix NEB Cat# M0531
Nextera XT Index Kit Illumina Cat# FC-131–1001
SPRIselect Beckman Coulter Cat# B23318
MinElute Reaction Cleanup Kit Qiagen Cat# 28204
QIAQuick PCR Purification Kit Qiagen Cat# 28104
Phosphate-Buffered Saline, 1X Thermo Cat# 10010031
RNase Thermo Cat# EN0531
Proteinase K Thermo Cat# AM2546
Protein G Dynabeads Thermo Cat# 10003D
2-Mercaptoethanol Sigma Cat# M6250–10ML
Buffer RLT Plus Qiagen Cat# 1053393
RNeasy Plus Micro Kit Qiagen Cat# 74034
Secondary Oligopaint probe: /5Alex647N/TGATCGACCACGGCCAAGACGGAGAGCGTGTG/ 3AlexF647N/ https://doi.org/10.1073/pnas.1714530115 N/A
Secondary Oligopaint probe: /5ATTO565N/ACACN/ACCTTGCACGTCGTGGACCTCCTGCGCTA/
3ATTO565N/		 https://doi.org/10.1073/pnas.1714530115 N/A
Secondary Oligopaint probe: /5Alex488N/CACAN/ACGCTCTTCCGTTCTATGCGACGTCGGTG/
3AlexF488N/		 https://doi.org/10.1073/pnas.1714530115 N/A
CD4 (L3T4) Microbeads Miltenyi Biotec 130-117-043
Polysine microscope slides Thermo Scientific Cat# P4981–001
Silicone isolators Electron Microscopy Sciences Cat# 70339–05
CD8-Biotin Miltenyi Biotec Cat# 130-118-074
Ethanol Decon Laboratories 2716
Dimethylformamide Sigma-Aldrich Cat# D4551
Polyvinylsulfonic acid (PVSA) Sigma Aldrich Cat# 278424
coverslips Fisher Scientific Cat# 12-548-5M
Nowrinkle rubber cement Elmer’s N/A
Slowfade Gold Antifade Reagent Invitrogen by Thermo Fisher Scientific Cat# S36936
Dries instantly top coat Sally Hansen’s Cat# 45114
Chromium Single Cell 3’ Library & Gel Bead Kit v2, 4 rxns 10X genomics Cat# PN-120267
Chromium Single Cell A Chip A Kit, 16 rxns 10X genomics Cat# PN-1000009
Chromium i7 Multiplex Kit, 96 rxns 10X genomics Cat# PN-120262
Critical Commercial Assays
Anti-Biotin MultiSort Ki Miltenyi Biotec 130-091-256
Tn5 Transposase Illumina Cat# FC-121–1030
SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian kit Takara Cat# 635006
NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat# E7645S
D1000 ScreenTape Agilent Cat# 5067–5582
D1000 Reagents Agilent Cat# 5067–5583
High Sensitivity D1000 ScreenTape Agilent Cat# 5067–5584
High Sensitivity D1000 Reagents Agilent Cat# 5067–5585
Genomic DNA ScreenTape Agilent Cat# 5067–5365
Genomic DNA Reagents Agilent Cat# 5067–5366
RNA ScreenTape Agilent Cat# 5067–5576
RNA ScreenTape Ladder Agilent Cat# 5067–5578
RNA ScreenTape Sample Buffer Agilent Cat# 5067–5577
Publicly accessible data
RNA-seq from Idd9.2 congenic mice Berry et al., 2015 GSE64674
TCF-1 ChIP-seq Dose et al., 2014 GSE46662
RNA-seq from fast and slow progressing T1D subjects Dufort et al., 2019 GSE78099
Deposited data
ChIP-seq, RNA-seq (bulk and single-cell), ATAC-seq and HiChIP This study GSE141853
Experimental Models: Organisms/Strains
Mouse: C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664
Mouse: NOD/ShiLtJ Jackson Laboratory IMSR Cat# JAX:001976, RRID:IMSR_JAX:001976
Software, Algorithms and Databases
FastQC (Andrews, 2017) https://www.bioinformatics.babraham.ac.uk/projects; RRID:SCR_014583
Trim Galore (Krueger, 2017a) https://www.bioinformatics.babraham.ac.uk/projects; RRID:SCR_011847
UCSC Genome Browser (Rosenbloom et al., 2015) https://genome.ucsc.edu; RRID:SCR_005780
GENCODE (Mudge and Harrow, 2015) https://www.gencodegenes.org; RRID:SCR_014966
Bowtie2 (Langmead and Salzberg, 2012) http://bowtie-bio.sourceforge.net/bowtie2
STAR (Dobin et al., 2013) https://github.com/alexdobin/STAR
Picard (BroadInstitute, 2017) http://broadinstitute.github.io/picard; RRID:SCR_006525
HTSeq (Anders et al., 2015) https://pypi.python.org/pypi/HTSeq; RRID:SCR_005514
DESeq2 (Love et al., 2014) https://github.com/Bioconductor-mirror/DESeq2; RRID:SCR_015687
R (Team, 2016) https://cran.r-project.org; RRID:SCR_001905
MACS2 (Zhang et al., 2008) https://github.com/taoliu/MACS
MMARGE (Link et al., 2018) https://github.com/vlink/marge
Homer (Heinz et al., 2010) http://homer.ucsd.edu/homer; RRID:SCR_010881
bedtools (Quinlan and Hall, 2010) https://bedtools.readthedocs.io/en/latest/#
Bedtools; RRID:SCR_006646
wigToBigWig http://hgdownload.cse.ucsc.edu/admin/exe/
GSEA (Subramanian et al., 2005) http://software.broadinstitute.org/gsea; RRID:SCR_003199
HiC-Pro (Servant et al., 2015) https://github.com/nservant/HiC-Pro
HiC-Pro, RRID:SCR_017643
Mango (Phanstiel et al., 2015) https://github.com/dphansti/mango
igraph (Csardi and Nepusz 2006) https://igraph.org/r/
ggplot2 (Wickham 2016) https://ggplot2.tidyverse.org/
Metascape (Zhou et al., 2019) http://metascape.org/gp/index.html#/main/step1
Metascape, RRID:SCR_016620
Circos (Krzywinski et al. 2009) http://circos.ca/
Circos, RRID:SCR_011798
Imaging Analysis Suite (Raj. et al. 2008) https://bitbucket.org/arjunrajlaboratory/rajlabimagetools/wiki/Home
ImageJ https://imagej.nih.gov/ij/
GEOquery (Davis and Meltzer 2007) https://bioconductor.org/packages/release/bioc/html/GEOquery.html
limma (Ritchie et al., 2015) https://bioconductor.org/packages/release/bioc/html/limma.html
LIMMA, RRID:SCR_010943
juicer (Durand et al., 2016) https://github.com/aidenlab/juicer/wiki/Juicer-Tools-Quick-Start
Juicer, RRID:SCR_017226
HiCPlotter (Akdemir and Chin, 2015) https://github.com/kcakdemir/HiCPlotter
RepeatMasker http://www.repeatmasker.org/
RepeatMasker, RRID:SCR_012954
lastz (Harris, 2007) http://www.bx.psu.edu/~rsharris/lastz/
Cellranger 10X genomics Version 2.1.0
Seurat (Butler et al., 2018 and Stuart et al., 2019) https://satijalab.org/seurat/vignettes.html
Seurat, RRID:SCR_016341
Version 3.0.2
DoubletFinder (McGinnis et al., 2019) https://github.com/chris-mcginnis-ucsf/DoubletFinder
Garnett (Pliner et al., 2019) https://cole-trapnell-lab.github.io/garnett/
Too-Many-Cells (Schwartz et al., 2019) https://github.com/GregorySchwartz/too-many-cells