REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
rabbit polyclonal anti-Nucleolin	Abcam	Cat# ab22758, RRID:AB_776878
mouse monoclonal anti-SC35	Abcam	Cat# ab11826, RRID:AB_298608
Alexa Fluor® 647 goat anti-rabbit IgG (H+L)	Thermo Fisher Scientific	Cat# A-21244, RRID:AB_2535812
DyLight® 650 goat anti-mouse IgG (H+L) Bethyl		Cat# A90-116D5, RRID:AB_10630715
Bacterial and Virus Strains
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
Disuccinimidyl glutarate (DSG)	Thermo Fisher Scientific	Cat# 20593
16% Formaldehyde (w/v), Methanol-free	Pierce	Cat# 28908
Doxycycline Sigma		Cat# D9891
Critical Commercial Assays
NEBNext End Repair Module	NEB	Cat# E6050
NEBNext dA-tailing Module	NEB	Cat# B6059
Instant Sticky End Master Mix	NEB	Cat# M0370
Deposited Data
Raw and analyzed data	This paper	GEO: GSE114242
ChIP-seq (e.g., Pol II, H3K4me3, etc) in mES cells	ENCODE; https://encodeproject.org	https://www.encodeproject.org/search/?type=Experiment&assembly=mm9&biosample_type=stem+cell
ChIP-seq (e.g., Pol II, H3K4me3, etc) in GM12878 cells	ENCODE; https://encodeproject.org	https://www.encodeproject.org/search/?type=Experiment&assembly=hg19&biosample_term_name=GM12878
GRO-seq data in mES cells	(Jonkers et al., 2014)	GEO:GSE48895
TAD Triplets identified using GAM in mES cells	(Beagrie et al., 2017)	https://media.nature.com/original/nature-assets/nature/journal/v543/n7646/extref/nature21411-s3.xlsx
Hi-C data in mES cells	(Dixon et al., 2012)	GEO:GSE35156
Hi-C data in GM12878 cells	(Rao et al., 2014)	GEO:GSE63525
Malat1 and U1 RAP-DNA in mES cells	(Engreitz et al., 2014)	GEO:GSE55914
Mouse ES cell super-enhancers	(Whyte et al., 2013)	http://www.cell.com/cms/attachment/2031389007/2048455341/mmc1.zip
Mouse ES cell enhancers	(Whyte et al., 2013)	http://www.cell.com/cms/attachment/2031389007/2048455344/mmc2.xls
Lamin Associated Domains in mES cells	(Peric-Hupkes et al., 2010)	https://ars.els-cdn.com/content/image/1-s2.0-S1097276510003217-mmc2.xls
Experimental Models: Cell Lines
F1 2-1 hybrid wild-type mouse ES cell line (129 x cast)	Kathrin Plath	(Engreitz et al., 2013)
pSM33 mES cell line	Kathrin Plath	(Engreitz et al., 2013)
GM12878 Human Lymphoblasts	Coriell Cell Repositories	GM12878, RRID:CVCL_7526
Human HEK293T	ATCC	Cat# CRL-3216, RRID:CVCL_0063
Experimental Models: Organisms/Strains
Oligonucleotides
SPRITE oligos and adaptors	This paper	See Table S5
Recombinant DNA
Software and Algorithms
Bowtie2 (v2.3.1)	Langmead Laboratory	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
ComputeGenomeMask	GATK package	https://gatkforums.broadinstitute.org/gatk/discussion/1499/computegenomemask
Bedtools (v2.26.0)	Quinlan Laboratory	http://bedtools.readthedocs.io/en/latest/
Imaris (8.4.1)	Bitplane Inc.	http://bitplane.com
Hi-Corrector Zhou	Laboratory	http://zhoulab.usc.edu/Hi-Corrector/
Cworld Dekker	Laboratory	https://github.com/dekkerlab/cworld-dekker
SPRITE computational pipeline	This study	https://github.com/GuttmanLab/sprite-pipeline/wiki
GraphPad Prism 7	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
R Software Package 3.3.1	The R Foundation	https://www.r-project.org/
Other
Resources related to the SPRITE protocol	This paper	http://www.lncrna.caltech.edu/protocols.php
Branson needle-tip sonicator (3 mm diameter (1/8″ Doublestep tip)	Branson Ultrasonics	Cat# 101-148-063