| Antibodies |
| Anti-CD31-Alexa Fluor 488 |
BioLegend |
303110 |
| Anti-CD34-FITC |
BioLegend |
343503 |
| Anti-CD29-APC |
BioLegend |
303008 |
| Anti-NCAM-Biotin |
BioLegend |
318319 |
|
Bacterial and virus strains
|
| NA |
|
|
|
|
|
|
Biological samples
|
|
|
| Lower extremity human skeletal muscle samples (collected from a female, 67-year-old individual) |
Duke University Medical Center |
NA |
|
|
|
|
Chemicals, peptides, and recombinant proteins
|
| Matrigel |
Corning |
354230 |
| mTeSR™ Plus |
STEMCELL Technologies |
05825 |
| Accutase |
BioLegend |
423201 |
| Chitin column |
Bio-Rad |
7372522 |
| Amicon Ultracel 30K |
Millipore |
UFC903024 |
| Dialysis membrane tube |
Spectra/Por |
D1614-11 |
| NEBuffer 3.1 |
NEB |
B7203S |
| CviQI |
NEB |
R0639L |
| T4 DNA ligase (400U/μl) |
NEB |
M0202S |
| 20mg/ml BSA |
NEB |
B9000S |
| Proteinase K |
Thermo Fisher |
AM2546 |
| Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v,) |
Spectrum |
136112-00-0 |
| T4 DNA polymerase |
NEB |
M0203L |
| NlaIII |
NEB |
R0125L |
| SPRI beads |
Beckman |
B23319 |
| DNA clean & concentrator kit |
Zymo |
D4013 |
| Gel extraction using DNA recovery kit |
Zymo |
D4002 |
| Roche Complete Protease Inhibitor |
Sigma |
5056489001 |
| PmeI |
NEB |
R0560L |
| RNaseOUT |
Invitrogen |
10777-019 |
| Q5® High-Fidelity DNA Polymerase |
NEB |
m0491L |
| FuGENE® HD Transfection Reagent |
Promega |
E2311 |
| Anza™ 13 Esp3I |
Invitrogen |
IVGN0136 |
|
|
|
|
Critical commercial assays
|
| iTaq™ Universal SYBR® Green Supermix |
Bio-Rad |
1725122 |
| Dual-Luciferase® Reporter Assay System |
Promega |
E1910 |
|
|
|
|
Deposited data
|
| HiCAR H1 |
This study |
GEO: GSE162819
|
| HiCAR GM12878 |
This study |
GEO: GSE162819
|
| HiCAR human muscle stem cells |
This study |
Synapse:syn26841404 |
| For published genomics datasets, see Table S3
|
Table S3
|
NA |
|
|
|
|
Experimental models: Cell lines
|
| H1 hESC |
WiCell |
WA01 |
| Human lymphoblastoid cell lines |
Coriell Institute |
GM12878 |
|
|
|
|
Experimental models: Organisms/strains
|
| NA |
|
|
|
|
|
|
Oligonucleotides
|
| Custom primers for HiCAR, see Table S1
|
Table S1
|
NA |
| sgRNA Oligos, see Table S1
|
Table S1 |
NA |
|
|
|
|
Recombinant DNA
|
| pTXB1-Tn5 |
Addgene |
60240 |
| Lentiguide-puro |
Addgene |
52963 |
| Lenti-dCas9-KRAB-blast |
Addgene |
89567 |
| Lenti dCAS-VP64_Blast |
Addgene |
61425 |
| pGL3-Promoter |
Promega |
E1761 |
| pRL-SV40 |
Promega |
E2231 |
|
|
|
|
Software and algorithms
|
| BWA |
(Li and Durbin 2010) |
http://bio-bwa.sourceforge.net/bwa.shtml
|
| Pairtools |
Python package |
https://github.com/mirnylab/pairtools
|
| HiGlass |
(Kerpedjiev et al. 2018) |
https://github.com/higlass
|
| EnrichedHeatmap |
(Gu et al. 2018) |
https://github.com/jokergoo/EnrichedHeatmap
|
| Cooltools |
Python package |
https://github.com/open2c/cooltools
|
| HiCRep |
(Yang et al. 2017) |
https://github.com/qunhualilab/hicrep
|
| Pairsqc |
(Lee et al. 2021) |
https://github.com/4dn-dcic/pairsqc
|
| MACS2 |
(Zhang et al. 2008) |
https://github.com/macs3-project/MACS
|
| Chip-R |
(Newell et al. 2021) |
https://github.com/rhysnewell/ChIP-R/
|
| Gimme |
(van Heeringen and Veenstra 2011) |
https://github.com/vanheeringen-lab/gimmemotifs
|
| MAPS |
(Juric et al. 2019) |
https://github.com/ijuric/MAPS
|
| Juicer:HiCCUPS |
(Durand et al. 2016) |
https://github.com/aidenlab/juicer
|
| FitHiC2 |
(Kaul, Bhattacharyya, and Ay 2020) |
https://github.com/ay-lab/fithic
|
| HiCAR nextflow pipeline |
(Ou, Ewels, and Bot,. 2022) |
DOI: 10.5281/zenodo.5889172
|
| Clusterprofile |
(Yu et al. 2012) |
https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
|
|
|
|
|
Other
|
| Detailed protocol for the preparation of HiCAR library |
In this study |
See Supplemental information, Method S1
|
