Hi-C Data Sets and Studies on the 4DN Portal

Below is a summary of the Hi-C data sets on the 4DN Data Portal. In addition to data generated by the 4DN Network, the Portal hosts reference data sets from landmark publications. Uniformly processed results for both 4DN and External data are available for download on the Browse page and can be visualized in the 4DN Visualization Workspace.

  Single Time Point and Condition

Data Set Project Replicate Sets Species Biosources Publication Lab
Micro-C on H1 and HFF cells 4DN 2 Micro-C
human H1-hESC
HFFc6
Krietenstein N et al. (2020)
(Mol. Cell )
Job Dekker, UMMS
Hi-C on H1 cells - protocol variations 4DN 3 in situ Hi-C
1 Dilution Hi-C
human H1-hESC Krietenstein N et al. (2020)
(Mol. Cell )
Job Dekker, UMMS
Hi-C on HFF cells - protocol variations 4DN 6 in situ Hi-C
1 Dilution Hi-C
human HFF-hTERT
HFFc6
Krietenstein N et al. (2020)
(Mol. Cell )
Finn EH et al. (2019)
(Cell)
Job Dekker, UMMS
Hi-C on GM12878 cells - protocol variations External 5 Dilution Hi-C
23 in situ Hi-C
human GM12878 Selvaraj S et al. (2013)
(Nature Biotech.)
Sanborn AL et al. (2015)
(PNAS)
Rao SS et al. (2014)
(Cell)
Erez Lieberman Aiden, BCM
Bing Ren, UCSD
Hi-C and Micro-C on WTC-11 derived iPS cells 4DN 2 Micro-C
2 in situ Hi-C
human WTC-11 Job Dekker, UMMS
DNase Hi-C on tissues 4DN 2 DNase Hi-C
mouse
human
heart
brain
Deng X et al. (2015)
(Genome Biology)
Bertero A et al. (2019)
(Nature Comm.)
Christine Disteche, UW
Chuck Murry, UW
Hi-C on lympoblastoid cell lines from 1000G individuals 4DN 19 Dilution Hi-C
human GM19239
GM19193
GM18508
GM18516
GM18505
HG00733
GM19204
HG00732
HG00513
GM19238
HG00514
GM18522
GM19240
GM19099
HG00731
GM19141
GM18507
HG00512
GM18486
Gorkin DU et al. (2019)
(Genome Biology)
Bing Ren, UCSD
Hi-C on ENCODE3 cell lines ENCODE 21 Dilution Hi-C
2 in situ Hi-C
human T47D
SK-MEL-5
endometrial microvascular endothelial cells
Panc1
endothelial cell of hepatic sinusoid
SJCRH30
SK-N-DZ
HeLa-S3
astrocyte of the cerebellum
NCI-H460
Caki2
LNCaP clone FGC
ACHN
HepG2
DLD1
brain microvascular endothelial cell
A549
brain pericyte
G401
SK-N-MC
RPMI-7951
astrocyte of the spinal cord
Job Dekker, UMMS
Hi-C on other common cell lines External 6 Dilution Hi-C
9 in situ Hi-C
mouse
human
IMR-90
CC-2551
HUVEC cell
K562
KBM-7
HAP-1
CH12.LX
192627
Jin F et al. (2013)
(Nature)
Sanborn AL et al. (2015)
(PNAS)
Rao SS et al. (2014)
(Cell)
Erez Lieberman Aiden, BCM
Bing Ren, UCSD

  Time Course

Data Set Project Replicate Sets Species Biosources Publication Study Lab
Hi-C on WTC-11 differentiation to cardiomyocytes 4DN 4 DNase Hi-C
human WTC-11 Bertero A et al. (2019)
(Nature Comm.)
Cardiomyocyte Differentiation Chuck Murry, UW
Hi-C on H9 cells during cardiomyocyte differentiation 4DN 6 in situ Hi-C
human H9 Zhang Y et al. (2019)
(Nature Gen.)
Cardiomyocyte Differentiation Bing Ren, UCSD
DNAse Hi-C on RUES cell differentiation to cardiomyocytes 4DN 4 DNase Hi-C
human RUES2 Bertero A et al. (2019)
(Nature Comm.)
Cardiomyocyte Differentiation Chuck Murry, UW
Hi-C on mESC during neural differentiation External 5 in situ Hi-C
mouse mouse embryonic stem cell
46C
Bonev B et al. (2017)
(Cell)
Neural Differentiation Giacomo Cavalli, UM
Hi-C on synch. HeLa cells 4DN
External
59 in situ Hi-C
2 Dilution Hi-C
human HeLa-S3 Abramo K et al. (2019)
(Nature Cell Bio.)
Gibcus JH et al. (2018)
(Science)
Cell Cycle Job Dekker, UMMS
HiC on sync. chicken cells External 18 Dilution Hi-C
chicken DT40 Gibcus JH et al. (2018)
(Science)
Cell Cycle Job Dekker, UMMS
Hi-C on sync.G1E-ER4 4DN 5 in situ Hi-C
mouse G1E-ER4 Zhang H et al. (2019)
(Nature)
Cell Cycle Gerd Blobel, CHOP
Hi-C on hESC differentiated to pancreatic endoderm 4DN 4 in situ Hi-C
human CyT49 Endoderm Differentiation Bing Ren, UCSD
sisHi-C during early embryonic development External 14 in situ Hi-C
mouse embryo
Early 2-cell stage embryo
sperm
animal zygote
inner cell mass
Late 2-cell stage embryo
oocyte
R1 mESC line
cerebral cortex
8-cell stage embryo
Du Z et al. (2017)
(Nature)
Embryo Development Wei Xie, TSINGHUA

  Disrupted or Atypical Cells

Data Set Project Replicate Sets Species Biosources Publication Study Lab
Hi-C on Mouse Olfactory System cells 4DN 7 in situ Hi-C
mouse olfactory receptor cell
immediate neuronal precursor cell
globose cell of olfactory epithelium
Monahan K et al. (2019)
(Nature)
Olfactory Sensory Neurons Stavros Lomvardas, COLUMBIA
Hi-C on inverted or conventional neurons External 2 Dilution Hi-C
mouse retinal rod cell
retinal neural layer
Falk M et al. (2019)
(Nature)
Compartments and Nuclear Lamina Job Dekker, UMMS
Hi-C on thymocytes +/- Lbr External 2 Dilution Hi-C
mouse thymocyte
thymocyte with Lbr-/-
Falk M et al. (2019)
(Nature)
Compartments and Nuclear Lamina Job Dekker, UMMS
Hi-C on lamin A/C haploinsufficient hiPSC-derived cardiomyocytes 4DN 3 DNase Hi-C
human LMNA-R225X-het Bertero A et al. (2019)
(JCB)
Compartments and Nuclear Lamina Chuck Murry, UW
Liquified Chromatin Hi-C on K652 cells 4DN 19 in situ Hi-C
human K562 Houda Belaghzal et al. (2019)
(bioRxiv)
Compartments Job Dekker, UMMS
Hi-C on CTCF-AID tagged mESCs External 3 Dilution Hi-C
mouse ES-E14TG2a Nora EP et al. (2017)
(Cell)
CTCF Protein Function Benoit Bruneau, UCSF
Hi-C on CTCF-AID tagged F123-CASTx129 4DN 4 in situ Hi-C
mouse F123-CASTx129 Naoki Kubo et al. (2017)
(bioRxiv)
CTCF Protein Function Bing Ren, UCSD
Hi-C on sync. SCC1-AID or CTCF-AID tagged Hela External 17 Dilution Hi-C
human HeLa cell line Wutz G et al. (2017)
(EMBO journal)
CTCF Protein Function Jan-Michael Peters, IMP
Hi-C on CH12 +/- CTCF ZF domain External 2 in situ Hi-C
mouse CH12 Vian L et al. (2018)
(Cell)
CTCF Protein Function Rafael Casellas, NIH
TCC on hepatocytes +/- NIPBL External 3 TCC
mouse hepatocyte Schwarzer W et al. (2017)
(Nature)
Cohesin Protein Function Francois Spitz, PASTEUR
Hi-C on RAD21-AID tagged HCT-116 External 58 in situ Hi-C
human HCT116 Rao SSP et al. (2017)
(Cell)
Vian L et al. (2018)
(Cell)
Cohesin Protein Function Erez Lieberman Aiden, BCM
Rafael Casellas, NIH
Hi-C on HAP-1 +/- WAPL or SCC4 KO External 4 in situ Hi-C
human HAP-1 Haarhuis JHI et al. (2017)
(Cell)
Cohesin Protein Function Benjamin Rowland, NKI
HiC on sync. CAPH2-AID chicken cells CAPH-AID, CAPH2-AID, or SMC2-AID External 22 Dilution Hi-C
chicken DT40 Gibcus JH et al. (2018)
(Science)
Condensin-I and Condensin-II Protein Function Job Dekker, UMMS
Hi-C on activated B cells External 5 in situ Hi-C
mouse B cell derived cell line Vian L et al. (2018)
(Cell)
Transcription, ATP, and Replication inhibition Rafael Casellas, NIH
Micro-C on JM8.N4 Cells +/- transcription 4DN 3 Micro-C
mouse JM8.N4 Hsieh TS et al. (2020)
(Mol. Cell )
Transcription Xavier Darzacq, BERKELEY
DNase Hi-C in Hela-S3 cells +/- SF3B1 siRNA External 2 DNase Hi-C
human HeLa-S3 Kim JS et al. (2019)
(JBC)
Splicing Todd Waldman, GEORGETOWN
Hi-C on ES-E14 +/- Mll3-Mll4 4DN 6 in situ Hi-C
mouse ES-E14 Jian Yan et al. (2017)
(bioRxiv)
Enhancers (H3K4me1-writers) Bing Ren, UCSD
Hi-C on E14Tg2 cell line External 8 in situ Hi-C
mouse ES-E14TG2a Bonev B et al. (2017)
(Cell)
Gene activation (zfp608 or sox4) Giacomo Cavalli, UM
DNase Hi-C on Patski +/- Ds-TR and Dxz4 region modfications 4DN 6 DNase Hi-C
mouse Patski Bonora G et al. (2018)
(Nature Comm.)
X Inactivation Christine Disteche, UW
HiC on S2 cells +/- Heat Shock 4DN 2 in situ Hi-C
fruit fly S2 Ray J et al. (2019)
(PNAS)
Heat Shock John Lis, CORNELL
HiC on K562 cells +/- Heat Shock 4DN 2 in situ Hi-C
human K562 Ray J et al. (2019)
(PNAS)
Heat Shock John Lis, CORNELL
TCC on IMR90 +/- Adenovirus 4DN 4 TCC
human IMR-90 Haochen Li et al. (2017)
(bioRxiv)
Viral Genome Integration Lin Chen, USC