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
External
8 in situ Hi-C
human
heart left atrium,
heart left ventricle
heart left ventricle
Wouter de Laat, HUBRECHT
External
2 in situ Hi-C
mouse
granulosa cell,
Sertoli cell
Sertoli cell
David Zarkower, UMN
4DN
12 in situ Hi-C
human
H1-hESC
Job Dekker, UMMS
4DN
3 Micro-C
human
HFF-hTERT
Job Dekker, UMMS
4DN
17 in situ Hi-C
1 Dilution Hi-C
1 Dilution Hi-C
human
HFF-hTERT,
HFFc6
HFFc6
Job Dekker, UMMS
4DN
9 Micro-C
human
HeLa-S3
Job Dekker, UMMS
4DN
18 in situ Hi-C
human
HeLa-S3
Job Dekker, UMMS
4DN
3 Micro-C
human
H1-hESC
Job Dekker, UMMS
4DN
4 Micro-C
human
H1-hESC
Job Dekker, UMMS
4DN
11 in situ Hi-C
human
H1-hESC
Job Dekker, UMMS
4DN
2 Micro-C
human
H1-hESC,
HFFc6
HFFc6
Job Dekker, UMMS
4DN
19 Dilution Hi-C
human
HG00733,
GM19239,
GM19099,
GM18508,
HG00731,
GM19240,
HG00514,
GM19193,
GM19141,
GM19204,
GM18505,
GM19238,
HG00513,
GM18507,
GM18522,
GM18516,
HG00512,
HG00732,
GM18486
GM19239,
GM19099,
GM18508,
HG00731,
GM19240,
HG00514,
GM19193,
GM19141,
GM19204,
GM18505,
GM19238,
HG00513,
GM18507,
GM18522,
GM18516,
HG00512,
HG00732,
GM18486
Bing Ren, UCSD
ENCODE
21 Dilution Hi-C
2 in situ Hi-C
2 in situ Hi-C
human
endothelial cell of hepatic sinusoid,
Panc1,
HeLa-S3,
SK-MEL-5,
SK-N-MC,
astrocyte of the spinal cord,
endometrial microvascular endothelial cells,
SJCRH30,
RPMI-7951,
DLD1,
NCI-H460,
Caki2,
HepG2,
A549,
T47D,
ACHN,
G401,
LNCaP clone FGC,
astrocyte of the cerebellum,
SK-N-DZ,
brain microvascular endothelial cell,
brain pericyte
Panc1,
HeLa-S3,
SK-MEL-5,
SK-N-MC,
astrocyte of the spinal cord,
endometrial microvascular endothelial cells,
SJCRH30,
RPMI-7951,
DLD1,
NCI-H460,
Caki2,
HepG2,
A549,
T47D,
ACHN,
G401,
LNCaP clone FGC,
astrocyte of the cerebellum,
SK-N-DZ,
brain microvascular endothelial cell,
brain pericyte
Job Dekker, UMMS
4DN
2 DNase Hi-C
human,
mouse
mouse
brain,
heart
heart
Christine Disteche, UW,
Chuck Murry, UW
Chuck Murry, UW
External
6 Dilution Hi-C
9 in situ Hi-C
9 in situ Hi-C
human,
mouse
mouse
CC-2551,
192627,
HUVEC cell,
CH12.LX,
IMR-90,
HAP-1,
K562,
KBM-7
192627,
HUVEC cell,
CH12.LX,
IMR-90,
HAP-1,
K562,
KBM-7
Erez Lieberman Aiden, BCM,
Bing Ren, UCSD
Bing Ren, UCSD
External
5 Dilution Hi-C
23 in situ Hi-C
23 in situ Hi-C
human
GM12878
Erez Lieberman Aiden, BCM,
Bing Ren, UCSD
Bing Ren, UCSD
Time Course
Data Set
Project
Replicate Sets
Species
Biosources
Publication
Study
Lab
4DN
2 in situ Hi-C
human
HCT116
Hi-C in HCT116 cells
Yijun Ruan, JAX
4DN
2 in situ Hi-C
mouse
trophoblast cell,
extraembryonic cell
extraembryonic cell
Effie Apostolou, CORNELL
4DN
7 in situ Hi-C
human
HUES8,
H1-hESC
H1-hESC
Early pancreatic differentiation
Danwei Huangfu, MSKCC
4DN
9 in situ Hi-C
mouse
Treg precursor,
double-positive, alpha-beta thymocyte,
CD4-positive, alpha-beta T cell,
double negative thymocyte,
CD8-positive, alpha-beta thymocyte,
regulatory T cell,
CD4-positive, CD25-positive, alpha-beta regulatory T cell
double-positive, alpha-beta thymocyte,
CD4-positive, alpha-beta T cell,
double negative thymocyte,
CD8-positive, alpha-beta thymocyte,
regulatory T cell,
CD4-positive, CD25-positive, alpha-beta regulatory T cell
Regulatory T-Cell maturation
Jesse Dixon, SALK
4DN
4 DNase Hi-C
human
RUES2
Endothelial differentiation
Chuck Murry, UW
4DN
4 in situ Hi-C
mouse
cerebellum vermis lobule,
cerebellum vermis lobule IX,
cerebellum - PND 6,
cerebellum - PND 22
cerebellum vermis lobule IX,
cerebellum - PND 6,
cerebellum - PND 22
Tomoko Yamada, NW
4DN
9 in situ Hi-C
zebrafish
Zebrafish Embryo
Hi-C on Zebrafish embryos
Brad Cairns, UTAH
4DN
5 in situ Hi-C
mouse
G1E-ER4
Cell Cycle
Gerd Blobel, CHOP
4DN
4 in situ Hi-C
human
CyT49
Endoderm Differentiation
Bing Ren, UCSD
External
14 in situ Hi-C
mouse
R1 mESC line,
Late 2-cell stage embryo,
embryo,
Early 2-cell stage embryo,
sperm,
cerebral cortex,
8-cell stage embryo,
animal zygote,
oocyte,
inner cell mass
Late 2-cell stage embryo,
embryo,
Early 2-cell stage embryo,
sperm,
cerebral cortex,
8-cell stage embryo,
animal zygote,
oocyte,
inner cell mass
Embryo Development
Wei Xie, TSINGHUA
External,
4DN
4DN
59 in situ Hi-C
2 Dilution Hi-C
2 Dilution Hi-C
human
HeLa-S3
Cell Cycle
Job Dekker, UMMS
External
5 in situ Hi-C
mouse
46C,
mouse embryonic stem cell
mouse embryonic stem cell
Neural Differentiation
Giacomo Cavalli, UM
4DN
6 in situ Hi-C
human
H9
Cardiomyocyte Differentiation
Bing Ren, UCSD
4DN
4 DNase Hi-C
human
WTC-11
Cardiomyocyte Differentiation
Chuck Murry, UW
External
18 Dilution Hi-C
chicken
DT40
Cell Cycle
Job Dekker, UMMS
4DN
4 DNase Hi-C
human
RUES2
Cardiomyocyte Differentiation
Chuck Murry, UW
Disrupted or Atypical Cells
Data Set
Project
Replicate Sets
Species
Biosources
Publication
Study
Lab
4DN
7 in situ Hi-C
mouse
regulatory T cell
Foxp3 in Treg cell development
Jesse Dixon, SALK
4DN
1 in situ Hi-C
mouse
double-positive, alpha-beta thymocyte
TCF1 protein in thymocytes
Golnaz Vahedi, UPENN
4DN
1 in situ Hi-C
mouse
double-positive, alpha-beta thymocyte
TCF1 protein in thymocytes
Golnaz Vahedi, UPENN
4DN
2 in situ Hi-C
mouse
scid.adh
TCF1 protein in thymocytes
Golnaz Vahedi, UPENN
4DN
12 in situ Hi-C
hamster,
human
human
olfactory receptor cell
Olfactory Sensory Neurons
Stavros Lomvardas, COLUMBIA
4DN
2 in situ Hi-C
human
HCT116
Cohesin Protein Function
Jennifer Cremins, UPENN
4DN
4 in situ Hi-C
human
H1-hESC
caRNA Function
Sheng Zhong, UCSD
4DN
2 in situ Hi-C
mouse
F123-CASTx129
Sequence requirements of CTCF insulation
Bing Ren, UCSD
External
2 Dilution Hi-C
mouse
retinal neural layer,
retinal rod cell
retinal rod cell
Compartments and Nuclear Lamina
Job Dekker, UMMS
External
2 Dilution Hi-C
mouse
thymocyte,
thymocyte with Lbr-/-
thymocyte with Lbr-/-
Compartments and Nuclear Lamina
Job Dekker, UMMS
External
8 in situ Hi-C
mouse
ES-E14TG2a
Gene activation (zfp608 or sox4)
Giacomo Cavalli, UM
4DN
19 in situ Hi-C
human
K562
Compartments
Job Dekker, UMMS
4DN
3 Micro-C
mouse
JM8.N4
Transcription
Xavier Darzacq, BERKELEY
4DN
4 TCC
human
IMR-90
Viral Genome Integration
Lin Chen, USC
External
58 in situ Hi-C
human
HCT116
Cohesin Protein Function
Erez Lieberman Aiden, BCM,
Rafael Casellas, NIH
Rafael Casellas, NIH
External
17 Dilution Hi-C
human
HeLa cell line
CTCF Protein Function
Jan-Michael Peters, IMP
4DN
3 DNase Hi-C
human
LMNA-R225X-het
Compartments and Nuclear Lamina
Chuck Murry, UW
External
2 in situ Hi-C
mouse
CH12
CTCF Protein Function
Rafael Casellas, NIH
External
5 in situ Hi-C
mouse
B cell derived cell line
Transcription, ATP, and Replication inhibition
Rafael Casellas, NIH
External
3 Dilution Hi-C
mouse
ES-E14TG2a
CTCF Protein Function
Benoit Bruneau, UCSF
External
22 Dilution Hi-C
chicken
DT40
Condensin-I and Condensin-II Protein Function
Job Dekker, UMMS
External
4 in situ Hi-C
human
HAP-1
Cohesin Protein Function
Benjamin Rowland, NKI
External
2 DNase Hi-C
human
HeLa-S3
Splicing
Todd Waldman, GEORGETOWN
4DN
2 in situ Hi-C
fruit fly
S2
Heat Shock
John Lis, CORNELL
4DN
2 in situ Hi-C
human
K562
Heat Shock
John Lis, CORNELL
4DN
4 in situ Hi-C
mouse
F123-CASTx129
CTCF Protein Function
Bing Ren, UCSD
External
3 TCC
mouse
hepatocyte
Cohesin Protein Function
Francois Spitz, PASTEUR
4DN
7 in situ Hi-C
mouse
globose cell of olfactory epithelium,
immediate neuronal precursor cell,
olfactory receptor cell
immediate neuronal precursor cell,
olfactory receptor cell
Olfactory Sensory Neurons
Stavros Lomvardas, COLUMBIA
4DN
6 DNase Hi-C
mouse
Patski
X Inactivation
Christine Disteche, UW
4DN
6 in situ Hi-C
mouse
ES-E14
Enhancers (H3K4me1-writers)
Bing Ren, UCSD
High-Resolution Hi-C Datasets
Below is a list of high-resolution Hi-C experiment sets on the 4DN Data Portal with more than 1 billion reads.