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
4DN
2 Micro-C
human
HFFc6,
H1-hESC
Job Dekker, UMMS
4DN
2 Micro-C
2 in situ Hi-C
human
WTC-11
Job Dekker, UMMS
4DN
19 Dilution Hi-C
human
HG00732,
GM19141,
GM19240,
GM18507,
GM19099,
GM19239,
GM19204,
GM19193,
GM18522,
HG00731,
GM18508,
HG00512,
HG00514,
GM19238,
HG00733,
GM18486,
GM18516,
HG00513,
GM18505
Bing Ren, UCSD
ENCODE
21 Dilution Hi-C
2 in situ Hi-C
human
brain microvascular endothelial cell,
SK-MEL-5,
SJCRH30,
ACHN,
Caki2,
T47D,
NCI-H460,
astrocyte of the spinal cord,
HeLa-S3,
HepG2,
A549,
Panc1,
LNCaP clone FGC,
DLD1,
endothelial cell of hepatic sinusoid,
endometrial microvascular endothelial cells,
RPMI-7951,
G401,
astrocyte of the cerebellum,
SK-N-MC,
brain pericyte,
SK-N-DZ
Job Dekker, UMMS
4DN
2 DNase Hi-C
human,
mouse
brain,
heart
Christine Disteche, UW,
Chuck Murry, UW
External
6 Dilution Hi-C
9 in situ Hi-C
human,
mouse
HUVEC cell,
KBM-7,
IMR-90,
192627,
K562,
HAP-1,
CH12.LX,
CC-2551
Erez Lieberman Aiden, BCM,
Bing Ren, UCSD

  Time Course

Data Set
Project
Replicate Sets
Species
Biosources
Publication
Study
Lab
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
Late 2-cell stage embryo,
animal zygote,
cerebral cortex,
embryo,
oocyte,
inner cell mass,
R1 mESC line,
sperm,
Early 2-cell stage embryo,
8-cell stage embryo
Embryo Development
Wei Xie, TSINGHUA
External,
4DN
59 in situ Hi-C
2 Dilution Hi-C
human
HeLa-S3
Cell Cycle
Job Dekker, UMMS
External
5 in situ Hi-C
mouse
mouse embryonic stem cell,
46C
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
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
Compartments and Nuclear Lamina
Job Dekker, UMMS
External
2 Dilution Hi-C
mouse
thymocyte with Lbr-/-,
thymocyte
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
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
immediate neuronal precursor cell,
globose cell of olfactory epithelium,
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