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
Nils Krietenstein et al. (2019)
(bioRxiv)
Job Dekker, UMMS
Hi-C on H1 cells - protocol variations 4DN 3 in situ Hi-C
1 Dilution Hi-C
human H1-hESC Nils Krietenstein et al. (2019)
(bioRxiv)
Job Dekker, UMMS
Hi-C on HFF cells - protocol variations 4DN 6 in situ Hi-C
1 Dilution Hi-C
human HFFc6
HFF-hTERT
Nils Krietenstein et al. (2019)
(bioRxiv)
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
human
mouse
brain
heart
Deng X et al. (2015)
(Genome Biology)
Bertero A et al. (2019)
(Nature Comm.)
Chuck Murry, UW
Christine Disteche, UW
Hi-C on lympoblastoid cell lines from 1000G individuals 4DN 19 Dilution Hi-C
human HG00731
GM19240
GM19239
GM18516
GM18486
GM19193
GM19141
GM19099
HG00514
HG00512
HG00732
GM18505
GM19238
GM18507
HG00513
GM18508
GM19204
GM18522
HG00733
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 astrocyte of the spinal cord
astrocyte of the cerebellum
HepG2
brain pericyte
LNCaP clone FGC
Caki2
SK-N-MC
HeLa-S3
ACHN
brain microvascular endothelial cell
A549
T47D
endometrial microvascular endothelial cells
SJCRH30
Panc1
DLD1
endothelial cell of hepatic sinusoid
RPMI-7951
G401
SK-N-DZ
NCI-H460
SK-MEL-5
Job Dekker, UMMS
Hi-C on other common cell lines External 6 Dilution Hi-C
9 in situ Hi-C
human
mouse
192627
HAP-1
KBM-7
IMR-90
K562
HUVEC cell
CH12.LX
CC-2551
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 Yanxiao Zhang et al. (2019)
(bioRxiv)
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 46C
mouse embryonic stem cell
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

  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 immediate neuronal precursor cell
olfactory receptor 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 neural layer
retinal rod cell
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 with Lbr-/-
thymocyte
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 Tsung-Han S. Hsieh et al. (2019)
(bioRxiv)
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