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Disrupted or Atypical Cells

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   September 9th, 2020 at 7:22pm

Disrupted or Atypical Cells

Data Set
Project
Replicate Sets
Species
Biosources
Publication
Study
Lab
Hi-C on mouse cerebellar granule neurons
4DN
24 in situ Hi-C
mouse
cerebellar granule cell
Perturbed cerebellar neuron time series
Tomoko Yamada, NW
Hi-C in lung tissue
4DN
1 in situ Hi-C
mouse
lung
Liu M et al. (2024)
(bioRxiv)
Hi-C in LUAD
Siyuan Wang, YALE
Hi-C on mouse cerebellar granule neurons - developmental series
4DN
4 in situ Hi-C
mouse
cerebellar granule cell,
granule cell precursor
Scrutton Alvarado NJ et al. (2025)
(Biology open)
Perturbed cerebellar neuron time series
Tomoko Yamada, NW
Hi-C on WTC-11 differentiated to cardiac muscle cell
4DN
3 in situ Hi-C
human
WTC-11
Grant ZL et al. (2025)
(bioRxiv)
Cardiomyocyte differention of TBX5 allelic series
Benoit Bruneau, UCSF
Hi-C on mononuclear cells from b-ALL patient
4DN
36 in situ Hi-C
human
mononuclear cell
Chromatin Structure in B-ALL
Jesse Dixon, SALK
Hi-C on hTert-RPE-1 with timecourse of NIPBL or Rad21 depletion
4DN
24 in situ Hi-C
human
RPE-hTERT
Popay TM et al. (2024)
(bioRxiv)
Dynamics of Cohesin-mediated Loop extrusion
Jesse Dixon, SALK
Hi-C on Maturing Regulatory T-cells with Fox3p disruption
4DN
7 in situ Hi-C
mouse
regulatory T cell
Liu Z et al. (2023)
(Nat Commun)
Foxp3 in Treg cell development
Jesse Dixon, SALK
Hi-C on DP2 cells isolated from CRE induced TCF1-KO mice
4DN
1 in situ Hi-C
mouse
double-positive, alpha-beta thymocyte
Wang W et al. (2022)
(Nature immunology)
TCF1 protein in thymocytes
Golnaz Vahedi, UPENN
Hi-C on DP2 cells isolated from CRE induced mice
4DN
1 in situ Hi-C
mouse
double-positive, alpha-beta thymocyte
Wang W et al. (2022)
(Nature immunology)
TCF1 protein in thymocytes
Golnaz Vahedi, UPENN
Hi-C on Scid.adh cells
4DN
2 in situ Hi-C
mouse
scid.adh
Wang W et al. (2022)
(Nature immunology)
TCF1 protein in thymocytes
Golnaz Vahedi, UPENN
Bruneau lab TBX5 allelic series
4DN
4 in situ Hi-C
human
WTC-11
Grant ZL et al. (2025)
(bioRxiv)
Cardiomyocyte differention of TBX5 allelic series
Benoit Bruneau, UCSF
Hi-C on human or hamster Olfactory Sensory Neurons infected with SARS-Cov2
4DN
12 in situ Hi-C
hamster,
human
olfactory receptor cell
Zazhytska M et al. (2022)
(Cell)
Olfactory Sensory Neurons
Stavros Lomvardas, COLUMBIA
Hi-C on HCT116 +/- WAPL
4DN
2 in situ Hi-C
human
HCT116
Emerson DJ et al. (2022)
(Nature)
Cohesin Protein Function
Jennifer Cremins, UPENN
Hi-C on H1 cells
4DN
4 in situ Hi-C
human
H1-hESC
Calandrelli R et al. (2023)
(Nat Commun)
caRNA Function
Sheng Zhong, UCSD
Hi-C on Sox2 tagged F123 cells
4DN
2 in situ Hi-C
mouse
F123-CASTx129
Huang H et al. (2021)
(Nat Genet)
Sequence requirements of CTCF insulation
Bing Ren, UCSD
Ren lab TBX5allelic series
CvDC
6 in situ Hi-C
human
WTC-11
TBX5 and cardiac differentiation
Bing Ren, UCSD
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 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
Liquified Chromatin Hi-C on K562 cells
4DN
19 in situ Hi-C
human
K562
Belaghzal H et al. (2021)
(Nat Genet)
Compartments
Job Dekker, UMMS
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
TCC on IMR90 +/- Adenovirus
4DN
4 TCC
human
IMR-90
Li H et al. (2017)
(bioRxiv)
Viral Genome Integration
Lin Chen, USC
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 sync. SCC1-AID or CTCF-AID tagged Hela
External
17 Dilution Hi-C
human
HeLa cell line
Wutz G et al. (2017)
(EMBO J)
CTCF Protein Function
Jan-Michael Peters, IMP
Hi-C on lamin A/C haploinsufficient hiPSC-derived cardiomyocytes
4DN
3 DNase Hi-C
human
LMNA-R225X-het
Bertero A et al. (2019)
(J Cell Biol)
Compartments and Nuclear Lamina
Chuck Murry, UW
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
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
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
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 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
DNase Hi-C in Hela-S3 cells +/- SF3B1 siRNA
External
2 DNase Hi-C
human
HeLa-S3
Kim JS et al. (2019)
(J Biol Chem)
Splicing
Todd Waldman, GEORGETOWN
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
Hi-C on CTCF-AID tagged F123-CASTx129
4DN
4 in situ Hi-C
mouse
F123-CASTx129
Kubo N et al. (2021)
(Nat Struct Mol Biol)
CTCF Protein Function
Bing Ren, UCSD
TCC on hepatocytes +/- NIPBL
External
3 TCC
mouse
hepatocyte
Schwarzer W et al. (2017)
(Nature)
Cohesin Protein Function
Francois Spitz, PASTEUR
Hi-C on Mouse Olfactory System cells
4DN
7 in situ Hi-C
mouse
globose cell of olfactory epithelium,
olfactory receptor cell,
immediate neuronal precursor cell
Monahan K et al. (2019)
(Nature)
Olfactory Sensory Neurons
Stavros Lomvardas, COLUMBIA
DNase Hi-C on Patski +/- Ds-TR and Dxz4 region modfications
4DN
6 DNase Hi-C
mouse
Patski
Bonora G et al. (2018)
(Nat Commun)
X Inactivation
Christine Disteche, UW
Hi-C on ES-E14 +/- Mll3-Mll4
4DN
6 in situ Hi-C
mouse
ES-E14
Yan J et al. (2018)
(Cell Res)
Enhancers (H3K4me1-writers)
Bing Ren, UCSD