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4DN Microscopy Data Overview

Microscopy Datasets

Below is a summary table of the microscopy datasets that are publicly available on the 4DN data portal. Many of these datasets don't include the raw image files; this is because the submitters in many cases have deemed the processed data to be much more useful to collaborators and outside users than raw images. If you are interested in obtaining raw images or any other type of file that isn't available on the data portal, please contact the data generating lab.

Sample Image
Dataset
Experiment Type
Publication
Biosource
Lab
Data File Availability
Genome-scale imaging in IMR90 cells
2 Experiment Sets
Multiplexed FISH
Su JH et al. (2020)
Cell
IMR-90
Xiaowei Zhuang
HARVARD
Raw: 0
Processed: 7
Multiplexed FISH in R1 mESCs
2 Experiment Sets
Multiplexed FISH
Jensen CL et al. (2023)
BioRxiv
R1 mESC line
Alistair Boettiger
STANFORD
Raw: 0
Processed: 3
Multiplexed FISH in Drosophila embryos
2 Experiment Sets
Multiplexed FISH
Messina O et al. (2023)
Nature
whole fruit fly
Nollmann Marcelo
Center for Structural Biochemistry
Raw: 0
Processed: 2
Multiplexed FISH in mouse ESC-E14
2 Experiment Sets
Multiplexed FISH
Le DJ et al (2024)
Biorxiv
ES-E14TG2a
Alistair Boettiger
STANFORD
Raw: 0
Processed: 5
IF in mouse ESC to NPC
5 Experiment Sets
Immunofluorescence
Li G et al (2024)
Biorxiv
F121-6
Doug Fowler
UW
Raw: 980
Processed: 0
DNA FISH in U2OS
2 Experiment Sets
DNA FISH
Zhang H et al (2023)
Nature Communications
U2OS
Huaiying Zhang
CMU
Raw: 0
Processed: 12
Chromatin tracing in mouse primary motor cortex
2 Experiment Sets
Multiplexed FISH
Zhuang X et al
bioRxiv
Primary Motor Cortex
Xiaowei Zhuang
Harvard
Raw: 0
Processed: 28
Chromatin tracing of single chromosomes
5 Experiment Sets
Multiplexed FISH
Wang S et al (2016)
Science
IMR-90
Siyuan Wang
YALE
Raw: 0
Processed: 5
Chromatin tracing of chrX
21 Experiment Sets
Multiplexed FISH
Patterson B et al (2023)
Science Advances
HES-3, H7-hESC, H9 and IMR-90
Siyuan Wang
YALE,
Bing Yang
YALE
Raw: 0
Processed: 21
Chromatin tracing of Sox9 in CNCC
5 Experiment Sets
Multiplexed FISH
Chen et al (2023)
Biorxiv
H9
Alistair Boettiger
STANFORD,
Joanna Wysocka
STANFORD
Raw: 0
Processed: 16
Chromatin tracing of Pitx1 in mouse limb bud
1 Experiment Set
Multiplexed FISH
Hung et al (2023)
Biorxiv
Mouse limb bud
Alistair Boettiger
STANFORD,
David Kingsley
STANFORD
Raw: 0
Processed: 15
Chromatin tracing of mouse HoxA locus
5 Experiment Sets
Multiplexed FISH
Murphy et al (2022)
Nature Genetics
Multiple
Alistair Boettiger
STANFORD
Raw: 0
Processed: 20
Chromatin tracing of chr3 in mESC with CTCF and cohesin depletion
40 Experiment Sets
Multiplexed FISH, RNA FISH
Hafner et al (2022)
Molec. Cell
Mouse Embryonic stem cells - ES-E14TG2a and TC1
Alistair Boettiger
STANFORD
Raw: 0
Processed: 162
Chromatin tracing of BX-C in Drosophila
7 Experiment Sets
Multiplexed FISH
Mateo LJ et al (2019)
Nature
Embryo
Alistair Boettiger
STANFORD
Raw: 0
Processed: 25
Chromatin tracing of 2-Mb on chr21
10 Experiment Sets
Multiplexed FISH
Bintu et al (2018)
Science
Multiple human cell lines
Alistair Boettiger
STANFORD,
Xiaowei Zhuang
HARVARD
Raw: 0
Processed: 11
Chromatin tracing of chrX
9 Experiment Sets
Multiplexed FISH
Cheng et al (2021)
Genome Biol
IMR-90
and
RPE-hTERT
Siyuan Wang
YALE
Raw: 0
Processed: 18
Chromatin tracing in mouse brain
1 Experiment Set
Multiplexed FISH
Takei et al (2021)
Science
cerebral cortex
Long Cai
CALTECH
Raw: 0
Processed: 18
Chromatin tracing in mESCs
1 Experiment Set
Multiplexed FISH
Takei et al (2021)
Nature
ES-E14TG2a.4
Long Cai
CALTECH
Raw: 0
Processed: 12
Chromatin Tracing of Sox2 and SE with engineered CTCF insertions
5 Experiment Sets
Multiplexed FISH
Huang et al (2021)
Nat Genet
F123-CASTx129 (engineered)
Bing Ren
UCSD
Raw: 0
Processed: 7
Chromatin tracing in mammalian tissue
1 Experiment Set
Multiplexed FISH
Liu et al (2020)
Nat Commun
Fetal mouse liver
Siyuan Wang
YALE
Raw: 0
Processed: 12
RNA FISH for TERRA in U2OS
2 Experiment Sets
(2 Experiment Sets with Raw Files)
RNA FISH
Xu et al (2022)
Front Mol Biosci
U2OS
Huaiying Zhang
CMU
Raw: 12
Processed: 6
SPT for GAGA transcription factor
30 Experiment Sets
(4 Experiment Sets with Raw Files)
SPT
Tang et al (2022)
Nat Struct Mol Biol
Fly larval hemocytes
Carl Wu
JHU
Raw: 345
Processed: 60
Super-resolution imaging of chromosome walks
1 Experiment Set
Multiplexed FISH
Nir et al (2018)
PLoS Genet
GM23248
Chao-Ting Wu
HARVARD
Raw: 0
Processed: 18
Synthetic condensation of tudor domain
13 Experiment Sets
(13 Experiment Sets with Raw Files)
OptoDroplet
Courchaine et al (2021)
Cell
NIH3T3
Karla Neugebauer
YALE
Raw: 1341
Processed: 1354
Live imaging of chromatin topology and transcription
3 Experiment Sets
(3 Experiment Sets with Raw Files)
SPT
Chen et al (2018)
Nat Genet
Fly embryos
Thomas Gregor
PRINCETON
Raw: 3
Processed: 3
SPT on U2OS cells
8 Experiment Sets
(1 Experiment Set with Raw Files)
SPT
Kenworthy et al (2022)
Biophys J
U2OS
Robert Coleman
EINSTEIN
Raw: 37
Processed: 169
Nascent Transcript RNA FISH - JQ1 treatment
26 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
Arjun Raj
UPENN
Raw: 0
Processed: 144
Nascent Transcript RNA FISH - Flavopiridol treatment
8 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
Arjun Raj
UPENN
Raw: 0
Processed: 112
Nascent Transcript RNA FISH - Triptolide treatment
4 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
Arjun Raj
UPENN
Raw: 0
Processed: 60
Nascent Transcript RNA FISH - DRB treatment
6 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
Arjun Raj
UPENN
Raw: 0
Processed: 36
Nascent Transcript RNA FISH +/- 4h GATA1 induction
6 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
Arjun Raj
UPENN
Raw: 0
Processed: 24
Nascent Transcript RNA FISH +/- 13h GATA1 induction
12 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
Arjun Raj
UPENN
Raw: 0
Processed: 84
Slc25a37 RNA FISH - Enhancer Deletion
5 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
(+/- enhancer deletions)
Arjun Raj
UPENN
Raw: 0
Processed: 45
hbb-b1 RNA FISH +/- Looping Factor
2 Experiment Sets
RNA FISH
Bartman et al (2018)
Mol Cell
G1-ER4
Arjun Raj
UPENN
Raw: 0
Processed: 12
SPT on U2OS cells for Spot-On analysis
45 Experiment Sets
(1 Experiment Set with Raw Files)
SPT
Hansen et al (2018)
eLife
U2OS
Xavier Darzacq
Berkeley
Raw: 19
Processed: 45
SPT on JM8N4 cells for Spot-On analysis
15 Experiment Sets
SPT
Hansen et al (2018)
eLife
JM8.N4
Xavier Darzacq
Berkeley
Raw: 0
Processed: 15
Dual color smFISH on fruit fly embryo
(nuclear cycle 13)
6 Experiment Sets
(1 Experiment Set with Raw Files)
RNA FISH
Zoller et al (2018)
Cell
Fly embryos
Thomas Gregor
PRINCETON
Raw: 54
Processed: 148
DNA FISH in F121-9 Cells
9 Experiment Sets
DNA FISH
Bizhanova et al (2020)
Chromosoma
F121-9-CASTx129
(Tier 2)
Paul Kaufman
UMMS
Raw: 105
Processed: 21
Immunofluorescence on
synchronized HeLa cells
135 Experiment Sets
Immunofluorescence
Abramo et al (2019)
Nat Cell Biol
HeLa lines
Job Dekker
UMMS
Raw: 1335
Processed: 135
SMSN (Barentine et al 2019 bioRxiv)
5 Experiment Sets
DNA FISH, Immunofluorescence
Barentine et al (2019)
bioRxiv
Multiple
David Baddeley
YALE
Raw: 21
Processed: 16
FISH for DNA SPRITE
19 Experiment Sets
DNA FISH
Quinodoz et al (2018)
Cell
F121-CASTx129
Mitchell Guttman
CALTECH
Raw: 797
Processed: 33
ChromEMT
3 Experiment Sets
Electron Tomography
Ou et al (2017)
Science
Multiple
Clodagh O'Shea
SALK
Raw: 6
Processed: 0
DNA FISH on Chr1
52 Experiment Sets
(5 Experiment Sets with Raw Files)
DNA FISH
Finn et al (2019)
Cell
HFF-hTERT
Tom Misteli
NCI
Raw: 600
Processed: 272
DNA FISH on Chr1 and Chr17
14 Experiment Sets
DNA FISH
Finn et al (2019)
Cell
HFF-hTERT
Tom Misteli
NCI
Raw: 0
Processed: 52
DNA FISH on Chr17
71 Experiment Sets
DNA FISH
Finn et al (2019)
Cell
HFF-hTERT
Tom Misteli
NCI
Raw: 0
Processed: 256
DNA FISH on Chr18
38 Experiment Sets
DNA FISH
Finn et al (2019)
Cell
HFF-hTERT
Tom Misteli
NCI
Raw: 0
Processed: 137
DNA FISH on Chr4
70 Experiment Sets
DNA FISH
Finn et al (2019)
Cell
HFF-hTERT
Tom Misteli
NCI
Raw: 0
Processed: 247