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
Chromatin tracing of 2-Mb on chr21
10 Experiment Sets
Alistair Boettiger
STANFORD,
Xiaowei Zhuang
HARVARD
Raw: 0
Processed: 11
Chromatin tracing of chrX
9 Experiment Sets
Siyuan Wang
YALE
Raw: 0
Processed: 18
Chromatin tracing in mouse brain
1 Experiment Set
Long Cai
CALTECH
Raw: 0
Processed: 18
Chromatin tracing in mESCs
1 Experiment Set
Long Cai
CALTECH
Raw: 0
Processed: 12
Chromatin Tracing of Sox2 and SE with engineered CTCF insertions
5 Experiment Sets
Bing Ren
UCSD
Raw: 0
Processed: 7
Chromatin tracing in mammalian tissue
1 Experiment Set
Siyuan Wang
YALE
Raw: 0
Processed: 12
Super-resolution imaging of chromosome walks
1 Experiment Set
Chao-Ting Wu
HARVARD
Raw: 0
Processed: 18
Synthetic condensation of tudor domain
13 Experiment Sets
(13 Experiment Sets with Raw Files)
Karla Neugebauer
YALE
Raw: 1341
Processed: 1354
Live imaging of chromatin topology and transcription
3 Experiment Sets
(3 Experiment Sets with Raw Files)
Thomas Gregor
PRINCETON
Raw: 3
Processed: 3
Robert Coleman
EINSTEIN
Raw: 37
Processed: 169
Nascent Transcript RNA FISH - JQ1 treatment
26 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 144
Nascent Transcript RNA FISH - Flavopiridol treatment
8 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 112
Nascent Transcript RNA FISH - Triptolide treatment
4 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 60
Nascent Transcript RNA FISH - DRB treatment
6 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 36
Nascent Transcript RNA FISH +/- 4h GATA1 induction
6 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 24
Nascent Transcript RNA FISH +/- 13h GATA1 induction
12 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 84
Slc25a37 RNA FISH - Enhancer Deletion
5 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 45
hbb-b1 RNA FISH +/- Looping Factor
2 Experiment Sets
Arjun Raj
UPENN
Raw: 0
Processed: 12
SPT on U2OS cells for Spot-On analysis
45 Experiment Sets
(1 Experiment Set with Raw Files)
Xavier Darzacq
Berkeley
Raw: 19
Processed: 45
SPT on JM8N4 cells for Spot-On analysis
15 Experiment Sets
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)
Thomas Gregor
PRINCETON
Raw: 54
Processed: 148
DNA FISH in F121-9 Cells
9 Experiment Sets
Paul Kaufman
UMMS
Raw: 105
Processed: 21
Immunofluorescence on
synchronized HeLa cells
135 Experiment Sets
Job Dekker
UMMS
Raw: 1335
Processed: 135
SMSN (Barentine et al 2019 bioRxiv)
5 Experiment Sets
David Baddeley
YALE
Raw: 21
Processed: 16
FISH for DNA SPRITE
19 Experiment Sets
Mitchell Guttman
CALTECH
Raw: 797
Processed: 33
Clodagh O'Shea
SALK
Raw: 6
Processed: 0
DNA FISH on Chr1 and Chr17
14 Experiment Sets
Tom Misteli
NCI
Raw: 0
Processed: 52
DNA FISH on Chr17
71 Experiment Sets
Tom Misteli
NCI
Raw: 0
Processed: 256
DNA FISH on Chr18
38 Experiment Sets
Tom Misteli
NCI
Raw: 0
Processed: 137
DNA FISH on Chr4
70 Experiment Sets
Tom Misteli
NCI
Raw: 0
Processed: 247