PMID- 35145120
OWN - NLM
STAT- MEDLINE
DCOM- 20220415
LR  - 20220531
IS  - 2052-4463 (Electronic)
IS  - 2052-4463 (Linking)
VI  - 9
IP  - 1
DP  - 2022 Feb 10
TI  - Simultaneous visualization of DNA loci in single cells by combinatorial 
      multi-color iFISH.
PG  - 47
LID - 10.1038/s41597-022-01139-2 [doi]
LID - 47
AB  - Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable 
      studying the three-dimensional (3D) organization of the genome at the single cell 
      level. However, there is a major unmet need for open access, high quality, 
      curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained 
      by applying our recently developed iFISH method to simultaneously visualize 16 
      small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in 
      human cells, in a single round of hybridization. We show how combinatorial color 
      coding can be used to precisely localize multiple loci in 3D within single cells, 
      and how inter-locus distances scale inversely with chromosome contact frequencies 
      determined by high-throughput chromosome conformation capture (Hi-C). We provide 
      raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a 
      free resource that can facilitate studies of 3D genome organization in single 
      cells and can be used to develop automatic FISH analysis algorithms.
CI  - (c) 2022. The Author(s).
FAU - Mota, Ana
AU  - Mota A
AUID- ORCID: 0000-0001-8592-9764
AD  - Bienko-Crosetto Lab for Quantitative Genome Biology, Department of Microbiology, 
      Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23 A, Solna, SE-17165, Sweden.
FAU - Schweitzer, Maud
AU  - Schweitzer M
AD  - Bienko-Crosetto Lab for Quantitative Genome Biology, Department of Microbiology, 
      Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23 A, Solna, SE-17165, Sweden.
FAU - Wernersson, Erik
AU  - Wernersson E
AD  - Bienko-Crosetto Lab for Quantitative Genome Biology, Department of Microbiology, 
      Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23 A, Solna, SE-17165, Sweden.
FAU - Crosetto, Nicola
AU  - Crosetto N
AUID- ORCID: 0000-0002-3019-6978
AD  - Bienko-Crosetto Lab for Quantitative Genome Biology, Department of Microbiology, 
      Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden.
AD  - Science for Life Laboratory, Tomtebodavagen 23 A, Solna, SE-17165, Sweden.
FAU - Bienko, Magda
AU  - Bienko M
AD  - Bienko-Crosetto Lab for Quantitative Genome Biology, Department of Microbiology, 
      Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165, Sweden. 
      magda.bienko@ki.se.
AD  - Science for Life Laboratory, Tomtebodavagen 23 A, Solna, SE-17165, Sweden. 
      magda.bienko@ki.se.
LA  - eng
GR  - StG-2016_GENOMIS_715727/EC | EU Framework Programme for Research and Innovation 
      H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 
      Excellent Science - European Research Council)/
GR  - 621-2014-5503/Vetenskapsradet (Swedish Research Council)/
GR  - CDA grant/Human Frontier Science Program (HFSP)/
PT  - Dataset
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20220210
PL  - England
TA  - Sci Data
JT  - Scientific data
JID - 101640192
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Algorithms
MH  - *Cell Nucleus
MH  - Chromosomes
MH  - *DNA
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - Single-Cell Analysis
PMC - PMC8831585
COIS- The authors declare no competing interests.
EDAT- 2022/02/12 06:00
MHDA- 2022/04/16 06:00
PMCR- 2022/02/10
CRDT- 2022/02/11 05:34
PHST- 2021/08/02 00:00 [received]
PHST- 2021/12/23 00:00 [accepted]
PHST- 2022/02/11 05:34 [entrez]
PHST- 2022/02/12 06:00 [pubmed]
PHST- 2022/04/16 06:00 [medline]
PHST- 2022/02/10 00:00 [pmc-release]
AID - 10.1038/s41597-022-01139-2 [pii]
AID - 1139 [pii]
AID - 10.1038/s41597-022-01139-2 [doi]
PST - epublish
SO  - Sci Data. 2022 Feb 10;9(1):47. doi: 10.1038/s41597-022-01139-2.