PMID- 33328483
OWN - NLM
STAT- MEDLINE
DCOM- 20210909
LR  - 20210909
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 10
IP  - 1
DP  - 2020 Dec 16
TI  - ProbeDealer is a convenient tool for designing probes for highly multiplexed 
      fluorescence in situ hybridization.
PG  - 22031
LID - 10.1038/s41598-020-76439-x [doi]
LID - 22031
AB  - Fluorescence in situ hybridization (FISH) is a powerful method to visualize the 
      spatial positions of specific genomic loci and RNA species. Recent technological 
      advances have leveraged FISH to visualize these features in a highly multiplexed 
      manner. Notable examples include chromatin tracing, RNA multiplexed error-robust 
      FISH (MERFISH), multiplexed imaging of nucleome architectures (MINA), and 
      sequential single-molecule RNA FISH. However, one obstacle to the broad adoption 
      of these methods is the complexity of the multiplexed FISH probe design. In this 
      paper, we introduce an easy-to-use, versatile, and all-in-one application called 
      ProbeDealer to design probes for a variety of multiplexed FISH techniques and 
      their combinations. ProbeDealer offers a one-stop shop for multiplexed FISH 
      design needs of the research community.
FAU - Hu, Mengwei
AU  - Hu M
AD  - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 
      06510, USA.
FAU - Yang, Bing
AU  - Yang B
AD  - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 
      06510, USA.
FAU - Cheng, Yubao
AU  - Cheng Y
AD  - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 
      06510, USA.
FAU - Radda, Jonathan S D
AU  - Radda JSD
AD  - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 
      06510, USA.
FAU - Chen, Yanbo
AU  - Chen Y
AD  - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 
      06510, USA.
FAU - Liu, Miao
AU  - Liu M
AD  - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 
      06510, USA.
FAU - Wang, Siyuan
AU  - Wang S
AD  - Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 
      06510, USA. siyuan.wang@yale.edu.
AD  - Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, 
      CT, 06510, USA. siyuan.wang@yale.edu.
AD  - Yale Combined Program in the Biological and Biomedical Sciences, Yale University 
      School of Medicine, New Haven, CT, USA. siyuan.wang@yale.edu.
AD  - Molecular Cell Biology, Genetics and Development Program, Yale University School 
      of Medicine, New Haven, CT, USA. siyuan.wang@yale.edu.
AD  - Biochemistry, Quantitative Biology, Biophysics and Structural Biology Program, 
      Yale University School of Medicine, New Haven, CT, USA. siyuan.wang@yale.edu.
AD  - M.D.-Ph.D. Program, Yale University School of Medicine, New Haven, CT, USA. 
      siyuan.wang@yale.edu.
AD  - Yale Center for RNA Science and Medicine, Yale University School of Medicine, New 
      Haven, CT, USA. siyuan.wang@yale.edu.
AD  - Yale Liver Center, Yale University School of Medicine, New Haven, CT, USA. 
      siyuan.wang@yale.edu.
LA  - eng
GR  - 1R33CA251037/CA/NCI NIH HHS/United States
GR  - U01 CA260701/CA/NCI NIH HHS/United States
GR  - 1DP2GM137414/NH/NIH HHS/United States
GR  - 1R01HG011245/HG/NHGRI NIH HHS/United States
GR  - R01 HG011245/HG/NHGRI NIH HHS/United States
GR  - T32 GM007499/GM/NIGMS NIH HHS/United States
GR  - 2T32GM007499/NH/NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20201216
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
RN  - 0 (DNA Probes)
SB  - IM
MH  - Animals
MH  - DNA Probes/*metabolism
MH  - Genome, Human
MH  - Humans
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Mice
MH  - Time Factors
MH  - User-Computer Interface
PMC - PMC7745008
COIS- S.W. is one of the inventors on a patent applied for by Harvard University 
      related to MERFISH. Other authors declare no competing interests.
EDAT- 2020/12/18 06:00
MHDA- 2021/09/10 06:00
PMCR- 2020/12/16
CRDT- 2020/12/17 05:41
PHST- 2020/07/09 00:00 [received]
PHST- 2020/10/28 00:00 [accepted]
PHST- 2020/12/17 05:41 [entrez]
PHST- 2020/12/18 06:00 [pubmed]
PHST- 2021/09/10 06:00 [medline]
PHST- 2020/12/16 00:00 [pmc-release]
AID - 10.1038/s41598-020-76439-x [pii]
AID - 76439 [pii]
AID - 10.1038/s41598-020-76439-x [doi]
PST - epublish
SO  - Sci Rep. 2020 Dec 16;10(1):22031. doi: 10.1038/s41598-020-76439-x.