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Dataset Fig3a_DNAunderwind

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Project

Project
394-Fukute-DNAunderwind
Title
Mechanical regulation of DNA underwinding in the nucleus
Description
This project investigates how DNA is underwound in the mechanical environment of the nucleus, by performing super-resolution imaging of underwound DNA and nuclear proteins in mouse cells.
License
CC BY
Funding
This work was supported by JST, CREST, Grant Number JPMJCR2023, Japan (J.F., K.M.), JST, CREST, Grant Number JPMJCR22L5, Japan (T.A.), JST, SPRING, Grant Number JPMJSP2110, Japan (J.F.), MEXT/JSPS, KAKENHI, Grant Number JP23KJ1255, Japan (J.F.), and MEXT/JSPS, KAKENHI, Grant Number JP20K20180 and JP23K17196, Japan (K.M.).

Dataset

Title
Lattice-SIM images of ribosome DNA, bio-psoralen, fibrillarin, and DAPI in nucleus
Description
Lattice-SIM images of ribosome DNA, fibrillarin, DAPI and bio-psoralen in nucleus. The underwound DNA was labeled with biotinylated psoralen, which preferentially binds to underwound DNA rather than relaxed DNA, before cell fixation. Channel1;ribosome DNA, Chennel2;psoralen, Channel3;fibrillarin (a marker for fibrillar component of the nucleoli), Channel4;DAPI
License
CC BY
Submitted at
None
Released at
None
Updated at

Biosamples

Description
MC3T3-E1 mouse osteoblast-like cells in which underwound nuclear DNA was fluorescently labeled with psoralen
Organisms
Mus musculus (NCBI:txid10090)
Strains
Cells
Cell lines
MC3T3-E1 cell ()
Intrinsic variables
Extrinsic variables
The biotinylated psoralen was applied to the cell and crosslinked to DNA by UV irradiation. After cell fixation, NeutrAvidin Protein, DyLight^{TM} 488 was applied and other staining was conducted. The ribosome DNA was labeled with Cy3- labeld probes for mouse ribosome DNA (BAC clone RP23- 225M6, Chromosome Science Laboratory).

Ontologies

UBERON
Anatomical entities
Gene ontology: Biological processes
Gene ontology: Cellular components
nucleus (GO:0005634)
Gene ontology: Molecular functions

Genetics

Gene names
NA
Protein names
rRNA 2'-O-methyltransferase fibrillarin (P35550)
Genetic methods
antibody (FBbi_00000401)
Protein tags
NeutrAvidin Protein (DyLight^{TM} 488)
Probes
DAPI (FBbi:00000056)
Oligo Primer
Genotype

Treatments

Reagent or Compound
Concentrations
FoldDilution

Imaging Methods

Dimensions
2560x2560x1x4x1
X scales
0.05 micrometer
Y scales
0.05 micrometer
Z scales
T scales
Channels
4 channel
Microscopy types
(Lattice-pattern structured illumination microscopy)
Detection methods
scientific complementary metal oxide semiconductor (sCMOS)
Visualization methods
Cy3 NeutrAvidin Protein (DyLight^{TM} 488) Alexa Fluor 568 DAPI
Illumination methods
scientific complementary metal oxide semiconductor (sCMOS)
Sources of contrast
Contrast enhancing methods
Resolution enhancing methods
structured illumination microscopy (SIM)
Image parameters
Sample preparation methods
formaldehyde fixed tissue

Instruments

Body
Elyra7 super-resolution microscope (Zeiss)
Model
Light source
Detector
Objective
Plan-Apochromat 40×/1.4 oil objective lens
Filter set
Dichroic