Data Gallery

Featured PaintScape™ Data

Data examples and biological insights from jebFISH™ genome analysis on the PaintScape™ platform
in situ Chromosome Traces in Single Cells
PaintScape-data-chromotrace-IMR90-ChromoPaint-MPX-cell14
PaintScape chromosome traces from jebFISH 3D genome analysis on IMR90 cells with the 400+ plex ChromoPaint HuCL PanChromo MPX panel
(all chromosome view of a single nucleus)
Visualization of
Translocations
PaintScape data image from jebFISH on MCF7
jebFISH analysis of MCF-7 with the ChromoPaint PanChromo MPX kit visualized a translocation from Chr 6 to 3 as well as aneuploidy of Chr 3.
(Only Chr 3 and 6 displayed for clarity).
Structural Genome Insights across Cell Populations
PaintScape-data-MCF7-distance-heatmap with ecDNA and tranlocation
jebFISH analysis of MCF-7 with a 400+ plex ChromoPaint HuCL PanChromo MPX panel revealed structural aberrations including translocations, multi-loci proximities, and ecDNA indication
PaintScape chromotrace of Chr 20 in MCF7 cells revealed ecDNA formation
jebFISH 3D genome visualization on the PaintScape platform with the ChromoPaint kit revealed focal amplifications of segments of Chr 20 in MCF-7 cells and visualization of ecDNA (circled in blue)

Chromopaint DATA spotlight

jebFISH with the ChromoPaint assay kit visualized ecDNA and focal amplifications of Chr 20 in MCF-7 cells

The ChromoPaint HuCL PanChromo MPX Assay was used to perform jebFISH 3D genome visualization of MCF-7 cells on the PaintScape instrument platform. The LociPaint probe panel in the kit simultaneously painted multiple genomic targets along all chromosomes. The jebFISH analysis visualized several known chromosomal aberrations and focal amplifications including focal amplifications of chromosome 20 (shown here). PaintScape visualization of the focal amplifications (e.g., Target 363) also further indicated ecDNA formation (circled in blue).

Focal amplifications of genome targets 363, 364, and 365 were visualized in individual nuclei of the MCF-7 sample (one sample nuclei shown)
jebFISH enabled seeing the focal amplifications in the context of the rest of Chr 20 (colored in purple) and revealed when they appeared in ecDNA (blue circle)
Those amplified regions of Chr 20 correlate with known regions of clustered breakpoints and DEREs (distant estrogen response elements) observed in ER+ breast cancer cells*

* Hsu, Pei-Yin et al. Cancer Cell (2013)

PAINTSCAPE DATA SPOTLIGHT

PaintScape visualized and revealed structural genome changes to Chr 11 in human fibroblast cells after infection with human cytomegalovirus (hCMV)*

A high-plex jebFISH genome painting of chromosome (Chr) 11 with the PaintScape platform on a human fibroblast cell line was used to directly visualize and compare the folding of Chr 11 (with p- and q- arm detail) before and after infection with hCMV. Figure A below shows the in situ Paintscape image with a single cell zoom-in and the arm detail from the control (no infection) cell sample. Figure B compares the p- and q- arm traces at three timepoints: before (no infection), 24-hr post infection, and 72-hr post infection.

* In collaboration with Giovanni Bosco Lab (Dartmouth) and Felicia Goodrum Lab (Dartmouth).

Results revealed by PaintScape

In control cells (no infection), interactions of specific regions of the p- and q-arms were observed; but changes occurred in the post infection samples.
In virus-infected cells, notable Chr 11 restructuring was observed, e.g., a section of the q-arm extended out in the 24-hr post infection sample. (Fig. B)
As infection time progressed, the Chr 11 p- and q-arms interacted less (Fig. C)
Figure A | PaintScape in situ visualization of Chr 11 in control cells (no infection)
jebFISH analysis of Chr 11 on human fibroblast cells with PaintScape
Figure B | PaintScape Chr 11 traces with p-arm/q-arm detail at different timepoints revealed notable differences
PaintScape Chr11 ChromoTrace with p- and q-arm detail--hCMV-control
control cells
(no infection)
PaintScape Chr11 ChromoTrace with p- and q-arm detail--hCMV-24hr post infection
24hr post hCMV infection
PaintScape Chr11 ChromoTrace with p- and q-arm detail--hCMV-72hr post infection
72hr post hCMV infection
Figure C | PaintScape inter-target distance heatmaps from the three timepoints further highlighted Chr 11 genome restructuring in hCMV infected cells
PaintScape-data-Chr11-distance-heatmap-0hr-hCMV-post-infxn
control cells
(no infection)
PaintScape-data-Chr11-distance-heatmap-24hr-hCMV-post-infxn
24hr post hCMV infection
PaintScape-data-Chr11-distance-heatmap-72hr-hCMV-post-infxn
72hr post hCMV infection

KEY: p-arm targets in red; q-arm targets in blue.

PaintScape revealed differences in Chr 11 conformation with notable genome restructuring in hCMV infected cells such as an extended out section of the q-arm 24-hr post infection. Not only was Chr 11 folding directly visualized in each single cell, but also inter-target distance data was tabulated and pooled for sub- and whole cell populations and revealed differences in the cell population profiles at 24-hr and 72-hr post infection compared to the control pre-infection cell sample. Heatmaps of inter-target distances shown above.*

* In collaboration with Giovanni Bosco Lab (Dartmouth) and Felicia Goodrum Lab (Dartmouth).

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