Platform overview

ChromoPaint™ HuCL PanChromo MPX Assay

419-plex assay for in situ 3D genome analysis in human cell lines (HuCL) with jebFISH™ Technology
ChromoPaint™ 400+ plex genome target panel for jebFISH analysis on human cell lines

Genome target locations

419 genomic loci targets

Complete assay kit for highly multiplexed jebFISH direct in situ visualization of the 3D genome in human cell lines (HuCL)

The ChromoPaint™ HuCL PanChromo MPX Assay breaks new ground as the first commercially available kit for genome-wide, high-multiplex direct visualization of the 3D genome.

The ChromoPaint kit includes reagents with optimized solutions for performing a 419-plex jebFISH in situ 3D genome visualization on the PaintScape™ platform instruments. The assay not only leverages powerful jebFISH chemistry, but also sophisticated barcoding for efficient simultaneous detection and identification of the 419 genome targets.

In addition to the LociPaint™ genome painting probes, each assay kit also contains reagents and solutions for sample preparation, imaging, and readout reagents—including jebReader™ readout probes with sophisticated, proprietary barcoding. Optimized for use on human cell lines.

Kit Includes

ChromoPaint HuCL PanChromo MPX panel
Sample prep reagents
Imaging and barcode readout reagents
Very high-multiplex: paints 419 genome targets simultaneously
Simultaneously paints across all 23 chromosomes
Directly visualize focal amplifications, segmented copy number variations, and other ploidy aberrations
Visualize translocations and ecDNA
See multi-loci proximities directly in situ
Ability to visualize p-arm and q-arm segments

ChromoPaint DATA examples

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-showing-ecDNA-tranlocations
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)

What is jebFISH ?
Why the 3D genome ?
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