Expansion in situ genomic sequencing datasets
Data files
Oct 10, 2024 version files 672.87 MB
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README.md
706 B
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TableS1_control_reads.txt
80.58 MB
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TableS2_imr90_reads.txt
36.35 MB
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TableS3_progeria_reads.txt
555.85 MB
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TableS4_cell_stats.txt
95.54 KB
Abstract
Microscopy and genomics are both used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. While emerging multiplexed imaging methods can simultaneously localize genomic regions and nuclear proteins, their ability to accurately measure DNA-protein interactions is constrained by the diffraction limit of optical microscopy. Here, we describe expansion in situ genome sequencing (ExIGS), a technology that enables sequencing of genomic DNA and superresolution localization of nuclear proteins in single cells. We applied ExIGS to fibroblast cells derived from an individual with Hutchinson-Gilford progeria syndrome to characterize how variation in nuclear morphology affects spatial chromatin organization. Using this data, we discovered that lamin abnormalities are linked to hotspots of aberrant euchromatin repression that may erode cell identity. Further, we show that lamin abnormalities heterogeneously increase the repressive environment of the nucleus in tissues and aged cells. These results demonstrate that ExIGS may serve as a generalizable platform for connecting nuclear abnormalities to changes in gene regulation across disease contexts.
README: Expansion in situ genomic sequencing datasets
https://doi.org/10.5061/dryad.rr4xgxdhm
Description of the data and file structure
Tables S1-S3 contain spatially-resolved genomic reads generated using expansion in situ genome sequencing (ExIGS). Each table contains a description of columns at the top. Table S1 contains ExIGS reads from human skin (control) fibroblasts, Table S2 contains reads from IMR-90 fibroblasts, and Table S3 contains reads from progeria (HGPS) fibroblasts from passage 19, 22, and 25.
Table S4 is a list of all cells from Tables S1-S3, as well as summary statistics about the expansion immunofluorescence imaging for each cell.
Methods
The table contains reads generating using expansion in situ genome sequencing (ExIGS). Please see our manuscript for more details.