zack chiang
@zchiang.bsky.social
microscopy x epigenomics | buenrostro lab | harvard/broad
to be fair, it's been quite important to genome assembly and related areas for some time, but I think we're just scratching the surface with functional, multi-modal, and temporal readouts
combined with the speed and low cost, there's a lot of potential for both diagnostic and screening tech imo
combined with the speed and low cost, there's a lot of potential for both diagnostic and screening tech imo
November 19, 2024 at 12:41 AM
to be fair, it's been quite important to genome assembly and related areas for some time, but I think we're just scratching the surface with functional, multi-modal, and temporal readouts
combined with the speed and low cost, there's a lot of potential for both diagnostic and screening tech imo
combined with the speed and low cost, there's a lot of potential for both diagnostic and screening tech imo
my friend Sai is a co-corresponding on this, so I suspect that's his doing!
critics normally complain single-cell atlases don't have any real biology, now they also gonna complain when it's too interventional, there's no winning I guess 😛
critics normally complain single-cell atlases don't have any real biology, now they also gonna complain when it's too interventional, there's no winning I guess 😛
November 15, 2024 at 7:12 PM
my friend Sai is a co-corresponding on this, so I suspect that's his doing!
critics normally complain single-cell atlases don't have any real biology, now they also gonna complain when it's too interventional, there's no winning I guess 😛
critics normally complain single-cell atlases don't have any real biology, now they also gonna complain when it's too interventional, there's no winning I guess 😛
Happy to provide more info if needed! And thanks for pointing out the omission, we'll definitely add it to our methods section
November 14, 2024 at 7:47 PM
Happy to provide more info if needed! And thanks for pointing out the omission, we'll definitely add it to our methods section
Thanks! We add an oligo with an acrydite group to link it to the gel during polymerization, then use a complementary fluorescent oligo for visualization
November 14, 2024 at 7:12 PM
Thanks! We add an oligo with an acrydite group to link it to the gel during polymerization, then use a complementary fluorescent oligo for visualization
We then show these changes are found within tissues and during aging. To learn more, check out our preprint! www.biorxiv.org/content/10.1...
Thank you to all co-authors, the Buenrostro lab, and everyone at Harvard SCRB and the Broad Institute who made this work possible!
Thank you to all co-authors, the Buenrostro lab, and everyone at Harvard SCRB and the Broad Institute who made this work possible!
Expansion in situ genome sequencing links nuclear abnormalities to hotspots of aberrant euchromatin repression
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 multiplex...
www.biorxiv.org
November 11, 2024 at 7:33 PM
We then show these changes are found within tissues and during aging. To learn more, check out our preprint! www.biorxiv.org/content/10.1...
Thank you to all co-authors, the Buenrostro lab, and everyone at Harvard SCRB and the Broad Institute who made this work possible!
Thank you to all co-authors, the Buenrostro lab, and everyone at Harvard SCRB and the Broad Institute who made this work possible!
To show the power of this approach, we applied ExIGS to progeria cells with nuclear lamina abnormalities
By combining expansion and 3D genome sequencing in the same nucleus, we can literally see how the abnormal lamin topology changes the structure of chromosomes
6/
By combining expansion and 3D genome sequencing in the same nucleus, we can literally see how the abnormal lamin topology changes the structure of chromosomes
6/
November 11, 2024 at 7:33 PM
To show the power of this approach, we applied ExIGS to progeria cells with nuclear lamina abnormalities
By combining expansion and 3D genome sequencing in the same nucleus, we can literally see how the abnormal lamin topology changes the structure of chromosomes
6/
By combining expansion and 3D genome sequencing in the same nucleus, we can literally see how the abnormal lamin topology changes the structure of chromosomes
6/
In situ sequencing measures the 3D location and genomic position of each DNA fragment, letting us trace the path of every chromosome in the nucleus
We also do expansion IF imaging to measure which fragments co-localize with protein landmarks
5/
We also do expansion IF imaging to measure which fragments co-localize with protein landmarks
5/
November 11, 2024 at 7:33 PM
In situ sequencing measures the 3D location and genomic position of each DNA fragment, letting us trace the path of every chromosome in the nucleus
We also do expansion IF imaging to measure which fragments co-localize with protein landmarks
5/
We also do expansion IF imaging to measure which fragments co-localize with protein landmarks
5/
Expanding the genome evenly is hard because DNA is a polymer, so here we use the Buenrostro lab's favorite enzyme Tn5 to make fragments beforehand
We then do Illumina sequencing, but instead of on a flowcell, all enzymatics are performed ~inside~ the expanded nucleus
4/
We then do Illumina sequencing, but instead of on a flowcell, all enzymatics are performed ~inside~ the expanded nucleus
4/
November 11, 2024 at 7:33 PM
Expanding the genome evenly is hard because DNA is a polymer, so here we use the Buenrostro lab's favorite enzyme Tn5 to make fragments beforehand
We then do Illumina sequencing, but instead of on a flowcell, all enzymatics are performed ~inside~ the expanded nucleus
4/
We then do Illumina sequencing, but instead of on a flowcell, all enzymatics are performed ~inside~ the expanded nucleus
4/
Fortunately, we had Fei Chen & Ed Boyden, the inventors of expansion microscopy on board!
In ExM, samples are physically enlarged in gels, allowing superresolution imaging without fancy microscopes
3/
In ExM, samples are physically enlarged in gels, allowing superresolution imaging without fancy microscopes
3/
November 11, 2024 at 7:33 PM
Fortunately, we had Fei Chen & Ed Boyden, the inventors of expansion microscopy on board!
In ExM, samples are physically enlarged in gels, allowing superresolution imaging without fancy microscopes
3/
In ExM, samples are physically enlarged in gels, allowing superresolution imaging without fancy microscopes
3/
In 2020, we (Andrew Payne, Paul Reginato) showed in situ genome sequencing, which we used to reveal the 3D genome at the very first stages of life: www.science.org/doi/10.1126/...
However, the resolution of IGS is capped by nuclear volume and the diffraction limit of light
2/
However, the resolution of IGS is capped by nuclear volume and the diffraction limit of light
2/
In situ genome sequencing resolves DNA sequence and structure in intact biological samples
A technical approach allows simultaneous sequencing and imaging of genomes in human fibroblasts and early mouse embryos.
www.science.org
November 11, 2024 at 7:33 PM
In 2020, we (Andrew Payne, Paul Reginato) showed in situ genome sequencing, which we used to reveal the 3D genome at the very first stages of life: www.science.org/doi/10.1126/...
However, the resolution of IGS is capped by nuclear volume and the diffraction limit of light
2/
However, the resolution of IGS is capped by nuclear volume and the diffraction limit of light
2/