Thread by @z_chiang

Introducing IN SITU GENOME SEQUENCING, a new technology to resolve DNA sequence🧬 and structure🔬

A team effort with @Andrew_C_Payne, @PaulReginato, @eboyden3, @JD_Buenrostro, and Fei Chen

science.sciencemag.org/content/early/…

This is how it works: (1/8)

We started with a basic question: how can we sequence DNA while preserving 3D genome structure?

Instead of extracting DNA, we developed a method to construct sequencing libraries within fixed nuclei (2/8)

Next, we use in situ sequencing to read out the libraries via fluorescence microscopy.

This is a single nucleus: each spot is an amplified DNA fragment, the colors indicate the 4 DNA bases, and each frame represents a round of sequencing (3/8)

The trick is that instead of directly in situ sequencing the genomic DNA, we read out unique spatial barcodes.

Then we perform Illumina sequencing and integrate across barcodes, yielding 100-1000s of spatially-resolved reads per nucleus (4/8)

We first examined known features of spatial genome organization in cultured PGP1 (aka @geochurch) fibroblasts.

We then applied our method to intact early mouse embryos at the zygote, 2-cell, and 4-cell stage (5/8)

Our method is sequencing-based, so we can leverage genotype information to compare maternal and paternal chromosome organization across developmental stages.

Our method is also imaging-based, so we can compare structures across cells within a single intact embryo (6/8)

Check out the paper for more! Thanks to all co-authors, reviewers, and the editorial team @ScienceMagazine who helped us sneak this in at the buzzer of this very weird year (7/8)

science.sciencemag.org/content/early/…

If you'd like to explore the data for yourself, head on over to our interactive Shiny app! (8/8)

buenrostrolab.shinyapps.io/insituseq/