Sam Dieltiens
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samdieltiens.bsky.social
Sam Dieltiens
@samdieltiens.bsky.social
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PhD student @ Stein Aerts Lab of Computational Biology
VIB.AI & KU Leuven 🧬🖥️
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Reposted by Sam Dieltiens
hannahdckmnkn.bsky.social
Our new preprint is out! We optimized our open-source platform, HyDrop (v2), for scATAC sequencing and generated new atlases for the mouse cortex and Drosophila embryo with 607k cells. Now, we can train sequence-to-function models on data generated with HyDrop v2!
www.biorxiv.org/content/10.1...
Data collected with the new sequencing platform HyDrop v2 is shown. First, a schematic overview of the bead batches of the microfluidic beads is followed by a tSNE and a barplot showing the costs in comparison to 10x Genomics. Then, a track of mouse data (cortex) is shown together with nucleotide contribution scores in the FIRE enhancer in microglia. Here, the HyDrop and 10x based models show the same contributions. On the right, the Drosophila embryo collection is explained; in the paper HyDrop v2 and 10x data are compared to sciATAC data. Then, a nucleotide contribution score is also shown, whereas HyDrop v2 and 10x models show the same contribution, just as in mouse.
April 4, 2025 at 8:52 AM
Reposted by Sam Dieltiens
niklaskemp.bsky.social
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
April 3, 2025 at 2:30 PM
Reposted by Sam Dieltiens
biorxiv-genomic.bsky.social
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species https://www.biorxiv.org/content/10.1101/2025.04.02.646812v1
April 3, 2025 at 7:34 AM