Sara Simmonds 🧬

🚨Big news! Five years in the making, our Zebrahub paper is now published in #Cell 🎉. We’ve built a timecourse atlas of zebrafish embryonic development, combining #scRNAseq data and #lightsheet live imaging, and delved deep into the dynamics of key progenitors. cell.com/cell/fulltext/S0092… Explore the datasets here: zebrahub.sf.czbiohub.org Led by @Merlin_Lange with key contributions by @ale_agranados, @Shruthi94Vijay, @jobragantini, @Sarah_E_Ancheta and @yangjoonkim #zebrahub #devbio #cell #Biology #imaging @CellCellPress @czbbiohub #CZBiohubS

📡🧵 Excited to release two #bioRxiv preprints! The first preprint is: "Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis" doi.org/10.1101/2024.10.18.6… We present a comprehensive time-resolved single-cell multiomic atlas of zebrafish development. Integrating scATAC-seq and scRNA-seq from 94,000+ cells, we map gene regulatory networks across six key stages of embryogenesis (10 to 24 hpf). A major accomplishment by @yangjoonkim co-led by @Merlin_Lange with experiments by @Shruthi94Vijay #Zebrahub-Multiome is a sequel to zebrahub.org, our transcriptomic and imaging atlas of zebrafish development. #zebrafish #development #ATACseq #cell #biology #sequencing @czbiohub #CZBiohubSF @cziscience Note: We sent two preprints simultaneously yesterday, and this is the first one to come out... I will append to this thread when the second one is out...

📡🧵 Excited to release our preprint: Ultrack: Pushing the Limits of Cell Tracking Across Biological Scales doi.org/10.1101/2024.09.02.6… A tour-de-force by @jobragantini, #Ultrack is a versatile, highly accurate, and fast ILP-based cell tracking software for 2D, 3D, and multicolor datasets. It has convenient @napari_imaging and @FijiSc plugin interfaces and built-in HPC cluster support. github.com/royerlab/ultrack #cell_tracking #microscopy #devbio @czbiohub