Better late than never! Last month, we posted our preprint on single-cell RNA sequencing of the #zebrafish sox17 lineage — a collaboration among several labs including us, @stefanmaterna.bsky.social and @thelovelylab.bsky.social. A few key takeaways below: 1/3 www.biorxiv.org/content/10.6...

Transcriptional divergence of the zebrafish sox17 lineage begins during gastrulation

The endoderm is specified at the onset of gastrulation and subsequently undergoes extensive migration before forming an epithelial sheet that gives rise to multiple organs, including the gut and respi...

biorxiv.org

We are #hiring! Come join us at Utrecht University (NL) and help centralize our ongoing #genomics efforts into a new core unit, embedded in our inter-divisional lab. We are looking for a Postdoc in molecular biology and a Bioinformatics engineer. Please apply/forward to those interested.

IMPORTANT study from @hocinerekaik.bsky.social @denisduboule.bsky.social and a significant validation of SCBEMs, #gastruloids in particular, as a discovery tool www.biorxiv.org/content/10.6... 🧵

Our research work on using #singlecell co-mapping to study early embryonic development is now published: doi.org/10.7554/eLif....

Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development

A robust and quantitative map links chromatin modification and gene expression of cells during zebrafish embryogenesis.

doi.org

With @burgesslab.bsky.social, not one, but TWO freshly caught T2T zebrafish reference genomes for the Tübingen and AB strains 🎣 🎣 🎉

Javan Okendo@javanokendo.bsky.social · 9mo ago

🎉 Excited to share our new preprint presenting a complete de novo assembly of the zebrafish genome; a major advance for zebrafish genomics and research! 🧬 Full paper: www.biorxiv.org/content/10.1... @zebrafishrock.bsky.social @izfs.bsky.social @zfinmod.bsky.social @modelzebrafish.bsky.social

CONCLUSIONS: To promote the best science being done, we need to look at the incentives of science publishing and funding. Long-term funding produces better science. Short-term and topical agendas encourages irreproducibility. Funding model organisms generates science we can build on! 🪰🪱🦠🐠🐁🐸 6/6 🧵

A new #zebrafish reference genome assembly (GRCz12tu) has been posted at GenBank! Special thanks to @burgesslab.bsky.social, NCBI, and the GRC for their immeasurable work 🔥 It is not yet annotated, but that will be forthcoming. www.ncbi.nlm.nih.gov/datasets/gen... h/t Monte Westerfield on ZR! Slack

Very important work #epigenomics, as we almost never image the cells when performing CnR/CnT experiments

Konrad Chudzik@konrad-chudzik.bsky.social · last yr.

🚨 Preprint alert 🚨 Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇 doi.org/10.1101/2025...

New story from @marloes3105.bsky.social shows new insights towards optimizing the in vitro models of mouse embryogenesis.

Marloes Blotenburg@marloes3105.bsky.social · last yr.

Very happy to share that our paper on stem cell culture conditions is now out! doi.org/10.1371/jour... We found that modulating mESC culture conditions influences gastruloid elongation and lineage specification, and helps with making the protocol more reproducible in our hands! more below 🧵⬇️ [1/7]