Jeff Farrell

#zebrafish genome update, our T2T assembly of the inbred strain of AB (M-AB) generated by my buddy Nori Sakai has now been released at NCBI and will be a second reference genome for zebrafish (GRCz12ab):

Just because I am seeing new reposts of this: this outage was resolved last week, about 48 hours after we found out about it. Thankfully, there has not been a second one 😎

Ok, friends! If you’re a Daniocell user, it’s now available again outside of the NIH. Very sorry for any inconvenience this posed for any of you and thanks for your patience. We’re taking additional steps to hopefully prevent similar outages in the future. Happy surfing 🎣

Hey friends - Daniocell is experiencing a temporary outage right now. The NICHD server it is hosted on got dropped from the NIH’s firewall list & so currently can’t be accessed outside the NIH. The relevant IT teams are working to resolve it. Sorry for any inconvenience. It’ll be back soon!!

It was super fun working on this interview with Saanjbati Adhikari about my path during my scientific training.

Thank you Kevin for creating something truly incredible. ZebrafishRock has been such an important contribution to our community. I’m glad that the Slack will live on - see you there, and hopefully at a meeting some time soon. Be well!

Congrats, Bailey!

@mads100tist.bsky.social calling attention to the awesomeness of #zebrafish #devbio and community. #SDB

Sure, but it’s a few extra steps. (1) Use a small screwdriver to unscrew the front panel of your Switch. (2) Use a hot glue gun to glue that front panel to the screen of your Mac laptop. (3) Start DaniocellDesktop and shrink the window to show through the front panel. (4) Voila! How easy is that?

Big props to Alicia Evans, Matt Breymaier, and the NICHD BSPC team for key contributions. It feels strange to announce new things these days, but hopefully this tool will bring some of you a little joy and some great new hypotheses. (4/4)

After installing, it'll download a copy of the Daniocell data for you and runs locally on your computer, meaning your interactions are private and can persist long-term. Check out the tutorials and give it a try: daniocell.nichd.nih.gov/desktop/ (3/4)

DaniocellDesktop lets you define custom cell populations, perform differentially expressed gene analysis, and generate publication-ready plots to show gene expression patterns, co-expression, and temporal changes for any genes or cell populations you wish. (2/4)

DaniocellDesktop logo, depicting a fish on a laptop screen.

If you love Daniocell, but wish it could generate analyses specific to YOUR genes & cell types of interest, check out DaniocellDesktop - a new point-and-click app for Mac and Windows that enables reanalysis of the Daniocell data without programming: daniocell.nichd.nih.gov/desktop/ (1/4)

MIC-Drop-seq: Scalable single-cell phenotyping of mutant vertebrate embryos Pooled perturbation screens can reveal cellular regulatory networks, yet scaling these techniques for large-scale screens in animals remains challenging. To address this, we developed MIC-Drop-seq, wh...

To dissect the gene regulatory networks used to build organisms, we need Perturb-seq-like tools that work in whole animals.

For this purpose, we developed MIC-Drop-seq, a tool that couples high-throughput CRISPR in zebrafish embryos with single-cell RNAseq.

www.biorxiv.org/content/10.1...

Jeff Farrell about to start his seminar

5 people at dinner

It was so awesome to have @jeffreyafarrell.bsky.social here to give a departmental seminar today!!

I am looking for postdocs to join my group at NIH. Are you interested in Development, Evolution, Genetics, Genomics, and Human health? Please apply! www.training.nih.gov/jobs/pdf-mb-...

We also did some such comparisons between ZF and human in our 2023 dev cell paper and some code you could use as a starting point is in the GitHub repo.

Hey Ivan! The data is available from the Daniocell front page, but LMK if you have questions

Kevin, I think what you do is super important, and I’m thankful for everything that Zebrafish Rock! has done!!! It helps me keep up with the community and helps make people aware of cool resources they should know about. Sorry there are some unappreciative jerks, but many of us love ZR deeply.

An example of what we in the NIH Intramural program can accomplish. Excited to share our latest paper in close collaboration with Nick Ryba's group. We examined how inflammation transforms representation in somatosensory neurons to cause pain. Lots of surprises here: www.nature.com/articles/s41...

“These findings support the use of zebrafish as a useful comparative model for studying the meninges, provide a foundational description for future zebrafish meningeal research”

New work from @biomarina-vg.bsky.social & Weinstein Lab at NIH 🐟

An optogenetic toolkit for robust activation of FGF, BMP, and Nodal signaling in zebrafish Cell signaling regulates a wide range of biological processes including development, homeostasis, and disease. Accessible technologies to precisely manipulate signaling have important applications in ...

Happy to share a new preprint from my lab! We characterize the on/off kinetics, light dosage-dependence, and more for a suite of optogenetic signaling activators in zebrafish embryos 💡 www.biorxiv.org/content/10.1...

Congratulations, Mike!!!

If you want to make it easy for editors to find reviewers for your manuscript, pre-print it so that prospective reviewers can quickly scan through it to make sure it's within their expertise and not going to be a slog. I am 5x more likely to accept if I can spend 5 minutes looking at the figs.

Hell yeah! Another stunning finding! Congratulations Andi, Victoria, and Andreas!!

The life of each of us began when a sperm and an egg came together. But what happens at a molecular level?

Our latest work in Cell led by @vdeneke.bsky.social & Andreas Blaha reveals a conserved fertilization complex that bridges sperm and egg in vertebrates! (1/11)

www.cell.com/cell/fulltex...

100% Yiqun crushing it as always, obviously.

Our study provides an approach to uncover biology in scRNAseq data from other cell types and tissues, offers a comprehensive view of cellular processes in notochord and prechordal plate development, and sheds light on cell-type-specific regulation of shared processes. (10/)

Moreover, for xbp1 (a UPR TF) to fully activate the 'gland-like' cargo-specific UPR response in the hatching gland requires the developmentally programmed expression of a co-factor, bhlha15/mist1. (9/)

We found that even though there is a shared, 'core' UPR, those genes are actually activated by different UPR TFs in the two tissues. Additionally, in each tissue, the same TFs that activate the 'core' UPR also activate the 'cargo-specific' UPR genes. (8/)