Jeff Farrell

Our lab website is mildly out of date, but up to date publications are here: www.ncbi.nlm.nih.gov/myncbi/jeffr...

If you or someone you know is driven and curious and might be a good fit for my lab, please let me know.

Postbacs typically carry out a independent 2 year project with mentoring from me and a postdoc in the lab, present publicly, have support to apply to MD or PhD, and receive a healthy stipend and insurance. Apply centrally (www.training.nih.gov/research-tra...) and notify me.

Postdocs should send a cover letter about their past work, their interests, and why they want to come to my lab (or what they want to do if they already have ideas), info for three references, and their CV.

Lab interests include development of intestinal epithelium and stroma, ‘messy’ outcomes/errors during cell fate decisions, developmental programs of uncharacterized cell types, or large-scale sc genomics. PDs also can propose any project that my lab would be well suited to support in some way.

I’m recruiting new members to the Farrell Lab this summer. We will have space for 1 postdoc (since Abhinav is leaving to start his own lab at U Arizona!!) and 2 postbacs, since my current two will leave for PhD programs at the end of the summer. More details in thread:

Developmental regulation of intestinal best4+ cells best4 +/CFTR-high expressing cells are a recently described intestinal epithelial cell type potentially altered in inflammatory bowel disease and colorectal cancer. However, their developmental origin...

The work is just beginning! Abhinav's new lab (starting this year!) will study their function and how they communicate with other cell types. We will keep studying their development. Read Abhinav's thread for more details or better yet, read it! Feedback welcome. www.biorxiv.org/content/10.6...

We began testing their function, focusing on pH regulation. In ZF, they're not req'd for proper gut pH homeostasis, but their intracellular pH varies spatially. Eliminating spatial variation non-autonomously affects goblet cell mucus modifying enzymes, suggesting best4+ cells coordinate other cells.

While conserved, best4+ cells are absent in mice, so zebrafish will be a key in vivo model. We made fish that label best4+ cells to live image them (they extend dynamic projections to touch other cells!) and the first in vivo models that remove best4+ cells.

We tested best4+ cell development from birth to differentiation. We IDed the conserved best4+ cell gene expression program, lineage traced them to ID their progenitors, tested the signals that specify them, IDed the TF that confers their identity, and IDed a TF required for their spatial diversity.

Happy New Year! NEW LAB PREPRINT testing how best4+ intestinal epithelial cells develop! best4+ cells are conserved across vertebrates and altered in IBD & colorectal cancer. But they were first molecularly IDed in 2019. We barely know anything about them yet! What do they do?? HOW DO THEY GET MADE?

#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...