Bertie Gottgens

A single-cell atlas of transcribed cis-regulatory elements in the human genome Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolut...

A pipeline for single cells was published by our colleagues from RIKEN a while back on bioRxiv: www.biorxiv.org/content/10.1...
We have adapted the pipeline, but not yet published on it. I'd say that at this stage, it may be more useful to look at known enhancers rather than as a discovery tool.

OK; open chromatin does not necessarily equate activity. If you used 5' reagents for single cell RNA-Seq, you could check for enhancer-originated transcripts. For some enhancers, it's supposed to correlate with activity. Doesn't work with 3' scRNA-Seq.

Are you asking how to validate that the TF activity predictions are "wrong"? Or that the ATACSeq is "wrong"? I'd say the 1st thing to measure is whether protein is expressed (RNA expression does not necessarily equate protein). If there is little to no protein, TF activity prediction probably wrong.

Congratulations to Bart and Luke and thank you very much to all of our collaborators at the @scicambridge.bsky.social and beyond, as well as our funders, principally @wellcometrust.bsky.social

Collaborative science is just so much fun! From our brilliant collaboration with Liz Robertson from @dunnschool.bsky.social; embryology, single cell omics and computational biology deliver new insights into the intricacies of blood and endothelial development. www.sciencedirect.com/science/arti...

Potential new treatment to tackle commonest form of childhood cancer A combination of two drugs could improve outcomes and reduce the need for toxic chemotherapy for B-cell acute lymphoblastic leukaemia, the commonest cancer in childhood and one that can be particularl...

It's great to see work from Dr Simon Richardson @simonrichardson.bsky.social and Prof Brian Huntly featured on @cam.ac.uk news this week.

They developed a treatment to tackle a common childhood blood cancer, hoping to offer safer & more effective care.

Read more: www.cam.ac.uk/stories/B-AL...

Photo of seminar with headshot of Sumru Bayin and title of her talk

Today we welcomed Dr Sumru Bayin for our Group Leader Seminar! Dr Bayin is CSCI's Affiliate PI, and Group Leader at @gurdoninstitute.bsky.social. She was hosted by @bertiegottgens.bsky.social and presented on 'Age-dependent regenerative mechanisms in the brain.' Thanks to all who joined!

Congratulations to my friend Muzz; a brilliant scientist with unrivalled energy and determination ; and a great leader of people

Congratulations to my friend Muzz; a brilliant scientist with unrivalled energy and determination ; and a great leader of people

Very sorry to hear of the passing of Professor Roger Pedersen, whose visionary leadership helped establish the @scicambridge.bsky.social. I will never forget how Roger personally taught my group how to dissect early post-implantation mouse embryos; watching him at the microscope was truly inspiring

Institute logo and text: A place of possibility, a poem created with the words of those who work and study at the Cambridge Stem Cell Institute

CSCI is now on Bluesky! We're happy to share our first post as a link to a poem from postdoc Kirsty Ferguson about working in the Institute, started at the Annual Retreat this year. See Kirsty's collaborative poem here: tinyurl.com/cscipoem

Wonderful news; many congratulations

We are hiring 😀

Postdoctoral position – Stem cells, Cancer, and Aging

We study cell fate decision and lineage specification in hematopoietic stem and multipotent progenitor populations to modulate lineage output for therapeutic purpose in diseases and aging contexts.

Looks very interesting; left me wondering about the pros and cons of using a fusion protein with the TF itself; like an evolution of for example Dam-ID which lacks precision in terms of location but doesn’t require antibodies

Very good to have you join

Question: As many of our community are getting ready to travel to the ASH annual meeting, who likes their terminology of Classical versus Malignant Hematology?

Picture of a screen with a presentation titled “journal club, Delás lab, Nov 2024)

It’s been such exciting times in the very very new Delás lab. So glad I can share here now!

We had our first journal club - yes, don’t laugh. It was exciting. Everyone (undergrads to postdoc) presented a section and discussed. Starting is hard but moments like this make all the difference!

Eomes directs the formation of spatially and functionally diverse extra-embryonic hematovascular tissues bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

New preprint from a super fun collaboration with Liz Robertson’s group. Nice combo of in vivo embryo, ESC differentiation and sc-omits; delivering new insights into extraembryonic blood and endothelial development . Big Thanks to Bart and Luke for pushing this. www.biorxiv.org/content/10.1...

Characterising stem cell biology as an offshoot of dev biol is neither helping the latter nor is it correct. In my field (blood stem cells) many of the pioneers came from a medicine or physics background (eg Till & McCulloch). I am not denying that there are overlaps btw.

A time- and single-cell-resolved model of murine bone marrow hematopoiesis The paradigmatic hematopoietic tree model is increasingly recognized to be limited, as it is based on heterogeneous populations largely defined by non…

Very happy to share our latest paper:”Time and single-cell resolved model of murine bone marrow hematopoiesis”:
www.sciencedirect.com/science/arti...
With the groups of Kamil Kranc and Donal O’Carroll, we have generated a new hematopoiesis model fit for the single cell genomics era.

Fluorescence microscopy pictures of spinal cord development and cellular models

I am excited to share that I will be starting my lab at UCL as part of the LMCB @LMCB_UCL in 2024. We will be studying how cis-regulatory elements controls cell fate decisions during development. We are recruiting at all levels. Learn more and reach out!