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Plate CUT&Tag (Meers Lab version)

We published a detailed protocol for our Plate-CUT&Tag method on @protocolsio.bsky.social to accompany our recent preprint (www.biorxiv.org/content/10.1...) give it a try! Feedback welcome! dx.doi.org/10.17504/protocols.io.n2bvjed5wgk5/v1

dx.doi.org

This protocol describes a method for carrying out CUT&Tag-Direct in 96 well microplates for high-throughput processing of samples by a single operator with only standard lab...

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Intermediately Methylated Regions in Normal Cells Are Epimutation Hotspots in Cancer

While you're at it, check out this nice new preprint from Dave's lab that makes use of Plate-CUT&Tag data to characterize chromatin states at intermediately 5mC-methylated regions that play key roles in AML: www.biorxiv.org/content/10.1... 4/3

biorxiv.org

DNA methylation is altered in all cancers, but the mechanisms responsible for these changes are not well understood. Using data from 100 primary samples, we show that regions with intermediate methyla...

This work was spearheaded by Brittany Johnson, the very first Meers Lab member who has now moved on to a PhD at @ibisatnu.bsky.social, with big assists from Gabe Boyle and @sarthylab.bsky.social at Seattle Children's and David Spencer here at WashU. Hoping this is the first of many for the lab! 3/3

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Michael Meers @mpmeers.bsky.social · 05/09/2025

Inspired by Derek Janssens' work on AutoCUT&RUN/Tag that streamlined those methods for highly parallel sample processing on a liquid handling robot, we simplified that a bit by allowing any user to process 96 samples at once without any specialized equipment, with a nice use case for AML 2/3

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Death, taxes, and "the PI is too inexperienced and requires a senior co-mentor for this student's F31" 🙃

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Reposted by Michael Meers

Sri Kosuri @srikosuri.bsky.social · 06/07/2025

I wrote down some of my thoughts down on the current race to build virtual cell models. Overall, excited and wary about the work ahead. Also, it's my first post to Substack; getting more excited about it as a replacement for X and Blue Sky. srikosuri.substack.com/p/the-elusiv...

srikosuri.substack.com

The elusive virtual cell

Rosetta Stone or Moby Dick?

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Reposted by Michael Meers

Evgeny Kvon @evgenykvon.bsky.social · 02/07/2025

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

nature.com

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

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Michael Meers @mpmeers.bsky.social · 24/06/2025

This is fantastic stuff Evgeny! Great to see it come together so nicely. Congratulations!

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Reposted by Michael Meers

Evgeny Kvon @evgenykvon.bsky.social · 23/06/2025

How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/

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Michael Meers @mpmeers.bsky.social · 20/05/2025

With apologies to @jeremymberg.bsky.social, I borrowed directly and heavily from this thread of his to craft my comment on this policy proposal, which I'm posting here for anyone who would like to use it as a template. Please heed Jeremy's exhortation and post a comment by Friday!

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Michael Meers @mpmeers.bsky.social · 20/05/2025

Typical of this White House: a non-expert decrying all that’s wrong, using “evidence” that amounts to anecdotes, offering mealy-mouthed “solutions” (wtf is “gold standard science” anyways?) as a pretext to destroy without any strategy to build. www.whitehouse.gov/briefings-st...

whitehouse.gov

Remarks by Director Kratsios at the National Academy of Sciences

Remarks by Director Kratsios at the National Academy of Sciences REINVIGORATING AMERICA’S SCIENTIFIC ENTERPRISE AS PREPARED FOR DELIVERY Washington, D.C.

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Reposted by Michael Meers

Jeremy Berg @jeremymberg.bsky.social · 20/05/2025

My quote of the day My dad used to say: “Don't tell me what you value. Show me your budget, and I'll tell you what you value." Joseph R. Biden, Jr.

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Michael Baym @baym.lol · 14/05/2025

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

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Jeremy Berg @jeremymberg.bsky.social · 23/04/2025

ACTION ITEM-----ACTION ITEM Implementation of Schedule F This is what a lot of us have been worried about. This allows for many civil service positions to replaced with political appointees. This could include NIH institute directors and even POs. BUT THERE IS A COMMENT PERIOD... 1/n

media.tenor.com

the word alert is in a purple circle

ALT: the word alert is in a purple circle

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Reposted by Michael Meers

Jeremy Yoder says no war @jbyoder.org · 20/02/2025

So I did this today: banged out a couple hundred words of a pitch while managing lab, sent it to the opinion page editor at the newspaper my parents still somehow get in print, and got back a "yes" in, I absolutely kid you not, under 15 minutes

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Jeremy Berg @jeremymberg.bsky.social · 18/02/2025

ATTENTION If you are on a study section that was scheduled to meet, please post or DM me with information regarding: 1. The name of the study section 2. The scheduled date 3. Whether the meeting actually occurred THANK YOU

media.tenor.com

a man wearing a top hat and a purple jacket is asking for more .

ALT: a man wearing a top hat and a purple jacket is asking for more .

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But that's not good enough to infer nuc binding bc C&R occasionally releases flanking nucs that happen to be next to the TF, which is why we did multi-timepoint mapping to see when the same bound locus went from >150 to <150. If it is happening, I think it's prob a minority of events at steady state

We think about this Q a lot--as noted above, we used CUT&RUN fragment size to infer that some nuc binding probably occurs, but our thought is that these events are likely transient so won't be efficiently captured via a re-ChIP-style method. FWIW C&R shows ~20% nuc-sized frags for FOXA1 ⬇️

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MRAF also met on Feb 10-11 after being posted Jan 13 (this one hurts because mine might easily have gone here instead of MRAA): www.federalregister.gov/documents/20...

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Center for Scientific Review; Notice of Closed Meetings

So it appears that the closely related MRAB study section *did* meet on Feb 6-7, after being posted on the federal register on Jan 13, 24 days prior: www.federalregister.gov/documents/20.... This suggests that the 35 day notice requirement that people have been tossing about might not be accurate?

federalregister.gov

Search, browse and learn about the Federal Register. Federal Register 2.0 is the unofficial daily publication for rules, proposed rules, and notices of Federal agencies and organizations, as well as e...

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@jeremymberg.bsky.social confirmed by SRO that NIGMS MRAA SRG scheduled to meet today will be rescheduled to a later date if you're still keeping track of these things

Michael Meers @mpmeers.bsky.social · 17/02/2025

Just confirmed by the SRO that it will be rescheduled to an as-yet-to-be-determined later date

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Yeah it appears not to be there, though the search function is a little unwieldy so it's possible I missed it (probably wishcasting though)

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Michael Meers @mpmeers.bsky.social · 17/02/2025

So it sounds like the MRAA Study Section for ESI MIRA may not meet tomorrow as scheduled? Anyone have confirmation of this?

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Reposted by Michael Meers

Vijay Ramani @vram142.bsky.social · 17/02/2025

A thread. Things are bad. But we’ve already lost if they smother the passion & joy we have for science. So here’s a proposal: if you’re a biologist in any way impacted by *exasperated wave* & want to chat, drop me an e-mail at myfirst.mylast[at]ucsf.edu. Let’s schedule a 30min chat about [...] (1/n)

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Michael Meers @mpmeers.bsky.social · 16/02/2025

Thank you @michelemunz.bsky.social for quoting me for this piece. Incidentally Eric Schmitt made a factually incorrect statement in it: this does NOT mean more money for lifesaving research, it means LESS--this is a CUT to future therapies and cures, full stop. www.stltoday.com/funding-cuts...

stltoday.com

Funding cuts will hamper research

ST. LOUIS — Missouri universities are sounding the alarm over the attempt by President Donald Trump's administration to cut grants supporting biomedical research — a move that could result in

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Jeremy Berg @jeremymberg.bsky.social · 16/02/2025

Thanks to all of the NIHers and their friends who reached out to me. I am still here (DM me or Signal jeremymberg.78) I still have a very incomplete picture but based on what I have been told, the damage to NIH and to many wonderful people who work(ed) there is/was impossible for me to imagine 1/n

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Michael Meers @mpmeers.bsky.social · 13/02/2025

A Senator voting to put one’s most vulnerable constituents at risk of illness and death is a dereliction of duty of the highest order. Here is a list of those whose shameful acts should eternally stain their legacies: www.nytimes.com/interactive/...

nytimes.com

Live Count: The Senate Votes on Robert F. Kennedy Jr. to be Health Secretary (Gift Article)

Follow the count live.