Carl Manner

@peiferlabunc Isn’t that the only point of co-first?

People say science twitter has lost its mojo, but we just main-character'd a guy for being insufficiently committed to mentoring, and it was the one guy who has a public, standing offer to be an informal advisor to literally any scientist in the world

@arjunrajlab Idk, if you’re using something like histone marks to define binding probability I could see that there’s a layer of abstraction there. But if you (for example) endogenously flag tag a TF, then isn’t signal above background essentially equivalent to binding?

I common hear that ChIP seq et al are not quantitative. What does that mean? If a peak is like 3x higher, should I not interpret that as higher binding probability? What is the evidence for or against?

The 7 hottest days on Earth in the last 100,000+ years all happened in the last week: July 6 ~ 17.23°C / 63.01°F July 7 ~ 17.20°C / 62.96°F July 4 ~ 17.18°C / 62.93°F July 5 ~ 17.18°C / 62.92°F July 8 ~ 17.17°C / 62.90°F July 10 ~ 17.12°C / 62.81°F July 9 ~ 17.11°C / 62.79°F

@ATinyGreenCell Or a mobius strip alternative to Okazaki fragments for circular dsdna.

So do we begin the decades long meme project to prove Elinne wrong by engineering a viable mechanism for polymerizing DNA 3' to 5' or....?

@ProfTomEllis Ah. How long are the longest ~10% of transcripts?

@CJManner These are synthetic alleles due to recoding 5% of the protein coding region of each gene. At the 3’UTR the alleles are mostly identical.

Help me pls hive mind 🙏 - What's the latest decent company for outsourcing RNAseq of S.cerevisiae yeast for differential expression analysis? 6 samples, low price and >1 month turnaround. Need paired end reads. >> Used Novogene last time and felt we could do better

@AugustPamplona @davidrliu Electrocompetent is the way to go. Or zymo mix and go for subcloning efficiency.

@davidrliu Competent cells seemed like voodoo to me the couple of times I was involved in trying.

Three of the more costly and frequently used reagents in molecular biology are rolling circle amplification (RCA) mix, chemically competent MachOne (or other E. coli) cells, and Gibson assembly mix. Postdoc Julian Willis—who is starting his own lab in the UK soon—developed homemade recipes for each that reduce costs ~3x (or more at large-scale). Links to each recipe: RCA mix: #gid=2101654780" target="_blank" rel="nofollow noopener">docs.google.com/spreadsheets/d… Chemically competent MachOne cells: #gid=1515614288" target="_blank" rel="nofollow noopener">docs.google.com/spreadsheets/d… Gibson assembly mix: #gid=399255283" target="_blank" rel="nofollow noopener">docs.google.com/spreadsheets/d…

@rhuttenhain I love benchling for molecular biology tools it has integrated, but am consistently disappointed in the relatively few reference genomes available and how outdated they are. If you’re working in human or mouse systems, it’s near perfect. If you use other models, less so.

I am seeking advice regarding the decision on an electronic notebook that we will be using in the lab: Which electronic notebook are you using and what do you like about it? #newPI

@OurOcean The copy pasta is coming soon, right?

It's #FishyFriday! 🐟 Did you know that the sunfish is one of the largest bony fish in the sea? 🌞 They can grow up to 10 feet long and weigh 4,000+ pounds! ow.ly/zwr950OF5WF

This recent talk features ChromBPNet, our upcoming flagship predictive sequence model of base-resolution chromatin accessibility profiles (ATAC-seq, DNase-seq, scATAC-seq cluster pseudobulks) with built-in de-novo enzyme bias correction. 1/

this was not at all depressing to write prospect.org/culture/books/…

@musharbash_b Tulum, Quintana Roo, MX

What’s a good city to abscond to for 2-4 weeks and finish writing a big journal article? Asking for me.

@ATinyGreenCell reddit.com/r/espresso/com…

@CJManner Thats super cool! Would love to read that thread :)

So after polishing up the experimental evolution robot and making an algae add-on, what should I work on next?

Prime editors can tweak DNA in ways that Cas9 -- and even base editors -- cannot. Clinical trials are expected to begin by 2025. In the last few days, three papers have pushed the method forward.🧵

@kearney_melissa Hot take: we should do away with traditional grading in favor of contract grading or - preferably - complete degrading (pass/fail).

Contrarian take: It is not a terrible, horrible, unforgivable sin for a student to ask for a regrade or a new grade. Sometimes graders make mistakes! And lots of students are super stressed out over grades. Why so much anger over this from professors on twitter? Geez.

I will veto this extreme ban and need everyone’s help to hold it. - RC