#cssinglecells23 — Public Fediverse posts

Last session of the conference! Continuing theme of "Cell identity in situ"

Parker Côté, DFCI
in Li Lab
https://ki.mit.edu/people/clinical-investigators-research-fellows/hojun-li

The #transcriptional dynamics of human #hematopoiesis at #SingleCell resolution

do #StemCells and #ProgenitorCells in #hematopoietic system (#HSPC) change with age?

HSPCs exist on a continuum of cell types

They identified #GeneExpression programs active in uncommitted cells, looking across human development (fetal to aged)

https://www.biorxiv.org/content/10.1101/2021.08.25.457678v1

#CSSingleCells23

Second half of the "variation and information" session #CSSingleCells23
led off by Sam Morris of WashU
http://morrislab.wustl.edu/

Multi-omic lineage tracing: insights into reprogramming cell identity

her piece in *Development*, "The evolving concept of cell identity in the single cell era"

working on "induced hepatocytes", start with fibroblasts, via "induced endoderm progenitors"

new work on #adipocytes
https://www.biorxiv.org/content/10.1101/2023.06.01.543318v1

#reprogramming
#StemCells
#CellIdentity
#CellFate

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Yogesh Goyal at Northwestern Feinberg
https://www.goyallab.org/

Topic:
Tracing rare cell plasticity and diverse fate decisions in single cancer cells

Begins with reference to (and pic of) Monod's *Chance and Necessity*
#CellFate
#SingleCell
#CSSingleCells23

Emphasizing non-genetic differences between cells, something we can only see at single-cell resolution

Refers to Luria & Delbruck 1943 about bacterial resistance (to phage), relevant to cancer resistance to therapy (selected)

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Last speaker of the day is the keynote:
Xiaowei Zhuang
Harvard University
https://zhuang.harvard.edu/pi.html

Spatially resolved #SingleCell genomics and cell atlas of the #brain

Explaining MERFISH, now I get it 🤓

Now have adapted to #epigenome: https://pubmed.ncbi.nlm.nih.gov/36272405/

and to thick tissue:
https://www.biorxiv.org/content/10.1101/2023.07.21.550124v1

Now discussing this epic MERFISH atlas of the whole mouse brain
https://www.biorxiv.org/content/10.1101/2023.03.06.531348v1

use imputation to infer cell-cell interactions (several hundred cell types), cool

#CSSingleCells23

Polly Fordyce at Stanford
http://www.fordycelab.com/

Question: How do #transcription factors activate transcription?
Outside the DNA binding domain of a TF, there are numerous disordered domains, including activation domains that interact with co-activators--
very little known about that

activation domains are disordered, poorly conserved, and binding to co-activators is very low affinity

developed a #microfluidic platform to measure, tech called STAMMP

#CSSingleCells23

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Susanne Rafelski
is Deputy Director of Allen Institute for Cell Science
https://alleninstitute.org/person/susanne-rafelski/

"Integrated intracellular organization and its variations in human iPS cells"

How we can "know" a cell... observables:
molecular census (omics)
environment
organization
behavior

use #human #hiPSC as model

https://alleninstitute.org/news/the-interior-design-of-our-cells-2/

#SingleCell #imaging #CSSingleCells23 #OpenScience

Julia Salzman from Stanford
http://salzmanlab.stanford.edu/

now explaining
SPLASH: Statistically Primary aLignment Agnostic Sequence Homing

We want to rapidly survey large #genomic areas, for regulatory sites, #splicing, etc. How do we look at sequencing data today? Through a lens of alignment with reference genomes. This can fail (e.g. cancer cells with shattered genomes, #V(D)J #recombination in immune cells)

Her metaphor: we need ground penetrating radar for #genomics

#CSSingleCells23

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Yannik Severin at ETH Zurich
https://imsb.ethz.ch/research/snijder_group/people/yannik_severin.html
now speaking on
"Multiplexed high-throughput immune cell imaging reveals molecular health-associated phenotypes"

Seeking to be able to screen #immunecells for responses to drugs
#singlecell resolution, to see morphology, subcellular

developed #multiplexed #PBMC characterization, trained #CNN -- as in #NeuralNetwork
https://www.science.org/doi/10.1126/sciadv.abn5631

#CSSingleCells23

Rosalind Xu is up!
From Moffitt lab at Harvard Med and Children's Hospital
https://moffittlab.github.io/people.html

"A single-cell spatial atlas of the mouse gut reveals spatial- and microbiota-dependent sensation"

Using MERFISH which was developed for brain, so she had to develop protocol that works in gut

#SingleCell
#CSSingleCells23
#microbiota
#intestinal
#Transcriptomics

Lacramioara Bintu from Stanford introducing the first speaker of the conference! She is Prisca Liberali from FMI in Basel, joining us virtually.

"Decoding the design principles of tissue organization"

Model system is intestinal #organoids
#selforganization

#CSSingleCells23

One #stemcell can generate an entire, organized, organoid

#multiplexed #SingleCell analysis of organoids, using to understand #regeneration after intestinal damage

A screen with 400K organoids and 3000 compounds!

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