#scrnaseq — Public Fediverse posts

The main #ECCB2026 conference may be over, but today lots of great people are meeting to discuss single-cell standards and collaborations:
Single-cell and spatial data FAIRification, community standards and training
organised by @fbastian @SIB & @elixir_europe
eccb2026.org/communities-day#single-cell-and-spatial-data-fairification
#scRNAseq #SingleCell #FAIRdata #bioinformatics #OpenData #GenevaLovesData

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

2D embeddings for high-dimensional data, the battle rages on

#umap #tsne #scrnaseq

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012403

I made a short video of the strange things UMAP and t-SNE can do to your data. The algorithms are shown mostly working as intended, yet with some surprising consequences.

#umap #tsne #scrnaseq #wtf

https://www.youtube.com/watch?v=gwqU9OoFwjQ

Last talk of the #CSSingleCells23 conference:
Karin Pelka, Gladstone/UCSF
https://pelkalab.org/

Spatially organized #immune hubs in #colon #cancer
#ColonCancer
#scRNAseq

https://pubmed.ncbi.nlm.nih.gov/34450029/

Then: predict cellular interaction networks via correlations of gene program activities across #tumors

anti-tumor hubs in tumors, ISGs including CXCR3 ligands, differs between tumor types (MMR+ or -)

have data from clinical trial (biopsies before and after treatment)
https://pubmed.ncbi.nlm.nih.gov/36702949/

1/2

First speaker of the session (Cell identity in situ)
is Elana Fertig
of Convergence Institute at Johns Hopkins
https://fertiglab.com/

She has background in weather prediction (!) ⛈️ which has convergence with predictive medicine (such as huge data sets)

Looks at #PancreaticCancer with spatial #proteomics
now #scRNAseq

Developed CoGAPS matrix factorization, can identify cell state transitions

Using PhysiCell to build models
http://physicell.org/

#cancer
#SingleCell
#CSSingleCells23

1/2

"predicts new biology missed by today's genomics"
#spatial #transcriptomics #genomics
#scrnaseq
#CSSingleCells23

works by unified detection of sample-specific sequence variation... sample can be different cells, sequence is raw reads

method chooses an "anchor" sequence then looks for neighboring sequence that varies. thus is independent of any reference genome

https://www.biorxiv.org/content/10.1101/2022.06.24.497555v4
https://www.biorxiv.org/content/10.1101/2023.03.17.533189v2

New insights into universally expressed human genes
https://www.biorxiv.org/content/10.1101/2022.12.06.519414v1

2/3

" Instead, #Hepatoblastoma #tumors contain a large suppressive #myeloid compartment which poses opportunities for targeting. Specifically, therapeutic antibodies
targeting the #tumor antigen #GPC3 to induce ADCP by #macrophages, in combination with myeloid
#ImmuneCheckpointBlockade (#CD47/SIRPa, or VISTA) could be a feasible strategy to explore in future studies"

Krijgsman et al. from Vercoulen lab in the #UMCUtrecht, on #bioRXiv:
https://www.biorxiv.org/content/10.1101/2023.06.28.546852v1

#scRNAseq #spatial #CyTOF #immunology

Yesterday, in the afternoon plenty of #scRNAseq work, a.o. Céline Delloye-Bourgeois showing her group's latest work on #neuroblastoma development and #metastatic progression. Including some of our own scRNA-seq data. Very cool.

Furthermore, more #SingleCell, also spatial, sequencing on #tumour heterogeneity and early stages. And work on cells that persist during/after #therapy, dubbed persister cells.

#anr2023

My first post on Mastodon after a whole lot of lurking and boosting, so I'm treating this as a mini #introduction for myself

I'm an #immunology PhD candidate at #ColumbiaUniversity medical center, and we just published a study of #TissueSpecifity of human #Tcell identity and clonal expansion in barrier sites, using #CyTOF, #scRNAseq, and #TCR #sequencing!

https://www.nature.com/articles/s41590-022-01395-9