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#scrnaseq — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #scrnaseq, aggregated by home.social.

  1. 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

  2. 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: github.com/nf-core/scnanoseq/r

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

  3. 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

    youtube.com/watch?v=gwqU9OoFwj

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

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

    pubmed.ncbi.nlm.nih.gov/344500

    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)
    pubmed.ncbi.nlm.nih.gov/367029

    1/2

  5. First speaker of the session (Cell identity in situ)
    is Elana Fertig
    of Convergence Institute at Johns Hopkins
    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
    physicell.org/

    #cancer
    #SingleCell
    #CSSingleCells23

    1/2

  6. "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

    biorxiv.org/content/10.1101/20
    biorxiv.org/content/10.1101/20

    New insights into universally expressed human genes
    biorxiv.org/content/10.1101/20

    2/3

  7. " 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:
    biorxiv.org/content/10.1101/20

    #scRNAseq #spatial #CyTOF #immunology

  8. 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

  9. 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!

    nature.com/articles/s41590-022