Single Cell Atlas
www.singlecellatlas.org

125 healthy adult/fetal tissues
5 M cells scRNAseq scATAC-seq scImmune
2 M cells CyTOF
190 M cells flow cytometry
50 tissues with spatial transcriptomics

#GenomeBiol 2024
link.springer.com/article/10.1...

#SpatialOmics #ImagingMassSpec #SpatialTranscriptomics

MISTy
Multiview Intercellular SpaTial modeling framework

View/spatial scale-specific features
Intraview - same location
Juxtaview - local neighborhood
Paraview - distnat

#GenomeBiol 2022
genomebiology.biomedcentral.com/articles/10....

#HistoneLactylation #Angiogenesis

VEGF-A➡️
⏫#EndothelialCell #Glycolysis #Lactate➡️
⏫H3K9la➡️
>50% CUT&Tag peaks within 3 kb promoters
Covering prolif/motility/junction/hypoxia

Oxygen-induced retinopathy ⬇️ by glycolytic inhibitors

#GenomeBiol 2024
genomebiology.biomedcentral.com/articles/10....

scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data - Genome Biology Analyzing mass spectrometry (MS)-based single-cell proteomics (SCP) data faces important challenges inherent to MS-based technologies and single-cell experiments. We present scplainer, a principled an...

scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data #GenomeBiol genomebiology.biomedcentral.com/articles/10....

Crescendo, a Harmony extension for #SpatialTranscriptomics #BatchCorrection

Generalized linear models "fit a gene’s counts with random effects for batch and user-defined cell-type identity"

vs ComBat-Seq scVI Seurat MNN limma

#GenomeBiol 2025
genomebiology.biomedcentral.com/articles/10....

Prime-seq
Barcoding Bulk RNAseq to save💸

"the shift to higher intronic fractions and the expression profile similarity is mainly due to the heat incubation, rather than the enzymatic digestion by Proteinase K"🙂

Wolfgang Enard lab #GenomeBiol 2022
genomebiology.biomedcentral.com/articles/10....