Chinese Immune Multi-Omics Atlas Human peripheral blood exhibits molecular and cellular heterogeneity across populations, yet the underlying mechanisms remain unclear. We present the Chinese Immune Multi-Omics Atlas (CIMA), character...

CIMA maps cell type–specific regulatory networks by integrating scRNA-seq, scATAC-seq & genetics across 10M+ PBMCs, revealing causal links to immune-mediated diseases.
#SingleCell #Genomics #Immunology #MultiOmics #scRNAseq #scATACseq #HumanGenetics @science.org www.science.org/doi/10.1126/...

I'd like to thank 🙏🏽 @cynthiasc.bsky.social for her 3 years at @lieberinstitute.bsky.social working in my team analyzing data generated by @kr-maynard.bsky.social et al.

Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)

#multiome #snRNAseq #scATACseq

OmnibusX: A unified platform for accessible multi-omics analysis. #MultiOmics #DataAnalysis #RNAseq #scRNAseq #scATACseq #SpatialTranscriptomics #BMCcomputationalBiology
journals.plos.org/ploscompbiol...

How is the progression of maturation regulated in forebrain inhibitory neurons? Excited to share our new study from the Mayer lab — stable differentiation, dynamic maturation, and stage-specific chromatin changes in GABAergic neurons.

#GABA #Neuroscience #scATACseq #scRNAseq

We also saw a shift in TF activity.

Footprinting showed increased NFI binding, especially NFIB, in late-born cohorts. These neurons activate maturation modules faster — possibly guided by chromatin remodeling during neurogenesis.
#TFfootprints #TranscriptionFactors #scATACseq
(5/n)

This shift was mirrored in chromatin accessibility.

scATAC-seq revealed stage-specific enhancer activation, with late-born cells opening distinct regulatory elements — especially in distal regions. A dynamic change in the regulatory landscape.
#Chromatin #Epigenetics #scATACseq
(4/n)

Great conversations and inspiring vibes at @events.embl.org — felt amazing to share my work and hear from incredible speakers!
#EESAgeing #SingleCell #Aging #ATACseq #RNAseq #Immunology #Multiomics #scRNAseq #scATACseq

🔬 Your immune system doesn’t just weaken with age—it evolves. We mapped how.
📊 We used single-cell multi-omics (RNA + ATAC) + bulk ATAC on PBMCs to build a cell-by-cell map of aging.
👉 Poster 83, EMBO | EMBL Symposium
#SingleCell #Aging #EMBL #Multiomics #scRNAseq #scATACseq

Integrated analysis of single-cell RNA-seq and ATAC-seq in lens epithelial cells: Unveiling the role of ATF6 as a key transcription factor

Integrated #scATACseq and #scRNAseq data reveals that ATF6 plays a pivotal role in maintaining the homeostasis of lens epithelial cells and facilitates EMT in epithelial cells by regulating p-STAT3 expression. #SecondaryCataracts #Cataracts #medsky

#OpenAccess: buff.ly/UXLfbrp

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning - Nature Communications Functional chromatin changes occur at different scales. Here, the authors introduce ChromatinHD, a method that characterises differential and predictive chromatin accessibility changes in a scale-adap...

Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414...

Happy 2025 everyone 🎆 !

Alevin-fry 0.11.0 was just released (last night). This speed up permit-list generation by making it multithreaded, but much more importantly, adds the `atac` command allowing barcode correction and counting & BED generation directly in the main branch of alevin-fry. 1/3 #scRNAseq #scATACseq

source: https://www.biorxiv.org/content/10.1101/2024.11.27.625728v1

MuMu: a sample multiplexing protocol for droplet-based simultaneous single nuclei RNA- and ATAC-seq systems. #SingleNuclei #MultiplexingProtocol #10X #scRNAseq #scATACseq @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...