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

TSNE plot and hierarchical clustering of cell types in snRNA-seq data from human ERC

In addition we generated the largest public ERC #snRNAseq dataset, 122k nuclei clustered into 38 fine resolution sub-clusters. Taking a close look at the cellular diversity of the brain region 🔍 🦠

Excited to share that our article on accurate sample deconvolution of pooled snRNA-seq data using sex-dependent gene expression patterns is live on NAR Genomics and Bioinformatics! 🎉

Check it out here: doi.org/10.1093/narg...

#NARGenomicsandBioinformatics #snRNAseq #Genomics #Bioinformatics

Combinatorial Cell-Adhesion and Activity Codes Instruct Cortical Modality Identity The emergence of functional sensory modalities requires precise cortical arealization and thalamocortical connectivity. While early morphogen gradients broadly initiate cortical patterning, how sensor...

New preprint on bioRvix! We show how cortical sensory-modality identity is instructed by a combinatorial cell-adhesion and activity codes, using #snRNAseq #spatialtranscriptomics #functional imaging. Congrats to everyone on this work! @guillelbendito.bsky.social @neuroalc.bsky.social

Para refinar la señal de habénula del vecino tálamo utilizamos nuestros datos de #snRNAseq para #deconvolución de nuestras muestras a granel #bulkRNA, estimando así la proporción de Hb. Estas proporciones las usamos para controlar diferencias en disecciones en el análisis de expresión diferencial 📊

Para contextualizar, integramos nuestros datos de #snRNAseq de Hb humana con datos #singlecell previamente publicados de Hb de ratón por el laboratorio de @gstuber.bsky.social. Algunos grupos de células neuronales como las LHb.2 enriquecidas por OPRM1 en humano aparecen conservadas entre especies 🐁

Creamos un mapa molecular con #snRNAseq de la Hb humana para entender la diversidad neuronal a un nivel molecular en esta región del cerebro única. Nuestros datos de 7 donadores control produjeron 16 mil núcleos y 17 grupos celulares, incluyendo 7 poblaciones neuronales laterales y 3 medias en Hb 🧪

Acá va en español 🇲🇽
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"¡Estamos orgullosos de anunciar que nuestro artículo ‘Análisis Transcriptómico de la Habénula Humana en Esquizofrenia’ es el artículo de portada de la edición de noviembre del American Journal of Psychiatry!" 🧠 #HabenulaLIBD #snRNAseq #Habénula doi.org/10.1176/appi...

To refine habenula signal from neighboring thalamus we utilized our #snRNAseq data to perform #deconvolution on our bulk samples, estimating proportion of habenula. These proportions were used to control for dissection differences in the differential expression analysis

We’ve created a #snRNAseq molecular atlas of the human Habenula to understand neuronal diversity on a molecular level in this unique brain region. Our snRNA-seq data on 7 control donors yielded 16k nuclei and 17 clusters, including 7 lateral & 3 medial Hb neuron populations 🧪

Transcriptomic Analysis of the Human Habenula in Schizophrenia | American Journal of Psychiatry Objective: The objective of this study was to define the molecular neuroanatomy of the human habenula (Hb) and identify transcriptomic differences between brains of individuals with schizophrenia and ...

Proud to announce our paper ‘Transcriptomic Analysis of the Human Habenula in Schizophrenia’ from @lieberinstitute.bsky.social is the cover article for the November issue of the American Journal of Psychiatry! 🧠 #HabenulaLIBD #snRNAseq #Habenula doi.org/10.1176/appi...

Opposite directions of association of higher physical activity and higher insulin resistance with human skeletal muscle cell type abundance and fiber type-level gene expression #snRNAseq #SingleNucleus #RNAseq #genomics 🧪🧬🖥️ www.biorxiv.org/content/10.1...

Resource Library - Precision Cell Systems Browse our collection of published protocols, peer-reviewed publications, and application notes featuring Precision Cell Systems technology.

Read the study: precisioncellsystems.com/resources/?_...

#SingleCell #snRNAseq #Automation #SamplePrep #Neuroscience #PrecisionCellSystems

(1/10) We’re excited to share our new preprint (doi.org/10.1101/2025...), which uncovers the spatiomolecular landscape of the human nucleus accumbens (NAc), by integrating snRNA-seq with Visium spatial transcriptomics across 10 control donors. 🧠 #NAcLIBD #snRNAseq #10xVisium

Highlights from an exciting Day 2 at @endocrinesociety.bsky.social #ENDO2025 including my talk on #snRNAseq in #ACC at the #adrenalcancer symposium! @unibirmingham.bsky.social @uhbtrust.bsky.social

We are excited to host rising junior Daniel (of #VassarBiochem) for #NationalMSSociety (#NMSS) Undergrad Summer Research Program! Working with #longread #snRNAseq data, he'll examine #CNStissue #lesions in #MS patients & GEX with #cytomegalovirus. Outside the lab, he enjoys trumpet & reading. 🧬

[2025-04-23] Journal club on "[...] deconvolution of pooled snRNA-seq using sex-dependent gene expr" YouTube video by Leonardo Collado Torres

Hi! Check my journal club talk: smart ML method to deconvolute pooled snRNA-seq using sex-specific expression🧬

Thanks @daylab.bsky.social & @rphillips3.bsky.social for this approach🙌

🎥 youtu.be/zpeCFwYfV3o
🛝 speakerdeck.com/manishabarse

#snRNAseq #ML #Bioinformatics @lieberinstitute.bsky.social

GIPR agonism and antagonism decrease body weight and food intake via different mechanisms in male mice - Nature Metabolism This study, together with a companion manuscript, show that, in mice, weight loss as a result of GIP receptor antagonism requires, and potentiates, functional GLP-1 receptor signalling in the brain, e...

Using Sable Promethion #Metabolic Cages, a key study in Nature ties metabolic & genetic evidence to reveal how GIPR antagonists, but not agonists, need GLP-1R signaling to reduce #BodyWeight in mice. 🧪

ow.ly/8pPn50VNQGL

#Obesity #Diabetes #Metabolism #Neuroscience #GIP #GLP #GLP1R #DVC #snRNAseq

The resulting cell type proportions had a large range across the different #DLPFC samples, and were not always correlated with the paired #snRNAseq proportions ⚠️

Testing these #deconvolution methods was made possible by a really cool multi-assay dataset from consecutive slices of #DLPFC tissue blocks 🧠1. Bulk RNA-seq 🧬 2. #snRNAseq as the reference 🦠 3. #RNAScope serving as a orthogonal measurement of cell type proportions 🔬

💥 Angela Dorigatti and Sabrina putting in the work! Making that easy single-cell spatial magic happen and repping hard for the Scroggins Lab on the Big campus! 💪🔬🔥
#WomenInSTEM #SingleCell #SpatialBiology #Teamwork #ScrogginsLab#SupportMomsAndBabies #WomenInSTEM #snRNAseq

Watch a new webinar showcasing how Lite Yang (Washington University in St. Louis) harnessed the power of Xenium #singlecellspatial and multiomic #snRNAseq to create detailed, multimodal maps of cell projections in the mouse #brain: bit.ly/4je4uiB

Detail of Figure 1: Schematic illustrating the strategy for isolating single nuclei from purified murine glomeruli, with podocyte-specific deletion of YAP or TAZ. UMAP plots show distinct clusters of podocytes.

📣📣📣 Latest news from the NephroLab Cologne – more specifically, from our 🦛 Hippo- Team:
Our snRNA-Seq study on YAP and TAZ in kidney podocytes is now online open access in JASN! 🥳 🎉 🐙
Huge thanks to everyone on the team and the incredibly thorough reviewers at […]

[Original post on social.cologne]

3 images of nuclei suspensions, featuring varying levels of debris and uniformity, followed by 2 bar plots showing yield and quality of each nuclei isolation method.

Data quality in #scRNAseq and #snRNAseq is really important. We spent 3 years testing different nuclei isolation protocols. The dataset I'm working on atm has a median value of 0.016% reads derived from mitochondria per cell.

Find out how in our new preprint. (;

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Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity - Nature Communications Circuit and cell type prioritization for complex disorders is crucial to direct future efforts. Here the authors integrate GWAS, human single-cell RNA-seq and fMRI analysis suggesting multi-modality c...

In @naturecomms.bsky.social , @hjerling-leffler.bsky.social and team at @ki.se integrated #GWAS with #snRNAseq data from the Human Brain Atlas revealing that the genetic risk for SCZ is enriched in the hippocampus & amygdala, further confirmed with fMRI. www.nature.com/articles/s41...

Unveiling adipose populations linked to metabolic health in obesity Metabolic disease risk in individuals with obesity is variable and influenced by so-far-unknown factors. Reinisch and Ghosh et al. uncovered distinct cell populations and transcriptional programs in adipose tissue that are strongly linked to metabolic disease. The findings suggest that visceral adipose tissue plasticity is key to maintaining metabolic health despite excess adiposity.

Reading now: Unveiling adipose populations linked to metabolic health in obesity by I Reinisch et al. #adipose #RNAseq #snRNAseq #SingleNucleus 🧬🖥️🧪

Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq Abstract. In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA)

Reading now: Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq by @delaneyksull.bsky.social @guillaumeolesan.bsky.social @pmelsted.bsky.social @lpachter.bsky.social et al. #RNAseq #scRNAseq #snRNAseq #SingleCell #SingleNucleus

Implementation and validation of single-cell genomics experiments in neuroscience - Nature Neuroscience Single-cell or single-nucleus RNA-sequencing experiments form a basis for biological insights about cell types and states, but they require orthogonal experiments to confirm the functional relevance o...

Authors present types of orthogonal and functional validation experiments to strengthen preliminary findings obtained using #scRNAseq & #snRNAseq transcriptomics, and details some of the challenges/limitations of these approaches.

www.nature.com/articles/s41...

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease - Nature Genetics Spatial and single-nucleus analyses in human postmortem Alzheimer’s disease (AD) brain tissues at early and late stages from individuals with and without Down syndrome, as well as in AD mouse models, ...

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s disease. 10x Genomics #visium + Parse Biosciences #snRNAseq
www.nature.com/articles/s41...

a black cat is sitting in front of an apple laptop computer . ALT: a black cat is sitting in front of an apple laptop computer .

Looking forward to getting my money's worth out of my MacBook next week. Time to hunker down. #transcriptomics #snRNAseq