#Cell-Cell-seq
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aliceyting.bsky.social
Today we report single-cell APEX-seq (scAPEX-seq)—a method for unbiased mapping of subcellular transcriptomes at single-cell resolution. It reveals cell states invisible to standard scRNA-seq and identifies regulators of CAR T function that improve solid tumor killing.

tinyurl.com/32pf6b8p
March 18, 2026 at 11:40 AM
wkhuber.bsky.social
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics
Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
jorg-vogel-lab.bsky.social
If you want to do single-cell RNA-seq on your favourite bacterium, here‘s our detailed Nature Protocol for microbial MATQ-seq. It profiles up to 600 genes in a single bacterial cell!

www.nature.com/articles/s41...
Transcriptomic profiling of individual bacteria by MATQ-seq - Nature Protocols
Bacterial single-cell sequencing via MATQ-seq combines index sorting, random priming and rRNA depletion, and offers high cell retention and transcript capture rates, making it ideal for experiments wi...
www.nature.com
April 9, 2025 at 9:15 AM
bartdeplancke.bsky.social
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics
This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.
www.nature.com
October 6, 2025 at 6:57 AM
kitazawa-taro.bsky.social
Please RP.
We are thrilled to announce that our lab’s first preprint is out!
”Whole-genome single-cell multimodal history tracing to reveal cell identity transition”

We report HisTrac-seq, a multiomic single-cell molecular recording platform.
www.biorxiv.org/content/10.1...
August 16, 2025 at 7:15 AM
plantcellatlas.bsky.social
Developed with input from @c-spirit.org & PCA, The BAR Single Cell Data Portal is now in beta, feat. curated scRNA-seq datasets, interactive data exploration, & the new SUPeR Viewer!

Explore the portal: bar.utoronto.ca/single_cell_...

#SingleCell #PlantScience
Promotional graphic announcing the BAR Single Cell Data Portal. The image features a six-panel visualization of single-cell data, with yellow, orange, and red cells representing different water and salinity conditions. Text highlights curated scRNA-seq datasets, CellxGene exploration, and a new single-cell portal viewer. Logos for BAR, Center for Sustainable Plant Innovation and Resilience, and Plant Cell Atlas appear along the bottom.
September 28, 2026 at 3:13 PM
caleblareau.bsky.social
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics
Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...
www.nature.com
January 8, 2025 at 1:30 PM
sebamorenor.bsky.social
Excited to share that our work on single-nucleus RNA-seq of the shoot apical meristem — the shoot stem cell niche — has found a home.
#Plantascience #scRNAseq #stemcells
www.science.org/doi/10.1126/...
Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem
snRNA-seq reveals shoot stem cell heterogeneity and traces their differentiation into primary stem cell types.
www.science.org
June 22, 2026 at 10:07 AM
rberrens.bsky.social
Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...
Long-read RNA sequencing of transposable elements from single cells using CELLO-seq - Nature Protocols
Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors fro...
doi.org
July 16, 2025 at 4:55 PM
mireyaplass.bsky.social
I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...
Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications
Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...
www.nature.com
July 14, 2025 at 10:31 AM
davisjmcc.bsky.social
Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)

Luckily for you, @aaronkwc.bsky.social has!

Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?

Check it out 👇
www.biorxiv.org/content/10.1...

🧪🧬💻
Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?
Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the re...
www.biorxiv.org
December 10, 2024 at 6:37 AM
natbiotech.nature.com
Tumor-reactive T cell receptors are rapidly identified from lymphocyte scRNA-seq data go.nature.com/49O5INm
rdcu.be/d8L1u
Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy - Nature Biotechnology
Tumor-reactive T cell receptors are rapidly identified from lymphocyte scRNA-seq data.
go.nature.com
February 13, 2025 at 6:21 PM
natbiotech.nature.com
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - @uwgenome.bsky.social @uwdeptmedicine.bsky.social go.nature.com/4rFTAHy
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - Nature Biotechnology
Single-molecule chromatin fiber sequencing exposes single-cell-level heterogeneity in the chromatin architecture of individual regulatory elements.
go.nature.com
December 3, 2025 at 7:43 PM
c-spirit.org
🌱 New plant single-cell resource!

Developed with input from C-SPIRIT & PCA, the BAR Single Cell Data Portal brings together scRNA-seq datasets, CellxGene & the new SUPeR Viewer to explore gene expression across plant cell types. 🔬🧬

🔗 bar.utoronto.ca/single_cell_...

#plantscience
September 28, 2026 at 4:15 PM
florianingelfinger.bsky.social
1/3 Deep generative modeling coming to cytometry! 🔬

CytoVI is now in Nature Methods: integrate flow cytometry, mass cytometry & CITE-seq, predict missing markers, and discover disease-associated cell states.

www.nature.com/articles/s41...
CytoVI: deep generative modeling of antibody-based single cell data - Nature Methods
CytoVI is a deep generative model for statistically rigorous analysis of antibody-based single-cell data.
www.nature.com
October 1, 2026 at 6:36 AM
james-gagnon.bsky.social
To dissect the gene regulatory networks used to build organisms, we need Perturb-seq-like tools that work in whole animals.

For this purpose, we developed MIC-Drop-seq, a tool that couples high-throughput CRISPR in zebrafish embryos with single-cell RNAseq.

www.biorxiv.org/content/10.1...
MIC-Drop-seq: Scalable single-cell phenotyping of mutant vertebrate embryos
Pooled perturbation screens can reveal cellular regulatory networks, yet scaling these techniques for large-scale screens in animals remains challenging. To address this, we developed MIC-Drop-seq, wh...
www.biorxiv.org
June 2, 2025 at 4:13 PM
michaelraissig.bsky.social
1/ Preprint alert:

🌾 The developing leaf of the wild grass Brachypodium distachyon at single-cell resolution

👉 doi.org/10.1101/2025...
A 70k-cell single-cell RNA-seq atlas of the developing grass leaf—from the shoot meristem to mature leaf tissues. @cerealcell.bsky.social @lbmountain.bsky.social
November 5, 2025 at 12:32 PM
erictopol.bsky.social
The potential for 2 cancer drugs in combination to impact Alzheimer's disease as an outgrowth or single-cell RNA -seq, review of electronic health records from 1.4 million patients, and whittling down 1,300 potential repurposed drugs to 2.
www.cell.com/cell/fulltex...
Cell-type-directed network-correcting combination therapy for Alzheimer’s disease
A multi-cell-type drug discovery strategy targeting dysregulated gene networks in neurons and glia identified letrozole and irinotecan as a combination therapy that significantly improved memory and r...
www.cell.com
July 21, 2025 at 2:42 PM
tmontsay.bsky.social

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
grothlab.bsky.social
DNA replication globally disrupts the epigenome. But does this create a chromatin-access opportunity for TF binding to facilitate cell identity change? Now 𝐫𝐞𝐩𝐥𝐢-𝐀𝐓𝐀𝐂-𝐬𝐞𝐪 shows 𝘥𝘦 𝘯𝘰𝘷𝘰 chromatin opening & TF binding occurs specifically post-replication, in cellular differentiation & reprogramming!
Post-replicative chromatin accessibility predicts cell fate change
Knudsen and colleagues use repli-ATAC-seq to compare replicated and unreplicated chromatin in two models of cell identity change. They find that lineage-specific elements are accessible earlier in rep...
www.cell.com
February 25, 2026 at 6:50 PM
We’re excited to present this integrative analysis of single-cell proteomics and transcriptomics of the human HSPC hierarchy. Now published in @science.org together with @fabiantheis.bsky.social, @erwinschoof.bsky.social, @porsebo.bsky.social.
www.science.org/doi/10.1126/...
🧵
Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics
Single-cell transcriptomics (scRNA-seq) has facilitated the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, the exclusive use of mRNA measurem...
www.science.org
August 22, 2025 at 6:03 AM
trevormnolan.bsky.social
🌱 Thrilled to see our latest collaborative work with @jennyrussinova.bsky.social @nvukas.bsky.social published in Cell! By combining single-cell RNA-seq and live imaging, we uncovered previously hidden brassinosteroid signaling states and their role in optimizing root growth. doi.org/10.1016/j.ce...
March 10, 2025 at 4:37 PM
tmontsay.bsky.social
scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified!
2/8
December 3, 2024 at 8:38 AM
veeninglab.com
Finally out, such an awesome piece of work, very proud of this one: www.cell.com/cell-systems... #MicroSky
October 4, 2025 at 8:48 AM
erictopol.bsky.social
Pancreatic cancer cells can hijack neurons to facility their growth and spread. Here's the single-cell map (spatial mics) of the process
www.cell.com/cancer-cell/...
Integrated single-cell and spatial transcriptomics uncover distinct cellular subtypes involved in neural invasion in pancreatic cancer
Chen et al. integrate sc/snRNA-seq with spatial transcriptomics to characterize cellular composition, lineage dynamics, and spatial architecture in PDAC tissues with varying neural invasion status, un...
www.cell.com
July 17, 2025 at 4:36 PM