#scRNAseq
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lpachter.bsky.social
One of the curiosities of genomics history is that James Watson was vehemently against cDNA sequencing (for ESTs), and fought with Craig Venter & Bernadine Healy who championed it. Tl;dr Watson ended up resigning from the HGP, Venter plowed ahead... and we now have #scRNAseq.
November 9, 2025 at 9:41 PM
kischober.bsky.social
I didn't see them really assigning a subset from adults as naive with high certainty in the first place (using CITEseq or ribosomal genes among others). Without that context, it's very hard to distinguish ET from mature naive from mature early TSCM/TCM in scRNAseq.
November 9, 2025 at 3:21 PM
stressbiology.bsky.social
Single-cell RNA sequencing reveals developmental trajectories and environmental regulation of callus formation in Arabidopsis
Zhixin Liu, Yixin Zhang ... Guoyong An, Xuwu Sun

link.springer.com/article/10.1...

#ScRNAseq #regeneration #dedifferentiation
Single-cell RNA sequencing reveals developmental trajectories and environmental regulation of callus formation in Arabidopsis - Stress Biology
Plant cells exhibit an extraordinary regenerative potential, achieving cellular totipotency by dedifferentiating to form new tissues. While significant progress has been made in understanding cell fat...
link.springer.com
November 9, 2025 at 9:17 AM
jsantoyo.bsky.social
DESpace2: detection of differential spatial patterns in spatial omics data. #SpatialOmics #DifferentialSpatialPatterns #scRNAseq #Genomics #Bioinformatics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
DESpace2: detection of differential spatial patterns in spatial omics data
Spatially resolved transcriptomics (SRT) enables the investigation of mRNA expression in a spatial context. While several SRT analysis frameworks have been developed, the vast majority of them focus…
www.biorxiv.org
November 8, 2025 at 6:05 PM
medcomm.bsky.social
#Article in @MedComm_MC
Discovering Heterogeneous Leukocytes Subsets Associated With Alcoholic Steatohepatitis by #scRNAseq Analysis doi.org/10.1002/mco2...

#AlcoholicLiverDisease #AlcoholicSteatohepatitis #Bcell #ImmuneCell #Neutrophil #tSNEs
Discovering Heterogeneous Leukocytes Subsets Associated With Alcoholic Steatohepatitis by scRNAseq Analysis
In this study, we explored comprehensive profiling of heterogeneous immune leukocytes at a single-cell level using scRNAseq analysis to discover the regulation of inflammatory-mediated liver fibrosis...
doi.org
November 7, 2025 at 8:16 AM
eurobioimaging.bsky.social
At this week's #VirtualPub, we welcome Elena Buglakova, @embl.org, on “Cross-scale cross-modality data integration: from scRNAseq to electron microscopy” followed by the Tech Exchange.
Join us on 🗓️ Fri, Nov 7 at 1 pm CEST.
Register 🔽
www.eurobioimaging.eu/events/cross...
November 6, 2025 at 1:32 PM
fiosgenomics.bsky.social
Working with single-cell RNA-Seq data and wondering where to start with the analysis?
This blog includes the main steps:
https://www.fiosgenomics.com/single-cell-rna-seq-data-analysis-workflow
#omics #bioinformatics #singlecell #scRNAseq
November 6, 2025 at 12:02 PM
nf-co.re
Pipeline release! nf-core/scrnaseq v4.1.0!

Please see the changelog: github.com/nf-core/scrn...
Release 4.1.0 · nf-core/scrnaseq
What's Changed bumpt dev branch version by @fmalmeida in #447 Json schema improvements by @abartlett004 in #453 Change simpleaf protocol name from 10xv4 to 10xv4-3p by @milos7250 in #452 updated -...
github.com
November 6, 2025 at 11:27 AM
horticulturer.bsky.social
Unveiled single-cell RNA & spatial metabolomics in Panax root tips, revealing gene patterns & ginsenosides biosynthesis. #PanaxGenomics #scRNAseq @oxfordacademic.bsky.social
Details: doi.org/10.1093/hr/u...
Integrated single-cell transcriptomics and spatial metabolomics unveil cellular differentiation and ginsenosides biosynthesis in Panax root tips
Abstract. Root tips, which represent the initial stage of taproot development, serve as an ideal model for investigating plant growth and secondary metabol
doi.org
November 5, 2025 at 3:19 PM
stanfordstomata.bsky.social
What a glorious day--waking up to see this lovely preprint that does it all--a comprehensive scRNAseq atlas of leaf development, hints at the txn of new cell types, and great hypotheses about how GRNs may differ among related TFs

(and in other news, some hope for American Democracy)
michaelraissig.bsky.social Michael Raissig @michaelraissig.bsky.social · 5d
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 2:16 PM
fiosgenomics.bsky.social
Discover the applications for single-cell analysis & learn about the common challenges and their resolutions in our whitepaper.
View it now! ⬇️
https://www.fiosgenomics.com/wp-content/uploads/2020/10/Fios-Genomics-White-paper-scRNA-Analysis-website.pdf
#bioinformatics #scRNAseq
November 5, 2025 at 11:50 AM
eurobioimaging.bsky.social
At this week's #VirtualPub, we welcome Elena Buglakova, @embl.org, on “Cross-scale cross-modality data integration: from scRNAseq to electron microscopy” followed by the Tech Exchange.
Join us on 🗓️ Fri, Nov 7 at 1 pm CEST.
Register 🔽
www.eurobioimaging.eu/events/cross...
November 4, 2025 at 1:32 PM
stemcellsciencenews.com
🥼 Dr. Olivier Lantz and colleagues performed scRNAseq and spatial analysis of both T cells and tumoral cells. #thymoma

T cells at all stages of T cell development, from immature to mature, were present in the tumor.

🆕 Discover more: https://bit.ly/47jMWyy
October 31, 2025 at 11:47 PM
biocompareeditor.bsky.social
For a rundown of the main scRNAseq methods available today, loosely organized by throughput, check out Biocompare's latest article from Caitlin Smith.
Comparing Single-Cell RNA Sequencing Options
A rundown of methods organized by throughput
www.biocompare.com
October 30, 2025 at 10:45 AM
prstats.bsky.social
Single-cell RNA-seq Analysis using R

24–27 Nov | Online

Learn to process, visualise, and interpret single-cell RNA-seq data using Seurat and related tools.
Instructor: Dr Frances Turner

prstats.org/course/single-cell-rna-seq-analysis-scrn01
#SingleCell #Bioinformatics #Rstats #Genomics #scRNAseq
Single cell RNA-Seq analysis | PR Statistics
This 4-day live course introduces single cell RNA-Seq analysis, covering experimental design, raw data processing, and advanced methods in R using Seurat. Participants will learn quality control, clus...
prstats.org
October 29, 2025 at 11:59 AM
jsantoyo.bsky.social
TemporalVAE: atlas-assisted temporal mapping of time-series single-cell transcriptomes during embryogenesis. #SingleCell #scRNAseq #TimeSeries #Embryogenesis #DeepLearning #Genomics #Bioinformatics @natcellbio.nature.com
www.nature.com/articles/s41...
October 29, 2025 at 9:31 AM
cytosurge.bsky.social
⌛ Time travel with us tomorrow!
🎤 Join us live on Oct 29, 3PM CET!
🥼 Not available at that time? No worries – just register, and we will send you the recording link. 👉 lnkd.in/eZ75MxcC

#scRNASeq #Transcriptomics #NGS #FluidFM
October 28, 2025 at 12:44 PM
jsantoyo.bsky.social
BestopCloud: an integrated one-stop solution for single-cell RNA sequencing data analysis. #SingleCell #scRNAseq #DataAnalysis #WebTool #OpenSource #Rshiny #BMCgenomics @NatureGenet
bmcgenomics.biomedcentral.com/articles/10....
October 26, 2025 at 5:49 PM
giulia-boezio.bsky.social
Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social

We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇

www.biorxiv.org/content/10.1...
Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding
The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...
www.biorxiv.org
October 26, 2025 at 5:15 PM
haoyin.bsky.social
Systematic comparisons among 4 subcellular-resolution #SpatialTranscriptomics methods

Stereo-seq v1.3
Visium HD FFPE
CosMx 6k
Xenium 5k

Human Tumors
Ground truth CODEX, +scRNAseq

#NatComm 2025
www.nature.com/articles/s41...
October 24, 2025 at 10:45 AM
nextflow.io
🧪 Converting raw single-cell RNA-Seq data into meaningful insights is not simple. Nikhila T. Suresh from Purdue University just walked through benchmarking @nf-co.re/scrnaseq pipeline on mouse prostate data, comparing alignment methods & documenting practical challenges for new users
October 23, 2025 at 2:59 PM
rebeccanicholl.bsky.social
Calling all single-cell fans; our virtual training course on single-cell RNA-seq with Python course closes for applications soon.

See you there?

#EMBL #Bioinformatics #Python #scRNAseq
training.ebi.embl.org EMBL-EBI Training @training.ebi.embl.org · 18d
Reminder: applications close for our single-cell RNA-seq with Python course next week.

Course dates: 2 – 6 February 2026
Course fee: from £240.00, funding is available.
Location: virtual, UK time zone

Apply by 2 November 2025: www.ebi.ac.uk/training/eve...

#Python #SingleCell #Bioinformatics
🧬📊🐍
training.ebi.embl.org EMBL-EBI Training @training.ebi.embl.org · Jul 25
Join us virtually for 'Single-cell RNA-seq analysis with Python' from 2 – 6 February 2026: www.ebi.ac.uk/training/eve...

This course covers the analysis of single-cell RNA sequencing (scRNA-seq) data using Python and command-line tools.

@ebi.embl.org
@events.embl.org

🧬🧪🖥️
#SingleCell #RNASeq
October 23, 2025 at 11:47 AM
evolvedbiofilm.bsky.social
Yi Song, Southern University of Science and Technology
Characterization of primary immune responder cells in roots based on scRNAseq dataset
#BGIspatialmicrobiome
October 22, 2025 at 7:13 AM
antoinezalc.bsky.social
It did a very good job on my initial submission from my postdoc manuscript. Funny though it says scRNAseq is now a standard technic. It’s is true now but not in 2020 haha
Looking forwards to testing it with our new manuscripts!
October 21, 2025 at 4:56 PM
mariabernabeu.bsky.social
Alina finally integrated the scRNAseq immune dataset with our recently published dataset of the 3D-BBB model being exposed to P. falciparum. We identified shared and dominant disrupted pathways (JAK-STAT!) in all cells. As well as parasite/immune-specific disruptive pathways on endothelial cells.
October 21, 2025 at 11:06 AM