#Transcriptome
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tomkindlon.bsky.social
From Germany:

Transcriptome analysis of classical blood cells reveals down-regulation of proinflammatory genes in the classical monocytes of Long-COVID patients

www.frontiersin.org/journals/imm...

Screenshot from latest Science for ME weekly update

#LongCovid #PASC
Transcriptome analysis of classical blood cells reveals down-regulation of proinflammatory genes in the classical monocytes of Long-COVID patients — Fricke et al. "UMAP clustering of cells revealed distinct expression profiles between patients and controls in classical and intermediate, but not non-classical, monocytes. Differential gene expression analysis, based on a fold change threshold greater than 3 and a p-value threshold below 10−18, identified 40 DEGs in classical, 13 in intermediate, and 6 in non-classical monocytes, while other cell types showed minimal changes."
November 11, 2025 at 1:41 AM
uwbiostat.bsky.social
Join us Thursday, Nov. 13 at 3:30 p.m. for: Statistical Frameworks for Dissecting Genetic Regulation in the Human Transcriptome presented by Pejman Mohammadi @uwmedicine.bsky.social and @seattlechildrens.org Research Institute. Details and abstract: bit.ly/498bfAJ
November 11, 2025 at 5:57 PM
lionlchristiaen.bsky.social
Could not be more happy/proud/relieved to finally see this longstanding study published. Bluetorial to follow. @msarscentre.bsky.social
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors | The EMBO Journal www.embopress.org/doi/full/10....
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors | The EMBO Journal
imageimageDuring development, multipotent cardiopharyngeal progenitors express both cardiac and pharyngeal muscle transcriptional programs. This study in the tunicate Ciona shows that cell cycle-regul...
www.embopress.org
November 4, 2025 at 6:05 AM
yelenab.bsky.social
Our latest on how cells get ready for fate transition! @noahbruderer.bsky.social @margauxfailla.bsky.social @lionlchristiaen.bsky.social

Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors www.embopress.org/doi/full/10....
Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors | The EMBO Journal
imageimageDuring development, multipotent cardiopharyngeal progenitors express both cardiac and pharyngeal muscle transcriptional programs. This study in the tunicate Ciona shows that cell cycle-regul...
www.embopress.org
November 4, 2025 at 12:05 PM
sinamajidian.bsky.social
Ke Chen presents "A scalable and improved heuristic for flow decomposition"
They developed a new algorithm to decompose a directed graph (generated from reads) into a minimum # weighted paths, with application to metagenome and transcriptome assembly.
November 6, 2025 at 2:46 PM
biorxivpreprint.bsky.social
Multi-ancestry Transcriptome-Wide Association Study Reveals Shared and Population-Specific Genetic Effects in Alzheimer's Disease https://www.biorxiv.org/content/10.1101/2025.11.03.686160v1
November 5, 2025 at 11:33 AM
genomebiolevol.bsky.social
@guyleonard.bsky.social et al. report a near-complete genome and transcriptome sequence dataset for green algae host Paramecium bursaria, an endosymbiotic model system.

🔗 doi.org/10.1093/gbe/evaf183

#genome #evolution
De Novo Genome Sequence Assembly of the RNAi-Tractable Paramecium bursaria 186b: An Endosymbiotic Model System
Abstract. How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a use
doi.org
October 31, 2025 at 10:54 AM
imetascience.bsky.social
🐭 #Lactiplantibacillus plantarum Hi188 promotes post-weaning growth in mice.
🧪 The #metabolite 5-HIAA activates hepatic #AhR, boosting IGF-1 production.
🧑‍💻 Metagenomic and host transcriptome data reveal that 5-HIAA is co-produced by the host–microbiota axis.
🔗 doi.org/10.1002/imo2...
#microbiome
Host–microbiota interaction drives 5‐hydroxyindole‐3‐acetic acid production to promote linear growth in infant mice
This study discovered that Lactiplantibacillus plantarum Hi188 promoted linear growth in postweaning mice. Transcriptomic analysis, untargeted metabolomics, and in vitro experiments showed that the e...
doi.org
October 30, 2025 at 3:06 PM
earlhaminst.bsky.social
A study from the Earlham Institute and @helmholtzmunich.bsky.social as part of a global collaboration has generated the first wheat pan-#transcriptome, revealing new sources of genetic diversity that could be critical in boosting the resilience of #wheat

#plantscience #foodsecurity
News: Wheat diversity discovery could provide an urgently-needed solution to global food security
Newly-discovered diversity in the wheat genome could offer vital new opportunities to improve and ‘climate-proof’ one of the world’s most important staple crops.
buff.ly
October 25, 2025 at 11:01 AM
biorxivpreprint.bsky.social
Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport https://www.biorxiv.org/content/10.1101/2025.10.23.684069v1
October 24, 2025 at 8:47 PM
biorxivpreprint.bsky.social
A Meta-Analysis of the Effects of Chronic Stress on the Prefrontal Transcriptome in Animal Models and Convergence with Existing Human Data https://www.biorxiv.org/content/10.1101/2025.10.23.683091v1
October 24, 2025 at 5:15 PM
verndolinsky.bsky.social
Functional recovery of islet β cells in human type 2 #diabetes: Transcriptome signatures unveil therapeutic approaches @dream-diabetes.bsky.social @chrisadoucette.bsky.social www.science.org/doi/10.1126/...
Functional recovery of islet β cells in human type 2 diabetes: Transcriptome signatures unveil therapeutic approaches
Human T2D beta cell function was restored, the rescuing mechanisms disentangled, and hits identified to promote T2D remission.
www.science.org
October 21, 2025 at 7:08 PM
sharkscience.bsky.social
Alzheimer’s disease signatures in the brain transcriptome of Estuarine Dolphins 🐬🦑🌿🧪🐟 www.nature.com/articles/s42...
Alzheimer’s disease signatures in the brain transcriptome of Estuarine Dolphins - Communications Biology
Transcriptomic analysis of brain samples collected from dolphins found beached in the Indian River Lagoon during algal bloom seasons shows Alzheimer’s disease related molecular signatures.
www.nature.com
October 17, 2025 at 4:05 PM
biorxivpreprint.bsky.social
GeneJEPA: A Predictive World Model of the Transcriptome https://www.biorxiv.org/content/10.1101/2025.10.14.682378v1
October 16, 2025 at 5:33 AM
landau.bsky.social
Big, beautiful trees!!

SMART-PTA for whole-genome+transcriptome on thousand of single cells from the normal human esophagus 🤯 Massively scaling up the power of scWGS to build deep phylogenies and chart somatic evolution from birth throughout life.

www.biorxiv.org/content/10.1...
October 14, 2025 at 2:37 PM
devbiol.bsky.social
#DBfeature 🐣

The chicken embryo brings new insights into the tissue specific evolutionary role of WFDC1 during amniote development

-T Metzker-Pinto, YTH Tran, I Buzzatto-Leite, L Lok, JF Sampar, HF Carvalho, G del Monte-Nieto, LE Alvares

tinyurl.com/3abhm3d5

#SpecialIssue on Avian model systems
(A–B) WFDC1 expression pattern during chicken and mouse eye development, respectively. The developmental stages are indicated at the top of each image. Sagittal (Ai) and coronal (Aii-iv, Bi-v) sections were presented. (C–E) UMAP visualization of the mouse retina cells according to their transcriptome similarities, representing the cell type (C), embryonic day (D) and WFDC1 expression level (E).
October 13, 2025 at 9:05 AM
prepub-singlecell.bsky.social
Finding the perfect promoter: Correlating single-cell transcriptome data with gene drive performance #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.10.08.681126v1
October 9, 2025 at 7:01 AM
mhagenauer.bsky.social
🧠 🧬 Our paper "A Meta-Analysis of the Effects of Acute Sleep Deprivation on the Cortical Transcriptome in Rodent Models" is now out in the Journal of Sleep Research! Very exciting.

Congratulations to all involved! 🎉
@cosetterhoads.bsky.social @huda-akil.bsky.social @ummni.bsky.social
cosetterhoads.bsky.social cosetterhoads.bsky.social @cosetterhoads.bsky.social · Oct 8
I’m excited to announce that my (first first-authored!) paper is live!

So grateful to @mhagenauer.bsky.social for her mentorship and guidance, to JSleepResearch for their fantastic reviewers, to Grinnell College’s summer internship funding, and of course to all my co-authors!
October 8, 2025 at 10:05 PM
earlhaminst.bsky.social
📃 New research published today in @natcomms.nature.com from the Earlham Institute and @helmholtzmunich.bsky.social presents the first wheat pan-transcriptome - revealing layers of hidden diversity spanning our modern wheat variations. 🧪

➡️ buff.ly/ZDIRnFW

@wheatinitiative.bsky.social @ukri.org
New wheat diversity discovery could provide an urgently-needed solution to global food security
Newly-discovered diversity in the wheat genome could offer vital new opportunities to improve and ‘climate-proof’ one of the world’s most important staple crops.
buff.ly
October 6, 2025 at 9:15 AM
helmholtzmunich.bsky.social
How Genomes Support Resilient Wheat

As part of the 10+ Wheat Genomes Project, researchers from #HelmholtzMunich & Earlham Institute built the first wheat pan-transcriptome, mapping gene activity across varieties.

👉 t1p.de/cxxdv

@wheatinitiative.bsky.social
New Wheat Diversity Discovery Could Help Secure Global Food Supplies
October 6, 2025 at 9:22 AM
wheatinitiative.bsky.social
Exciting news in wheat science!
A new study in @natcomms.nature.com shows the first wheat pan-transcriptome: uncovering hidden diversity across modern wheat lines 🌾
Congrats to @earlhaminst.bsky.social & @helmholtzmunich.bsky.social for this major advance!
➡️ buff.ly/XEQlCnT
#WheatConnect
De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome - Nature Communications
Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core…
buff.ly
October 6, 2025 at 1:00 PM
pritiagarwal.bsky.social
🚨 New preprint!
We profile the transcriptome of the C. elegans distal tip cell: a persistent leader cell that invades basement membrane to shape the gonad.

Our dataset defines the molecular signature of invasive leader cells & uncovers new regulators of collective cell invasion.
Stage-specific transcriptomics of a leader cell reveals cell machineries driving collective invasion
Collective cell invasion underlies organ development, epithelial repair, and cancer metastasis. Leader cells remodel extracellular matrix, sense guidance cues, reorganize their cytoskeleton, and coord...
www.biorxiv.org
October 3, 2025 at 6:24 AM
tkozawa.bsky.social
Great preprint by Upadhyaya et al. (2025) on using a #multiomics approach to study #PlantTOR signaling in the unicellular green alga #Chromochloris zofingiensis, particularly showing the upregulation of #AminoAcid biosynthesis pathways during TOR inhibition with AZD8055.
#Algae #Phosphoproteomics 🔗⬇️
Fig. 8. Summary of the mechanism of TOR inhibition-dependent accumulation of amino acids in Chromochloris zofingiensis. TOR inhibition by AZD8055 induces the expression of transcription factors G2- like, HSF, and bHLH, which bind to amino acid biosynthesis and nitrogen metabolism genes to potentially regulate their transcription. This process, which is independent of glucose-TOR signaling, leads to an accumulation of amino acids during TOR inhibition. Glucose addition via hexokinase1 (HXK1) also upregulates amino acid biosynthesis. Fig. 1. TOR inhibition prevents glucose-driven growth and suppresses photosynthesis in the green alga Chromochloris zofingiensis. (A) Representative C. zofingiensis (WT) cultures over the 96 h experiment with the following treatments: control, TOR inhibition by 1 µM AZD8055, 100 mM glucose addition, and 100mM glucose + 1 µM AZD treatment. (B) Cell density and (C) maximum PSII photosynthetic efficiency (Fv/Fm). For (B) and (C), datapoints represent biological replicates with lines representing means (n = 3). (D) PCA of WT 1 h and 24 h transcriptome, proteome, and metabolome with treatments: control, 1 µM AZD, 15 mM glucose, 15 mM glucose + 1 µM AZD, and 15 mM sorbitol as an osmotic control. For the transcriptome, normalized log2-transformed counts of 500 genes with highest variance were considered. For the proteome and the metabolome, the raw intensity values were log2-transformed, and proteins or metabolites with highest variance were used to calculate and plot the PCA. Modified Fig. 2. Phosphoproteomics of TOR-inhibited Chromochloris zofingiensis identifies novel TOR players. (B) The log2 fold changes of TOR-dependent phosphosites between TOR inhibition by 1 µM AZD, 15 mM glucose addition, 15 mM glucose + 1 µM AZD, and 15 mM sorbitol-treated C. zofingiensis (WT) cultures at 1 h and 24 h from cluster 4 were labelled according to their protein symbols and phosphorylated Ser/Thr residue on the left and by their ortholog name identified on the right. The phosphopeptides were labelled if they are known conserved TOR targets as “known targets” and if they are unknown as “novel targets”. RbcL, MAPK, PP2C, PP2C, and SnRK2 were identified as putative novel conserved TOR targets. White boxes in the heatmap indicate that the phosphopeptides were not detected. Data represent means of fold changes log2 intensities of phosphopeptides (n = 3-4 biological replicates).
October 2, 2025 at 4:27 PM
genometdcc.org
New highlight video! 🧪🧬💻
RAEFISH from Steven Wang at Yale unlocks whole-transcriptome imaging at single-molecule resolution. See 20,000+ RNAs light up in cells and tissues. Plus get direct gRNA detection in high-content CRISPR screens. Spatial biology just leveled up

www.youtube.com/watch?v=P2j6...
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution
YouTube video by GenomeTDCC
www.youtube.com
October 1, 2025 at 5:17 PM
richardmott.bsky.social
We have just published a paper in Genome Biology, rdcu.be/eIMLf. We explore the information flow between genome, gene body methylation, transcriptome, translatome and proteome in Arabidopsis. This is part of a BBSRC-funded collaboration with UCL, Rothamsted Research and University of Cambridge.
Information flow between omic levels in Arabidopsis thaliana
September 30, 2025 at 8:54 AM