#transcriptome — Public Fediverse posts

New publication: #Pseudomonas volatiles shape the root #transcriptome and #microbiome to promote plant growth under drought. #plantgrowth #rhizobacteria #volatiles
https://doi.org/10.1111/nph.71203

MolluscaGenes: A Transcriptomic Database for the Mollusca - has already proved a useful resource for me: https://www.biorxiv.org/content/10.64898/2026.05.05.723003v1 #mollusc #transcriptome #Genomics

MolluscaGenes: A Transcriptomic Database for the Mollusca - has already proved a useful resource for me: https://www.biorxiv.org/content/10.64898/2026.05.05.723003v1 #mollusc #transcriptome #Genomics

The liver #transcriptome is highly sensitive to metabolic cues. By characterizing nuclear protein #OGlcNAcylation in mouse #liver during the day, this study shows how shifts in a nutrient-sensitive #PTM may shape transcriptional regulation @PLOSBiology https://plos.io/3KuS7m1

The liver #transcriptome is highly sensitive to metabolic cues. By characterizing nuclear protein #OGlcNAcylation in mouse #liver during the day, this study shows how shifts in a nutrient-sensitive #PTM may shape transcriptional regulation @PLOSBiology https://plos.io/3KuS7m1

Pipeline release! nf-core/denovotranscript v1.2.1 - nf-core/denovotranscript v1.2.1!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.2.1

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/denovotranscript v1.2.1 - nf-core/denovotranscript v1.2.1!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.2.1

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

The #spider #Tibellus #oblongus (#Philodromidae) has a #Holarcticdistribution and is common in Central Europe, thus not being protected. It prefers #sunexposed #habitats, whether dry or moist, and is a free #hunter that is very well #camouflaged due to its elongated #bodyshape. Y. Korolkova et al. (2023) examined the #venomgland #transcriptome and a venom proteome analysis.

© #StefanFWirth #Rosenthal #Berlin 2025

Ref
Y. Korolkova et al. (2023)
https://doi.org/10.1038/s41597-023-02703-0

Photos
© S.F. Wirth

The #spider #Tibellus #oblongus (#Philodromidae) has a #Holarcticdistribution and is common in Central Europe, thus not being protected. It prefers #sunexposed #habitats, whether dry or moist, and is a free #hunter that is very well #camouflaged due to its elongated #bodyshape. Y. Korolkova et al. (2023) examined the #venomgland #transcriptome and a venom proteome analysis.

© #StefanFWirth #Rosenthal #Berlin 2025

Ref
Y. Korolkova et al. (2023)
https://doi.org/10.1038/s41597-023-02703-0

Photos
© S.F. Wirth

#Microbiota transplantation offers new hope against #cotton #leaf_curl #disease.

#CLCuD #rhizosphere #phylosphere #Gossypium # #microbiome #transcriptome

https://phys.org/news/2025-03-microbiota-transplantation-cotton-leaf-disease.html

#Microbiota transplantation offers new hope against #cotton #leaf_curl #disease.

#CLCuD #rhizosphere #phylosphere #Gossypium # #microbiome #transcriptome

https://phys.org/news/2025-03-microbiota-transplantation-cotton-leaf-disease.html

Pipeline release! nf-core/denovotranscript v1.2.0 - nf-core/denovotranscript v1.2.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.2.0

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/denovotranscript v1.2.0 - nf-core/denovotranscript v1.2.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.2.0

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Random question for #transcriptome #bioinformatics folks - is there ever a reason to screen transcriptome assemblies (lots of small contigs) against database using ANI tools (i.e. skani)?

Curious to know if there's a usage case for it.

Do or die: How #soybeans tackle #nematode invaders.

#agriculture #transcriptome #RNA

https://phys.org/news/2025-01-die-soybeans-tackle-nematode-invaders.html

Do or die: How #soybeans tackle #nematode invaders.

#agriculture #transcriptome #RNA

https://phys.org/news/2025-01-die-soybeans-tackle-nematode-invaders.html

I've been seeing a few #transcriptome wide association studies (TWAS) papers lately. This is another example, from #sorghum, combining GWAS and TWAS to study flowering time. Bonus - I imagine that there's a lot more value that can be gained from the 822 #RNAseq samples made publicly available

https://www.biorxiv.org/content/10.1101/2024.12.12.628249v1.full.pdf

#PlantScience #PlantDevelopment #Sorghum

I've been seeing a few #transcriptome wide association studies (TWAS) papers lately. This is another example, from #sorghum, combining GWAS and TWAS to study flowering time. Bonus - I imagine that there's a lot more value that can be gained from the 822 #RNAseq samples made publicly available

https://www.biorxiv.org/content/10.1101/2024.12.12.628249v1.full.pdf

#PlantScience #PlantDevelopment #Sorghum

Pipeline release! nf-core/denovotranscript v1.1.0 - nf-core/denovotranscript v1.1.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.1.0

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/denovotranscript v1.1.0 - nf-core/denovotranscript v1.1.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.1.0

#denovoassembly #rnaseq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/denovotranscript v1.0.0 - nf-core/denovotranscript v1.0.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.0.0

#denovo-assembly #rna-seq #transcriptome #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/denovotranscript v1.0.0 - nf-core/denovotranscript v1.0.0!

Please see the changelog: https://github.com/nf-core/denovotranscript/releases/tag/1.0.0

#denovo-assembly #rna-seq #transcriptome #nfcore #openscience #nextflow #bioinformatics

#Genetic signatures of #domestication identified in #pigs and #chickens.

#agriculture #anthropology #transcriptome

https://phys.org/news/2024-08-genetic-signatures-domestication-pigs-chickens.html

#Genetic signatures of #domestication identified in #pigs and #chickens.

#agriculture #anthropology #transcriptome

https://phys.org/news/2024-08-genetic-signatures-domestication-pigs-chickens.html

Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. https://doi.org/10.1038/s41598-024-60593-7 #SpinalMuscularAtrophy,Sma #SurvivalMotorNeuron,Smn #CircularRna,Circrna #Proteome #Transcriptome

Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes. https://doi.org/10.1038/s41598-024-60593-7 #SpinalMuscularAtrophy,Sma #SurvivalMotorNeuron,Smn #CircularRna,Circrna #Proteome #Transcriptome

The #genetic interplay in Impatiens #downy_mildew: A #transcriptome-based approach to enhancing #disease resistance.

#plants #agriculture #RLK

https://phys.org/news/2024-05-genetic-interplay-impatiens-downy-mildew.html

Team reports on relationship between contents of #diosgenin and #brassinosteroids in #Dioscorea zingiberensis.

#hypomethylation #transcriptome

https://phys.org/news/2024-04-team-relationship-contents-diosgenin-brassinosteroids.html

Unraveling the unique role of #DELLA #proteins in grapevine #flowering.

#VvDELLA1 #signaling #gibberellin #transcriptome

https://phys.org/news/2024-04-unraveling-unique-role-della-proteins.html

#Boron deficiency in #oilseed_rape #transcriptome resembles a #wounding and #infection response.

#canola #brassica

https://phys.org/news/2024-04-boron-deficiency-oilseed-rape-transcriptome.html

#Microgravity found to cause marked changes in #gene_expression rhythms in #humans.

#transcriptome

https://phys.org/news/2024-03-microgravity-gene-rhythms-humans.html

If you are annotating genes in a eukaryotic genome with #rnaseq , how do you handle antisense transcripts? It seems like they are quite common in many situations.

I'm using tophat + stringtie, and sometimes I see features being called on the wrong strand.

#transcriptome #transcriptomeAnalysis #RNA #mRNA

If you are annotating genes in a eukaryotic genome with #rnaseq , how do you handle antisense transcripts? It seems like they are quite common in many situations.

I'm using tophat + stringtie, and sometimes I see features being called on the wrong strand.

#transcriptome #transcriptomeAnalysis #RNA #mRNA

We sequenced and analyzed #transcriptome of pods from seven cacao genotypes inoculated #Phytophthora palmivora and controls. We identified potential cis-regulatory elements involved in cacao resistance to this pathogen. Paper here: https://rdcu.be/dy9zZ #PromoterMotif #DNA #RNA #Sequencing #Genomics #RNASeq #Bioinfirmatics

Differential cardiomyocyte transcriptomic remodeling during in vitro Trypanosoma cruzi infection using laboratory strains provides implications on pathogenic host responses. https://doi.org/10.1186/s41182-023-00552-6 #TrypanosomaCruzi #ChagasDisease #Transcriptome #Hl1 #InVitroModeling

Differential cardiomyocyte transcriptomic remodeling during in vitro Trypanosoma cruzi infection using laboratory strains provides implications on pathogenic host responses. https://doi.org/10.1186/s41182-023-00552-6 #TrypanosomaCruzi #ChagasDisease #Transcriptome #Hl1 #InVitroModeling

Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways. https://doi.org/10.3390/pathogens12111373 #Covid19 #Calu3Cells #HostPathogenInteraction #RnaSeq #Transcriptome

Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways. https://doi.org/10.3390/pathogens12111373 #Covid19 #Calu3Cells #HostPathogenInteraction #RnaSeq #Transcriptome

A novel quantification method for #ribonucleotides, which are needed in almost all #cellular processes

#transcriptome

https://phys.org/news/2023-11-quantification-method-ribonucleotides-cellular.html

A novel quantification method for #ribonucleotides, which are needed in almost all #cellular processes

#transcriptome

https://phys.org/news/2023-11-quantification-method-ribonucleotides-cellular.html

19-SEP-2023
RNA for the first time recovered from an extinct species

https://www.eurekalert.org/news-releases/1001963 #science #extinction #TasmanianTiger #RNA #transcriptome

Loic Binan of the Broad:
All-optical genetic screens of intracellular and intercellular #transcriptional circuits with Perturb-FISH

Various CRISPR-based methods to look (multiplexed) at outcomes after knockdown to explore gene expression circuits, those are great, but want richer data (morphology etc)

one guide per cell (knock down one gene per cell) see #transcriptome via MERFISH, then identify the perturbed gene via in situ T7 transcription (same chemistry as MERFISH)

#CSSingleCells23

1/2

Loic Binan of the Broad:
All-optical genetic screens of intracellular and intercellular #transcriptional circuits with Perturb-FISH

Various CRISPR-based methods to look (multiplexed) at outcomes after knockdown to explore gene expression circuits, those are great, but want richer data (morphology etc)

one guide per cell (knock down one gene per cell) see #transcriptome via MERFISH, then identify the perturbed gene via in situ T7 transcription (same chemistry as MERFISH)

#CSSingleCells23

1/2

#Philippines research offers hope for conserving enigmatic Rafflesia #plants https://news.mongabay.com/2023/07/philippines-research-offers-hope-for-conserving-enigmatic-rafflesia-plants/

The seed #transcriptome of Rafflesia reveals #HorizontalGeneTransfer and convergent #evolution: Implications for conserving the world's largest flower: Jeanmaire Molina et al. https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.10370

"They found no genes pointing to a symbiotic relationship between #Rafflesia and #fungi, suggesting that unlike #orchids, Rafflesia may not need nutrients from fungi for successful germination."

#Philippines research offers hope for conserving enigmatic Rafflesia #plants https://news.mongabay.com/2023/07/philippines-research-offers-hope-for-conserving-enigmatic-rafflesia-plants/

The seed #transcriptome of Rafflesia reveals #HorizontalGeneTransfer and convergent #evolution: Implications for conserving the world's largest flower: Jeanmaire Molina et al. https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.10370

"They found no genes pointing to a symbiotic relationship between #Rafflesia and #fungi, suggesting that unlike #orchids, Rafflesia may not need nutrients from fungi for successful germination."

Genes reveal surprising overlaps in brain diseases and disorders

Scientists find patterns in how disease-related genes switch on in the brain.
The study authors say this way of sorting brain diseases and psychiatric disorders could potentially identify new targets for treatments.   

#Neuroscience #Brain #Neurology #NeurologicalDiseases #Psychiatry #PsychiatricDiseases #MentalDiseases #NeurodegenerativeDiseases #Neurodegeneration #BrainDiseases #NeurogeneticDiseases #Neurogenetics #Transcriptome #Transcriptomics #Genomics #MolecularBiology #Biomedicine

https://alleninstitute.org/news/genes-reveal-surprising-overlaps-in-brain-diseases-and-disorders/

Shamless plug warning! ⚠️

Our last paper on #transcriptional heterogeneity of #pediatric #cancer is out.
Did you think a quiet #genome translates into a quiet #transcriptome? Think again!

#multiscale #clustering on a pan-cancer #RNASeq cohort revealed new diagnostic subtypes and helped us train a #cnn model to identify tumour components in #clinical #oncology samples.

Read it here, it's #openaccess: https://www.nature.com/articles/s41591-023-02221-x

#precisionmedicine #transcriptomics
#machinelearning #ml

📢 Don't miss: Tuuli Lappalainen @tuuliel_lab (@nygenome @KTHuniversity @scilifelab) will speak at our #DahlemColloquium!

📜 Functional variation in the human #genome: lessons from the #transcriptome
📆 27. FEB, 11:00 AM (CET)
📍 @MPI_MolGen, #Berlin
🔗 https://www.molgen.mpg.de/events/33625/3967495

Interesting study in #ScientificReports that did #transcriptome profiling of surgically-removed calcified aortic valves from patients with/without #ClonalHematopoiesis. The authors found broad changes to immune cell infiltrates but also to #antibody profiles that correlated with survival. This last point is cool because CH's impact on #myeloid biology is often discussed, but it can obviously have important effects on #lymphoid cells, too: https://www.nature.com/articles/s41598-022-24130-8 #science #medicine #cardiology