Latest updates for Spatial Transcriptomics

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Recent items include:

  • Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular hetero
  • Ten quick tips for spatial transcriptomics analysis
  • Spatial mapping of RNA turnover kinetics in the mouse brain

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journals.plos.org /2 weeks ago

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular hetero...

by Dee Velazquez, Caleb Hallinan, Roujin An, Kalen Clifton, Jean Fan Imaging-based spatially resolved transcriptomics (imSRT) technologies provide high-throughput molecular-resolu...

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journals.plos.org /1 month ago

Ten quick tips for spatial transcriptomics analysis

by Nagomi Kurogi, Koki Shimbara, Tatsuya Koreeda, Koki Tsuyuzaki Spatial transcriptomics (ST) enables genome-wide gene expression profiling while retaining spatial context within...

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rna-seqblog.com /1 month ago

Spatial mapping of RNA turnover kinetics in the mouse brain

Spatial RNA sequencing maps RNA synthesis and degradation across the mouse brain, revealing how different regions rapidly adjust gene expression in response to stimulation...

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rna-seqblog.com /2 weeks ago

CellART extracts single-cell information from high-resolution spatial transcriptomics

RNA sequencing references combined with CellART help identify individual cells and cell types within high-resolution spatial transcriptomics data across multiple...

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journals.plos.org /1 month ago

OT-knn: A neighborhood-aware optimal transport framework for aligning spatial transcriptomics data

by Jia Song, Qunhua Li Spatial transcriptomics (ST) measures gene expression while preserving spatial context within tissues, enabling detailed characterization of tissue organiza...

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rna-seqblog.com /1 month ago

A real-data approach to evaluating RNA transcript analysis methods

RNA sequencing data provide a real-world framework for comparing differential transcript usage methods across bulk, single-cell, spatial, long-read, and short-read transcriptomics....

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rna-seqblog.com /3 weeks ago

ResolVI improves accuracy in spatial transcriptomics analysis

ResolVI improves spatial RNA sequencing analysis by correcting RNA assignment errors and technical variation, helping researchers distinguish cell states and detect subtle gene exp...

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genengnews.com /1 month ago

Spatial Transcriptomics Tools May Link Tumor Organization to Treatment Response

A new spatial transcriptomics framework compares tumor “floor plans." In a study of 262 solid tumors, the team identified recurring spatial groups that may connect spatial structur...

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journals.plos.org /1 month ago

Spatially guided translation from histology images to transcriptomic profiles using foundation model-driven contrastive...

by Zi Huai Huang, Ziyang Xu, Pingzhao Hu Spatial transcriptomics (ST) enhances single-cell RNA sequencing by revealing transcript distribution, offering critical insights into het...

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rna-seqblog.com /1 month ago

SPIDER improves spatial transcriptomics data using single-cell RNA sequencing

SPIDER uses single-cell RNA sequencing references to reduce noise in spatial transcriptomics, improving gene expression patterns, tissue structure identification...

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rna-seqblog.com /1 month ago

New method allows scientists to follow gene activity over time in the same cells

Live-cell RNA sequencing uses engineered virus-like particles to repeatedly sample transcriptomes without destroying cells, enabling researchers to track gene expression changes ov...

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rna-seqblog.com /1 month ago

RNA variant imaging for cancer diagnosis

RNA Variant Imaging is attracting attention because it addresses a persistent blind spot in cancer diagnostics: many clinically relevant RNA isoforms, splice events, and fusion tra...

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rna-seqblog.com /2 weeks ago

Cell2space restores spatial context to single-cell RNA sequencing data

RNA sequencing combined with Cell2space reconstructs spatial domains and cell neighborhoods, helping researchers recover tissue organization lost during single-cell sample preparat...

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rna-seqblog.com /3 weeks ago

scFlowReport brings multiple single-cell RNA sequencing analyses into one workflow

RNA sequencing analysis with scFlowReport integrates differential expression, pathway enrichment, regulatory networks and cell communication into a reproducible workflow for compar...

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rna-seqblog.com /1 month ago

ARCADIA combines RNA sequencing and spatial proteomics to reveal how tissue location shapes cell behavior

ARCADIA integrates single-cell RNA sequencing with spatial proteomics to reveal how tissue neighborhoods influence B-cell maturation, T-cell activation, and other transcriptional p...

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rna-seqblog.com /1 month ago

An end-to-end computational framework for “Record-seq” transcriptional recording data

A new framework adapts RNA sequencing analysis for Record-seq, improving spacer extraction, transcription-unit quantification, normalization, differential expression, and modeling...

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rna-seqblog.com /1 month ago

HeartBeat.bio and Cubase Bio Partner to Advance 3D Spatial Transcriptomics for Cardiovascular Drug Discovery

HeartBeat.bio and Cubase Bio are combining cardiac organoids with 3D spatial transcriptomics and RNA sequencing to study...

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rna-seqblog.com /1 month ago

New AI approaches to help understand complex biological data

RNA sequencing combined with new AI models helps researchers analyze cellular relationships and biological patterns across scales, improving interpretation of complex single-cell a...

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rna-seqblog.com /1 month ago

POND-seq enables non-destructive RNA sequencing in living cells

POND-seq enables non-destructive RNA sequencing of living cells, allowing repeated measurement of transcriptomes and RNA-binding protein interactions as cells respond to changing c...

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journals.plos.org /1 week ago

Sparse neuronal C4 elevation induces network-wide transcriptomic and lipid-droplet remodeling in the cortical microenvir...

by Marta Sánchez-Carbonell, Sonia Bolshakova, Juan E. Ávila-Pagán, Yaseer A. Sabir, Clay Griffin-Derr, Dominik G. Stich, Sofia V. Cieslewicz, Sheyla Esther Carmen Sifuentes, Rhushi...

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webwire.com /1 month ago

New method allows scientists to follow gene activity over time in the same cells

The following press release was issued by the Broad Institute of MIT and Harvard. - - In recent years, scientists have built methods to measure a cell's transcriptome, or all t...

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genengnews.com /2 weeks ago

The Epitranscriptome Heads Toward Clinical Necessity

Short-read RNA sequencing reporting the modifications that alter protein output is starting to make epitranscriptomics indispensable for patient selection in precision medicines. T...

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rna-seqblog.com /1 month ago

Single-cell and single-embryo RNA sequencing

Single-cell and single-embryo RNA sequencing enables detailed analysis of gene expression and cell identity during the earliest stages of embryonic development...

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rna-seqblog.com /2 weeks ago

GP-DHT uses single-cell RNA sequencing to map gene regulatory networks

Single-cell RNA sequencing combined with GP-DHT helps predict transcription factor and target gene relationships, providing a...

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