Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Spatial organization shapes the turnover of a bacterial transcriptome.

  PMID 27198188 · PMC4874777 · eLife · 2016 · 8 claims · 5 setups

  Has reproduction · 71

  The E. coli transcriptome is spatially organized: mRNAs encoding inner-membrane proteins are enriched at the membrane, while mRNAs encoding cytoplasmic, periplasmic, and outer-membrane proteins are distributed throughout the cytoplasm.

  coli single-molecule fish time-resolved

• S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning.

  PMID 41556263 · PMC13042551 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  S3RL is a separable representation learning framework that denoises sparse spatial transcriptomic data and enhances biologically relevant signals by integrating gene expression, spatial coordinates, and histological image features.

  dorsolateral dlpfc nanostring spatial cell-type multi-platform

• SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data.

  PMID 42015285 · PMC13231777 · Genome biology · 2026 · 8 claims · 6 setups

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  SpaNiche integrates smoothed cell-type abundance and ligand-receptor expression matrices via graph-regularized joint NMF, across multiple spatial views, to identify colocalization patterns

  lymph colorectal prostate cerebral simulated spatial scrna-seq

• Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

  PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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  scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

  skin combined annotated scrna-seq single-cell spatial cell2location

• Single-cell and spatial transcriptomics define 20E-driven developmental reprogramming in silkworm wing disc.

  PMID 41730863 · PMC13039787 · Nature communications · 2026 · 8 claims · 7 setups

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  Wing morphogenesis (Wm) cells act as central progenitors/differentiation hub, giving rise to epithelial and cuticle lineages under lineage-specific transcription factors

  mori spodoptera scrna-seq stereo-seq snrna-seq

• Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer.

  PMID 41907400 · PMC13018967 · iScience · 2026 · 8 claims · 8 setups

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  Colorectal cancer fibroblast heterogeneity can be distilled into two overarching, transcriptomically distinct CAF populations marked by PDGFRA+ and ACTA2+ expression

  crc colonic gemm scrna-seq multiplex bulk

• Direct inference of SNP heterozygosity rates and resolution of LOH detection.

  PMID 18052545 · PMC2098867 · PLoS computational biology · 2007 · 6 claims · 7 setups

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  A large proportion of SNPs in dbSNP have high-variance HET rate estimates, limiting their reliability for LOH study design.

  dbsnp theoretical simulated hapmap snp probability sequential

• Reconstructing single-cell resolution from spatial transcriptomics with CellRefiner.

  PMID 41760664 · PMC13066420 · Nature communications · 2026 · 8 claims · 8 setups

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  CellRefiner is a physical/particle-based model (subcellular element method) that integrates scRNA-seq and spatial transcriptomics data to reconstruct single-cell resolution spatial data

  hypothalamic embryo hippocampus visual merfish seqfish slide-seqv2

• Dissecting the immunosuppressive microenvironment of LAMA3 + malignant cells and SPP1 + macrophages in esophageal squamous cell carcinoma using single-cell and spatial transcriptomics.

  PMID 41845425 · PMC13104401 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  A LAMA3+ epithelial subpopulation (C3) enriched at the invasive tumor front shows strong EMT signatures and is associated with poor prognosis

  escc epithelial scrna-seq tcga-escc scrna-seq spatial infercnv

• ISG15-driven immune modulation and tumor progression in breast cancer metastasis: insights from single-cell and spatial transcriptomics.

  PMID 41639695 · PMC12958617 · BMC medicine · 2026 · 8 claims · 8 setups

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  CSC proportion is elevated in lymph node metastatic tumor tissue (BRCA_LNMT) compared to primary tumor (BRCA_PT)

  4t1 brca tcga-brca top single-cell spatial bulk

• TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery.

  PMID 41689080 · PMC12910759 · Genome medicine · 2026 · 7 claims · 4 setups

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  TiRank is a framework that integrates scRNA-seq, ST, and bulk transcriptomes using an REO-transformation module and multitask transfer learning to align data into a unified embedding space for prioritizing clinically relevant spatial niches

  benchmark pan-cancer gastric independent scrna-seq bulk spatial

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

  Has reproduction · 85

  High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

  breast er+ epithelial malignant scrna-seq spatial copy

• Spatiotemporal Transcriptomics Characterizes Immune Microenvironment During Mouse Liver Aging.

  PMID 42010880 · PMC13096584 · Aging cell · 2026 · 8 claims · 8 setups

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  T cells are the immune cell population with the most pronounced transcriptomic alterations during liver aging

  liver nash cirrhotic hcc scrna-seq snrna-seq stereo-seq

• Lipids join the post-genomic era.

  PMID 17076911 · PMC1794566 · Genome biology · 2006 · 8 claims · 8 setups

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  Infrared-laser MALDI-MS can image biological tissue while avoiding the matrix-preparation artifacts of UV-laser MALDI

  biological intact mixtures yeast maldi esi faims

• A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.

  PMID 34140473 · PMC8211662 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 90

  The human post-implantation epiblast transitions from a naïve to a primed pluripotent state, with naïve markers (KLF4, KLF17, PRDM14, etc.) downregulated and primed markers (FGF2, DNMT3B, SOX11, etc.) upregulated between pre- and post-implantation stages

  embryo embryos single-cell logistic immunofluorescence

• Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

  PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

  Has reproduction · 50

  Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

  hnscc tcga-hnscc caf fibroblast single-cell bulk spatial

• CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

  PMID 41686262 · PMC13136879 · Cancer immunology research · 2026 · 8 claims · 8 setups

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  CLK1 is markedly upregulated in immune-cold colorectal tumors and correlates with increased MDSC infiltration and CD8+ T-cell exclusion

  colorectal tcga-coad ct26 tumor scrna-seq bulk multiplex

• NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development.

  PMID 41882195 · PMC13061640 · Nature neuroscience · 2026 · 8 claims · 8 setups

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  NeMO Analytics is a curated compendium assembling gene-level transcriptomic (and other multiomic) data from ~200 studies of neocortical development and in vitro models for interrogation by non-coding biologists

  midgestational macaque fetal radial scrna-seq bulk spatial

• Temporal trends in methane emissions from a small eutrophic reservoir: the key role of a spring burst.

  PMID 35126532 · PMC8815417 · Biogeosciences (Online) · 2021 · 8 claims · 7 setups

  Has reproduction · 72

  Acton Lake had cumulative areal CH4 emission rates of 45.6 ± 8.3 g CH4 m-2 in 2017 and 51.4 ± 4.3 g CH4 m-2 in 2018 (109 ± 14 and 123 ± 10 Mg CH4 whole-reservoir, respectively)

  whole-reservoir sediment-water water reservoir eddy active floating

• Hereditary chronic pancreatitis induced plasticity cooperates with mutant Kras in early pancreatic carcinogenesis.

  PMID 41419303 · PMC13151493 · Gut · 2026 · 8 claims · 8 setups

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  KC-Cpa1 mice show markedly increased pancreatic remodelling, fibrosis and metaplastic/PanIN lesion formation compared with KC mice

  pancreas cre acinar scrna-seq histology bulk single-cell