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 transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution.

  PMID 41388990 · PMC12776951 · The Plant cell · 2026 · 8 claims · 6 setups

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  MERFISH was successfully optimized for wheat inflorescence tissue, enabling localization of a 200-gene panel to cellular resolution across 4 developmental stages

  microdissected cryosectioned wheat merfish-imaged bulk merfish single-nucleus

• Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

  PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups

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  Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups

  tcga-brca breast scrna-seq epithelial ssgsea single-cell cell-cell

• Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

  PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups

  Has reproduction · 100

  Exploratory adaptation (stochastic gene-regulatory network perturbation) explains how GBM cells adapt phenotypically across spatially distinct tumor regions

  patient-derived low-grade tf-gene single-sample bulk differential gene

• Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.

  PMID 41736854 · PMC12927100 · iScience · 2026 · 7 claims · 6 setups

  Has reproduction · 70

  Early-stage (prodromal) aSyn pathology in M83+/+ mouse brainstem is associated with upregulation of ATP/energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)

  sagittal st-derived spatial immunofluorescence cell-cell

• Spatial single-cell multiomics reveals peripheral immune dysfunction in Parkinson's and inflammatory bowel disease.

  PMID 41545356 · PMC12847817 · NPJ Parkinson's disease · 2026 · 8 claims · 5 setups

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  Spatial single-cell multiomic imaging of sigmoid colon reveals both shared and unique features of peripheral immune dysfunction in PD and IBD

  sigmoid plasma stool epithelial cosmx meso gene

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals.

  PMID 40922549 · PMC12419799 · eLife · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  829 genes are overexpressed in regions of increased calcite spicule formation in S. ciliatum, including known sclerocyte-specific biomineralization genes.

  sycon ciliatum cnidarian sponges differential go-term blastp

• Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.

  PMID 41860215 · PMC13101498 · Applied and environmental microbiology · 2026 · 7 claims · 6 setups

  Has reproduction · 81

  Offshore Lake Michigan bacterioplankton show higher expression of DOM, N, and P acquisition/transporter genes than nearshore bacterioplankton

  bacterioplankton lake metatranscriptomics metagenomic nutrient

• Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

  PMID 41674979 · PMC12885896 · Translational cancer research · 2026 · 8 claims · 8 setups

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  A FAM-related gene prognostic model (FAMGM) built using CoxBoost and random survival forest was identified as the optimal model among 101 machine learning combinations, based on highest average C-index across TCGA-BRCA and GSE96058 cohorts

  tcga-brca gse96058 brca breast bulk single-cell spatial

• AJUBA: The Master Regulator Bridging EMT and Immune Evasion in Colorectal Cancer.

  PMID 41814682 · PMC13140425 · Mediators of inflammation · 2026 · 8 claims · 8 setups

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  AJUBA is markedly upregulated in CRC across multiple transcriptomic cohorts and is enriched in epithelial cells with activated EMT features

  tcga-crc crc paired hct116 bulk single-cell spatial

• Genotype differences in cognitive functioning in Noonan syndrome.

  PMID 19077116 · PMC2760992 · Genes, brain, and behavior · 2009 · 8 claims · 6 setups

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  Genotype differences account for some of the variation in cognitive ability in Noonan syndrome

  individuals participants parents standardized genetic pure-tone

• Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

  PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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  Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

  matched excised additional formalin-fixed 2-d lc-ms quantitative

• Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

  PMID 41771574 · PMC12951371 · Cancer genomics & proteomics · 2026 · 7 claims · 8 setups

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  Malignant cells from HCC tumors resolve into six transcriptionally distinct subpopulations, including a progenitor-like CSC subset expressing EPCAM, SOX9, and SOX4

  malignant tumor csc six single-cell spatial copy

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Intestinal macrophages modulate synucleinopathy along the gut-brain axis.

  PMID 41606336 · PMC12960212 · Nature · 2026 · 8 claims · 8 setups

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  ME-Macs engulf misfolded, aggregated αS and modulate αS pathology and neurodegeneration in PD mouse models

  3kl sorted me-macs snca immunohistochemistry digital mass

• Major transitions in early coral development: novel insights enabled by visualisation of a comprehensive transcriptomic dataset for Acropora millepora.

  PMID 41612263 · PMC12924552 · BMC biology · 2026 · 8 claims · 6 setups

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  Profiling gene expression across 26 life stages of A. millepora and building an interactive Shiny-based tool (DEView) enables comprehensive visualisation of developmental transcriptomic data.

  acropora millepora bulk differential pca

• Deciphering immune and cellular reprogramming during the progression from inflammatory bowel disease to colorectal cancer using multi-omics single-cell and spatial transcriptomics.

  PMID 42001187 · PMC13122952 · Journal of translational medicine · 2026 · 8 claims · 5 setups

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  CEACAM5 is consistently upregulated across Crohn's disease and ulcerative colitis samples and links epithelial activation in IBD to tumorigenic processes in CRC

  intestinal colorectal single-cell serum bulk single-cell spatial

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.

  PMID 41484656 · PMC12857045 · Genome biology · 2026 · 8 claims · 8 setups

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  pRIC-seq, an adaptation of RIC-seq for plants, enables genome-wide mapping of RNA-RNA spatial interactions in diploid and tetraploid cotton

  diploid tetraploid cotton nicotiana pric-seq gro-cap chip-seq

• 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