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).

• Integrated multi-omic atlas reveals the hierarchy of spatiotemporal regulatory networks of mouse gastrulation.

  PMID 41526381 · PMC12902073 · Nature communications · 2026 · 8 claims · 8 setups

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  BioCRE, a novel bi-orientation regression algorithm, more accurately links genes to candidate cis-regulatory elements (CREs) than existing tools Signac and ArchR

  gastrulating gastrula gold-standard embryo single-cell computational promoter

• 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

• scGeno: a Hidden Markov Model approach to denoise chromosome-scale genotypes from single-cell data.

  PMID 41982479 · PMC13075984 · Bioinformatics advances · 2026 · 7 claims · 4 setups

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  scGeno, a categorical HMM, infers chromosome-level genotype states in mixed-genotype organisms by modeling sequential single-cell allelic expression ratios along chromosomes

  wild-type dnmt1 synthetic embryo single-cell posterior down-sampling

• Cis-regulatory evolution shapes facial diversity in birds and mammals.

  PMID 42090501 · PMC13148318 · Science advances · 2026 · 8 claims · 6 setups

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  Mesenchymal populations show markedly greater transcriptomic/regulatory divergence between mouse and chicken than ectodermal populations, pointing to a central role of mesenchyme in shaping facial morphology

  embryo chicken embryos single-cell situ cross-species

• Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.

  PMID 33833454 · PMC7610777 · Nature genetics · 2021 · 8 claims · 8 setups

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  In human embryos, intra-adrenal sympathoblasts are directly derived from nerve-associated Schwann cell precursors (SCPs), similarly to chromaffin cells

  embryo sympathoadrenal embryonic adrenal scrna-seq velocity immunohistochemistry

• scSNViz: visualization and analysis of cell-specific expressed SNVs.

  PMID 41533688 · PMC12866635 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 7 setups

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  scSNViz is an R package for exploration, quantification, and visualization of expressed SNVs from cell-barcoded scRNA-seq data, supporting VAF estimation, SNV clustering, and 2D/3D visualization.

  prostate non-small cholangiocarcinoma neuroblastoma scrna-seq cell-level single-cell

• Stage- and cluster-specific regulation of chondrogenic gene programs by Sox9 in mouse embryonic limb buds.

  PMID 41809054 · PMC12969044 · iScience · 2026 · 8 claims · 7 setups

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  scRNA-seq across five limb bud stages identifies four Sox9-high populations (chondroprogenitors 1, 2, 3, and mature chondrocytes) with distinct temporal dynamics

  forelimb scrna-seq cut&run embryo single-cell cut&run velocity

• Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.

  PMID 41860983 · PMC13021174 · PLoS computational biology · 2026 · 8 claims · 8 setups

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  VeloVAE significantly outperforms previous RNA velocity methods in data fit, accuracy of inferred differentiation directions, and transcription rate estimation.

  pancreas developing induced embryo scrna-seq

• scDEBGCL: a deep embedding approach based on bipartite graph contrastive learning for single-cell RNA-seq data.

  PMID 41981652 · PMC13188691 · BMC biology · 2026 · 7 claims · 3 setups

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  scDEBGCL is a deep embedding method for scRNA-seq data based on bipartite graph contrastive learning, integrating contrastive learning, graph reconstruction, and ZINB-based data reconstruction losses.

  nine yan dpt scrna-seq trajectory

• Rtf1-dependent transcriptional pausing regulates cardiogenesis.

  PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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  Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

  zebrafish embryo embryonic mescs crispr situ shrna

• 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

• Cell fixation and preservation for droplet-based single-cell transcriptomics.

  PMID 28526029 · PMC5438562 · BMC biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  Methanol fixation stabilizes and preserves dissociated cells for weeks without compromising single-cell RNA-seq data quality

  hek293 dissociated facs-sorted hek drop-seq bulk trizol

• VISTA uncovers missing gene expression and spatial-induced information for spatial transcriptomic data analysis.

  PMID 41507434 · PMC12891734 · Communications biology · 2026 · 8 claims · 6 setups

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  VISTA predicts unmeasured gene expression in subcellular spatial transcriptomic data by integrating scRNA-seq and SST through variational inference and geometric deep learning with built-in uncertainty quantification

  brain breast embryo muscle imaging-based sequencing spot-based

• Dynamic regulation of spermatogenesis and hybrid sterility revealed by single-cell analysis in yak and cattle.

  PMID 41622528 · PMC12916010 · Molecular biology and evolution · 2026 · 7 claims · 8 setups

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  Cattle and yak testes contain seven types of spermatogonia, ten spermatocyte subtypes, and ten spermatid types with largely conserved transcriptional programs governing spermatogenic fate transitions.

  testicular spermatocytes spermatids bc1 single-cell chromosome hematoxylin

• Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.

  PMID 41952215 · PMC13174004 · Genome biology · 2026 · 8 claims · 5 setups

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  No prior systematic, quantitative benchmark exists for CCI inference methods specifically developed for spatial transcriptomics across multiple platforms

  synthetic real simulated simulation spot-purity real-data

• Stage-specific epigenetic priming amplifies gene activation during lineage commitment.

  PMID 41894493 · PMC13025117 · Science advances · 2026 · 8 claims · 8 setups

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  Full-body Msl1 knockout causes embryonic lethality by E10.5, with morphological/developmental delay detectable already at E8.5

  embryos e9.5 mesc-derived bright-field western 10x

• miR-203 facilitates timely cell fate transitions via epigenetic modulation during early embryogenesis.

  PMID 41811946 · PMC12978216 · Science advances · 2026 · 8 claims · 8 setups

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  miR-203 is required for a timely totipotency-to-pluripotency transition during early mouse embryogenesis

  preimplantation 8-cell mice mir-203 qrt-pcr genotyping time-lapse

• Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources.

  PMID 42045691 · PMC13175893 · Nature genetics · 2026 · 6 claims · 7 setups

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  INSPIRE is a deep-learning method that unifies adversarial learning with a GNN-based encoder and integrated NMF to interpretably integrate multiple spatial transcriptomics datasets

  synthetic dorsolateral brain cortex simulated visium spatial