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).

• Partially shared multi-modal embedding learns holistic representation of cell state.

  PMID 41741805 · PMC13021527 · Nature computational science · 2026 · 8 claims · 5 setups

  Full-text index only

  APOLLO automatically learns partial information sharing between multiple data modalities using an autoencoder with a partially overlapping latent space trained via latent optimization.

  simulated paired single simulation scrna-seq multiplexed

• SOX2 phosphorylation during mitosis limits genomic damage.

  PMID 41213799 · PMC12863253 · Genes & development · 2026 · 8 claims · 8 setups

  Full-text index only

  SOX2 (but not SOX9) remains dynamically bound to mitotic chromatin throughout all mitotic stages in neural stem cells

  sox2-halo nscs flag-wt-sox2 live-cell immunocytochemistry frap

• Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution.

  PMID 36696508 · PMC9876548 · Science advances · 2023 · 7 claims · 8 setups

  Has reproduction · 50

  Chromatin accessibility continually decreases from mitotic entry until metaphase, then gradually increases as chromosomes segregate.

  l02 tissues hepatoma scatac-seq immunofluorescence atac-see

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

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

  Full-text index only

  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

• Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution.

  PMID 41513700 · PMC12891662 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Cytomix (TNFɑ+IFNɣ+IL1β) treatment of human colon organoids best recapitulates molecular features of human IBD compared to DSS or irradiation injury models.

  colon cytomix-treated scrna-seq immunofluorescence activated

• Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

  PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features

  breast same gene identified bulk high-content regulon

• A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.

  PMID 41518352 · PMC12790319 · European journal of immunology · 2026 · 8 claims · 5 setups

  Full-text index only

  Imaging-based spatial transcriptomics (CosMx SMI) captures tissue complexity and cellular composition more faithfully than scRNA-seq

  palatine same tonsil cosmx imaging-based immunofluorescence scrna-seq

• De novo H3.3K27M-altered diffuse midline glioma in human brainstem organoids to dissect GD2 CAR T cell function.

  PMID 41492091 · PMC12948678 · Nature cancer · 2026 · 8 claims · 8 setups

  Full-text index only

  FGF4 supplementation during organoid patterning specifically induces pontine/rostral hindbrain brainstem identity

  hes brainstem day developing bulk immunofluorescence scrna-seq

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

  hymenophyllum caudiculatum annotated rna-seq chlorophyll relative

• Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

  PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

  mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq

• Development of double-positive thymocytes at single-cell resolution.

  PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups

  Has reproduction · 86

  DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d

  thymocytes sorted thymocyte scrna-seq flow immunofluorescence

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.

  PMID 34282405 · PMC8285288 · Frontiers in cellular and infection microbiology · 2021 · 8 claims · 7 setups

  Full-text index only

  iPSC-derived pancreatic endocrine and exocrine (acinar/ductal) cultures express ACE2 and TMPRSS2, enabling SARS-CoV-2 entry

  ipsc-derived post-mortem vero-e6 immunofluorescence sars-cov-2 rt-qpcr

• Oxidative stress and GPX2 control pancreatic vs. non-pancreatic cell fate in human endoderm.

  PMID 41484137 · PMC12881361 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  GPX2 is a critical regulator of human posterior foregut differentiation, with oxidative stress acting as a key determinant of pancreatic vs. non-pancreatic cell fate

  hpsc-derived hpsc fetal bulk immunofluorescence flow

• Spatial cartography of human thymus enables the geopositioning of lineage transcription factors in rare mimetic thymic epithelial cells.

  PMID 41807357 · PMC13102919 · Nature communications · 2026 · 7 claims · 7 setups

  Full-text index only

  Generated a high-resolution spatial transcriptomic atlas of human fetal (13,14,17,18w) and paediatric (7w,2y,5y,6y) thymi using Stereo-seq, integrated with scRNA-seq and MACSima/Stereo-CITE proteomics

  fetal paediatric thymus stereo-seq scrna-seq macsima

• Spatiotemporal dynamics of ecto-5'-nucleotidase (CD73) in mouse retina under physiological conditions.

  PMID 41560519 · PMC12912271 · Development (Cambridge, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  CD73 expression in the neural retina is restricted to the rod-photoreceptor lineage and becomes robustly detectable from postnatal day (P) 3 onward, persisting into adulthood.

  cd73-bac-egfp cd73-creert2 scrna-seq cd73-knockout immunofluorescence genetic whole-mount

• Lamin C is required to establish genome organization after mitosis.

  PMID 34775987 · PMC8591896 · Genome biology · 2021 · 8 claims · 6 setups

  Has reproduction · 76

  Lamin C, not lamin A, is required for 3D organization of LADs and overall chromosome territory organization

  embryonic mefs mef damid-seq 3d-immunofish western

• Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.

  PMID 34089405 · PMC8179884 · Rice (New York, N.Y.) · 2021 · 8 claims · 7 setups

  Has reproduction · 43

  N22 performed better than IR64 under dual (low N + low water) stress overall, owing to better root architecture, chlorophyll/porphyrin synthesis and oxidative stress management

  root shoot leaf rice bulk root chlorophyll

• Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.

  PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 7 claims · 6 setups

  Has reproduction · 65

  UC patient-derived organoids histologically phenocopy primary UC tissue, showing disorganized stratified epithelium, reduced mucin/goblet cells, and non-uniform proliferation compared to non-IBD organoids

  patient-derived h3k27ac rna-seq chip-seq histology

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 7 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm via an evolutionarily conserved intronic enhancer

  e9.5 xenopus bulk rt-qpcr whole-mount