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).

• Single-Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression.

  PMID 34825784 · PMC8787427 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022 · 8 claims · 6 setups

  Has reproduction · 59

  Human NP contains six transcriptionally distinct NPC subpopulations: HT-CLNPs, effector NPCs, homeostatic NPCs, regulatory NPCs, fibroNPCs, and adhesion NPCs

  npcs scrna-seq-derived ht-clnp-i g-mdscs single-cell rt-qpcr immunohistochemistry

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.

  hcc tcga geo single-cell bulk microarray

• 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

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  Liver metastatic potential in RCC is marked by stem-like tumor states, metabolic plasticity, and microenvironmental remodeling.

  right-sided single integrated malignant single-cell copy dimensionality

• Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.

  PMID 37339216 · PMC10293804 · Proceedings of the National Academy of Sciences of the United States of America · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Subretinally transplanted stem cell-derived RPE (ESC- and iPSC-derived) retain RPE identity and survive in vivo for at least 30 days in immunocompetent rabbit eyes

  hpsc-derived day esc dutch qrt-pcr immunofluorescence transepithelial

• Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

  PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  Retrovirus-derived LTR8B acts as a trophoblast-specific cis-regulatory element within the PSG array, with LTR8B at PSG9 influencing other PSG family members as a master regulator

  sghpl-4 trophoblast placenta bewo chip-exonuclease crispr-cas9 chromatin

• Intergenic risk variant rs56258221 skews the fate of naive CD4(+) T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis.

  PMID 38901430 · PMC11293351 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 58

  rs56258221 (BACH2/MIR4464) associates with a distinct peripheral blood T cell immunophenotype in people with PSC

  peripheral liver facs-sorted cd4+ flow bulk cite-seq

• Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs.

  PMID 41932885 · PMC13219436 · Nature communications · 2026 · 8 claims · 8 setups

  Has reproduction · 91

  A fraction (15-50%) of the distal SOX9+ tip progenitor subdomain is sufficient to direct lung outgrowth through branch bifurcation, providing a mechanism for lung size control

  lung whole-mount immunofluorescence single-cell

• CHD7 regulates otic lineage specification and hair cell differentiation in human inner ear organoids.

  PMID 36396635 · PMC9672366 · Nature communications · 2022 · 8 claims · 7 setups

  Has reproduction · 50

  Loss of CHD7 or its chromatin remodeling (ATPase) activity causes complete absence of hair cells and supporting cells in inner ear organoids.

  pax2ng inner facs-isolated pax2ng+ western immunostaining scrna-seq

• Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq.

  PMID 33441952 · PMC7806779 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 47

  CDK12, ERBB2, and CLDN11 are overexpressed in metastatic lymph node gastric cancer and serve as candidate lymph node metastasis marker genes.

  tumour gastric qc-passed single-cell immunofluorescence immunohistochemistry

• Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.

  PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 78

  A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors

  hcc-associated hcc malignant cd8+ single-cell bulk metabolomics

• Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

  PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  CD39+CD8+ TILs are a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells within ccRCC tumors

  ccrcc tumor-reactive cd39 caix-specific single-cell bulk co-culture

• Enteroendocrine cell lineages that differentially control feeding and gut motility.

  PMID 36810133 · PMC10032656 · eLife · 2023 · 6 claims · 8 setups

  Has reproduction · 88

  Vil1-p2a-FlpO knock-in mice combined with lineage-specific Cre lines enable highly selective intersectional genetic access to major enteroendocrine cell lineages (serotonin/enterochromaffin, GLP1, CCK, somatostatin, GIP) in vivo

  neurod1-cre neurog3-cre intestinal vil1-p2a-flpo single-cell fluorescence-activated two-color

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 7 claims · 8 setups

  Has reproduction · 49

  LRP1 is the top hub gene with the highest diagnostic performance for distinguishing ectopic from eutopic endometrium in EMS

  ectopic geo training gwas microarray wgcna machine

• Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

  PMID 36253367 · PMC9576764 · Nature communications · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  The P. magna mitoribosome contains rRNA split into 13 fragments (LSU1-8, SSU1-4, mt-5S)

  mitoribosome polytomella cross-species single-particle novo comparative

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• Under the Shadow: Old-biased Genes Are Subject to Weak Purifying Selection at Both the Tissue- and Cell Type-Specific Levels.

  PMID 41092135 · PMC12569596 · Genome biology and evolution · 2025 · 8 claims · 6 setups

  Has reproduction · 93

  Age-related decrease in transcriptome conservation (ADICT) is commonly found in ageing tissues of nonmammalian species (chicken brain, killifish liver and skin, fruit fly brain).

  gallus nothobranchius drosophila heterocephalus bulk single-cell

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

  peripheral leukocytes plasma degs bulk single-cell plasma

• Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.

  PMID 41053409 · PMC12500777 · Cancer metastasis reviews · 2025 · 7 claims · 8 setups

  Has reproduction

  A 12-step CTC-specific scRNA-seq workflow spanning enrichment, single-cell sorting, sequencing, data pre-processing and downstream analysis is proposed to overcome methodological inconsistencies.

  breast ctcs nsclc neuroblastoma scrna-seq

• Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.

  PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  Reanalysis of scRNA-Seq identified 279 iMSC signature genes upregulated in BM MSCs of MM patients vs healthy donors, covering 82% of the top 50 previously defined iMSC genes

  facs-isolated mscs expanded single-cell bulk meta-analysis