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).

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.

  grch38 homogeneous per single single-cell clustering cell-type

• A single-cell survey of Drosophila blood.

  PMID 32396065 · PMC7237219 · eLife · 2020 · 8 claims · 6 setups

  Has reproduction · 94

  scRNA-seq of Drosophila larval hemocytes across unwounded, wounded, and wasp-infested conditions resolves 17 clusters spanning plasmatocytes, crystal cells, lamellocytes, and a non-hemocyte population.

  drosophila single-cell quantitative bulk

• FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

  PMID 34909283 · PMC8641482 · PeerJ · 2021 · 7 claims · 5 setups

  Has reproduction · 75

  The FEM algorithm converts each cell's gene expression matrix (GEM) into a functional expression matrix by applying Fisher's exact test enrichment per cell and per gene set, then encoding adjusted p-values as information content.

  peripheral pancreas liver pbmc scrna-seq differential dimensionality

• The liver as an immunological barrier redefined by single-cell analysis.

  PMID 32176810 · PMC7218664 · Immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 100

  Single-cell RNA-seq enables unbiased characterization of liver cell states, developmental trajectories and rare immune populations that bulk averaging obscures, redefining liver cell-type mapping.

  c57bl liver whole-liver hepatocytes scrna-seq facs-based plate-based

• Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.

  PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 6 claims · 7 setups

  Has reproduction · 50

  A computational method using high-quality scRNA-seq reference data can estimate per-sample, per-cell-type off-target contamination coefficients in sctRNA-seq datasets.

  brain cortex allen lcm-seq lcm-seq scrna-seq marker

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks.

  PMID 33138772 · PMC7607865 · BMC genomics · 2020 · 8 claims · 6 setups

  Has reproduction · 83

  scPPIN integrates scRNA-seq-derived p-values with PPINs to detect maximum-weight connected subgraphs (active/functional modules) via an exact Steiner-tree approach

  liver hepatocyte detected adipose single-cell differential protein-protein

• Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

  PMID 41647537 · PMC12869734 · Fundamental research · 2026 · 6 claims · 3 setups

  Has reproduction · 68

  scCluster, an end-to-end deep clustering model integrating gene expression and expressed variant (eSNP) features, stratifies cell subpopulations in cancer scRNA-seq data.

  raw real-world expressed gene deep

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups

  Has reproduction · 67

  A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.

  mammary five singlecellexperiment individual droplet-based quality doublet

• To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

  PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

  Has reproduction · 33

  C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

  coronary scrna-seq five type single-cell doublet copy

• 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

• WASP: a versatile, web-accessible single cell RNA-Seq processing platform.

  PMID 33736596 · PMC7977290 · BMC genomics · 2021 · 7 claims · 7 setups

  Has reproduction · 59

  WASP is a software platform for processing Drop-Seq-based scRNA-seq data generated with ddSEQ or 10x protocols, combining a Snakemake pre-processing pipeline with an R Shiny post-processing application.

  specified generic scrna-seq read reference

• 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

• Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation.

  PMID 35494238 · PMC9046238 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 60

  A customized bootstrapping/random-forest divide-and-conquer clustering pipeline integrating three scRNA-seq datasets robustly resolves cell states despite high cell-to-cell similarity within compartments

  bone endothelial independent integrated single-cell scrna-seq gene

• An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

  PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

  oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor

• 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

• Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.

  PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.

  luad tcga cd8+ degs single-cell cibersort survival

• Single-cell multiomics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response.

  PMID 39503729 · PMC11540304 · eLife · 2024 · 8 claims · 5 setups

  Has reproduction · 75

  CITE-seq multiomics reveals that each CML patient harbors a unique composition of stem and progenitor cells at diagnosis

  lin-cd34+ cml cite-seq facs differential

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.

  surgically mammary menopaused integrated single-cell scrna-seq mammary

• FAM3C/ILEI protein is elevated in psoriatic lesions and triggers psoriasiform hyperproliferation in mice.

  PMID 37226685 · PMC10331587 · EMBO molecular medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 83

  ILEI protein, but not mRNA, is elevated in psoriatic skin and correlates with disease severity

  skin full-thickness normal k5-ileiind immunohistochemistry scrna-seq bulk