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).

• Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

  PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another

  scrna-seq tcga-gbm gse131928 tumor gene pairwise principal

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• 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

• Interpretable and integrative analysis of single-cell multiomics with scMKL.

  PMID 40770488 · PMC12328712 · Communications biology · 2025 · 7 claims · 7 setups

  Has reproduction · 65

  scMKL outperforms SVM, EasyMKL, MLP, and XGBoost in classification accuracy (AUROC) across multiple single-cell cancer datasets

  mcf-7 t-47d small prostate 10x scrna-seq sciatac-seq

• Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model.

  PMID 36321803 · PMC9708074 · eLife · 2022 · 7 claims · 5 setups

  Has reproduction · 72

  Follicle cell-specific Lgl knockdown (Lgl-KD) causes loss of apical-basal polarity and invasive multilayering of the follicular epithelium without long-distance metastasis

  drosophila single-cell bulk immunofluorescence

• 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

• A cell atlas of the adult female Aedes aegypti midgut revealed by single-cell RNA sequencing.

  PMID 38839790 · PMC11153528 · Scientific data · 2024 · 8 claims · 4 setups

  Has reproduction · 95

  Established a protocol for isolating single cells from Ae. aegypti midgut and performing scRNA-seq (dissociation, density-gradient purification, viability QC, 10x Genomics library prep and sequencing).

  dissociated scrna-seq merged single-cell viability computational

• 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

• Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology.

  PMID 39941893 · PMC11817449 · Cancers · 2025 · 8 claims · 7 setups

  Has reproduction · 50

  A standardized, reproducible protocol can establish meningioma organoids (MEN-Os) from patient-resected tumor tissue without mechanical/enzymatic dissociation, using serum-free medium lacking growth factors or exogenous ECM.

  patient-resected men-os parent oct-embedded organoid brightfield h&e