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).

• Toward a Consensus in the Repertoire of Hemocytes Identified in Drosophila.

  PMID 33748138 · PMC7969988 · Frontiers in cell and developmental biology · 2021 · 8 claims · 8 setups

  Has reproduction · 74

  Comparative analysis of three scRNAseq studies identifies eight common, robust hemocyte subgroups associated with distinct functions (proliferation, immune response, phagocytosis, secretion)

  wandering feeding stage type single scenic immunolabeling

• 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

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

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.

  mammary aggregated single-cell quality doublet

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

  PMID 34909283 · PMC8641482 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 75

  The FEM algorithm converts a single-cell gene expression matrix into a functional expression matrix using multi-module gene set enrichment analysis, utilizing information from all expressed genes rather than discarding filtered genes.

  pbmc pancreas liver scrna-seq single-cell fisher's dimensionality

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

  Full-text index only

  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental

• Immunoregulatory Roles of Tumor-Originated Pericytes Identified by Single-Cell Analysis in Glioblastoma.

  PMID 41001759 · PMC12713092 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025 · 8 claims · 8 setups

  Has reproduction

  CD146 (MCAM) is a superior surface marker for sorting GBM pericytes, labeling nearly all PDGFRβ+ pericytes with strong specificity, unlike NG2 which labels fewer vessel-associated pericytes.

  facs-sorted frozen dissociated scrna-seq scrna-seq immunofluorescence fluorescence-activated

• transFusion: a novel comprehensive platform for integration analysis of single-cell and spatial transcriptomics.

  PMID 41645434 · PMC12930851 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  transFusion is a comprehensive, web-based platform for integrated analysis of scRNA-seq and 10x Visium spatial transcriptomics data requiring no parameter configuration

  breast scrna-seq 10x cellphonedb

• Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.

  PMID 41229397 · PMC12604667 · NAR genomics and bioinformatics · 2025 · 8 claims · 4 setups

  Has reproduction · 75

  scIGD is a Snakemake workflow that automates HLA allele-typing and allele-specific expression quantification from scRNA-seq data

  aida merkel-cell 20k myeloma scrna-seq

• Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

  PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq

  liver-derived muscle heart pooled 10x oxford hi-c

• 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

  Full-text index only

  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

• A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations.

  PMID 41792601 · PMC13077969 · BMC genomics · 2026 · 6 claims · 8 setups

  Full-text index only

  A new haplotype-resolved, chromosome-level reference genome assembly (SLU_Cpb5.0) was generated for C. picta bellii using combined PacBio HiFi, 10x Genomics Chromium, Hi-C, and Bionano optical mapping data from a single individual.

  genomic ultra-high tissues heart 10x pacbio hi-c

• Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

  PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 63

  Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.

  liver pbmc integrated gene scrna-seq differential ingenuity

• Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

  PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 92

  Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

  skeletal merged myogenic muscle scrnaseq batch-correction differential

• Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

  PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

  Full-text index only

  MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

  mip diagnostic is900-specific pgg

• pmid-41915012

  PMID 41915012 · PMC13142155 · 8 claims · 7 setups

  Full-text index only

  Inconsistent delta-method normalization across datasets introduces biases (e.g., B-cell separation) that persist even after integration with Harmony, scanorama, or BBKNN.

  10x brain ucsc datasets scrna-seq integration snrna-seq

• Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

  PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model

  breast anterior brain olfactory 10x starmap slide-seqv2

• scCNMF: an integrated analysis model for paired single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing data leveraging cell similarity and cis-regulatory potential.

  PMID 41800139 · PMC12962131 · PeerJ · 2026 · 7 claims · 2 setups

  Full-text index only

  scCNMF is an NMF-based model for vertical integration of paired scRNA-seq and scATAC-seq data that jointly incorporates a cell similarity matrix and a cis-regulatory potential (CRP) matrix

  publicly 10x paired

• Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8(+) T cells.

  PMID 37081150 · PMC10154250 · Nature immunology · 2023 · 8 claims · 7 setups

  Has reproduction · 37

  Orthogonal engineering with PD1d/IL-2v/IL-33 reprograms adoptively transferred CD8+ T cells into a novel synthetic effector state (C5/TSE) that deviates from canonical TOX+ exhaustion

  cd8+ b16-ova ot1 mice scrna-seq flow secretion

• A comparative analysis of blastoid models through single-cell transcriptomics.

  PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 60

  EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

  blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov

• Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.

  PMID 41736854 · PMC12927100 · iScience · 2026 · 7 claims · 6 setups

  Has reproduction · 70

  Early-stage (prodromal) aSyn pathology in M83+/+ mouse brainstem is associated with upregulation of ATP/energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)

  sagittal st-derived spatial immunofluorescence cell-cell