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).

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a comprehensive, publicly accessible database integrating bulk RNA-seq, scRNA-seq, and spatial transcriptomics data across 17 skin diseases and 63 independent datasets

  skin scrna-seq scrna-seq transcription cell-cell

• Current status of use of high throughput nucleotide sequencing in rheumatology.

  PMID 33408124 · PMC7789458 · RMD open · 2021 · 8 claims · 8 setups

  Has reproduction · 83

  RNA-Seq is the most represented HTS assay used in rheumatology research, primarily for biomarker identification in blood or synovial tissue.

  pubmed sequence blood patients systematic sra rna-seq

• MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

  PMID 29901703 · PMC6025204 · GigaScience · 2018 · 8 claims · 7 setups

  Has reproduction · 95

  The MetaMap pipeline recapitulates known infection agents in bona fide dual RNA-seq validation studies (Salmonella, HPV, HSV, rhinovirus)

  hela tumor lymphoblast rna-seq dual blastn-based

• Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

  PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  CLAD exhibits specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

  clad covid-19 million formalin-fixed single-cell single-nucleus integrated

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 7 claims · 6 setups

  Has reproduction · 53

  PulmonDB is a curated, web-based relational database (plus R package) integrating microarray and RNA-seq gene expression data with controlled-vocabulary annotation for COPD and IPF.

  lung rna-seq curated gene differential

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral