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).

• Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.

  PMID 35901050 · PMC9333241 · PloS one · 2022 · 5 claims · 8 setups

  Has reproduction · 55

  Several co-expressed gene modules are significantly associated with left ventricle ejection fraction (LVEF) and the DCM phenotype, enriched in fibrosis-related, small molecule transporting-related, and immune response-related pathways.

  heart degs gene rna-seq bulk differential gene

• nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data.

  PMID 35574063 · PMC9097006 · South African computer journal = Suid-Afrikaanse rekenaartydskrif · 2021 · 7 claims · 5 setups

  Has reproduction · 95

  nf-rnaSeqCount is a portable, reproducible Nextflow pipeline that maps RNA-seq reads to a reference genome and quantifies gene abundance for differential expression analysis

  black geo rna-seq rna-seq benchmarking quality

• Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

  PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 78

  CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

  cfdna na12878 genomic sperm targeted whole-genome whole-exome

• 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 publicly accessible database integrating data from 17 skin diseases and 63 independent datasets, including 1434 scRNA-seq, 63 spatial transcriptomics, and 1502 bulk RNA-seq samples

  skin scrna-seq single prurigo scrna-seq bulk spatial

• Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils.

  PMID 33948572 · PMC8080108 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

  Has reproduction · 35

  Neutrophils recruited to CF airways undergo rapid, broad transcriptional firing that upregulates anabolic genes and downregulates antimicrobial genes

  blood healthy transmigrated cfasn-transmigrated flow transmigration content

• A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

  PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

  Has reproduction · 78

  METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• PulmonDB: a curated lung disease gene expression database.

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

  Has reproduction · 53

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

  lung ipf copd curated hierarchical differential

• Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

  PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups

  Full-text index only

  QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies

  serum pooled duplicate full seldi-tof principal technical

• Proteomic surveillance of retinal autoantigens in endogenous uveitis: implication of esterase D and brain-type creatine kinase as novel autoantigens.

  PMID 18552983 · PMC2426731 · Molecular vision · 2008 · 7 claims · 6 setups

  Full-text index only

  Six novel candidate retinal autoantigens (β-actin, esterase D, tubulin β-2, brain-type creatine kinase, VDAC, aspartate aminotransferase) were identified by 2D-WB and mass spectrometry in EAU mice

  c57bl retinal recombinant eau two-dimensional maldi-tof one-dimensional

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

  Full-text index only

  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• 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