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).

Publications 1.3k Datasets 392.5k Experiments 13

System / cell line: normal ✕ Assay: integrated ✕ Clear

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

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

Has reproduction · 63

Independent human liver immune scRNA-seq datasets can be combined into an integrated meta-atlas in which all datasets co-cluster, despite differing cell-type proportions between studies.

liver combined normal differential scrna-seq integrated reference
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

Has reproduction · 85

Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

normal er+ epithelial malignant single-cell spatial copy
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
Characterization of a natural mutator variant of human DNA polymerase lambda which promotes chromosomal instability by compromising NHEJ.

PMID 19806195 · PMC2751832 · PloS one · 2009 · 8 claims · 8 setups

Full-text index only

The W438 hPolλ variant has reduced base substitution fidelity in vitro compared to wild-type R438

normal recombinant hpolλ short pcr-sscp ber m13mp2
Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

PMID 19011694 · PMC2582945 · PloS one · 2008 · 8 claims · 8 setups

Full-text index only

A 16-microRNA signature (9 up, 7 down) distinguishes osteoarthritic from normal cartilage.

patient-derived normal integrated taqman qrt-pcr northern
Protein expression patterns in primary carcinoma of the vagina.

PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical
Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 7 setups

Has reproduction

A ResNet classifier built on a 10-gene metabolic signature distinguishes all thyroid cancer differentiation states with ~92.7% average accuracy.

fuscc epithelial aggregated untargeted whole-exome bulk
p53 mutations in cervical carcinogenesis--low frequency and lack of correlation with human papillomavirus status.

PMID 8142262 · PMC1968818 · British journal of cancer · 1994 · 7 claims · 6 setups

Full-text index only

Somatic mutation in the p53 gene hotspot regions occurs infrequently in cervical carcinomas

cervical tumour paired hpv-positive immunocytochemistry pcr sequencing
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

conserved putative mirna-target normal comparative machine mirna
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.

PMID 19036792 · PMC2686442 · Nucleic acids research · 2009 · 8 claims · 7 setups

Full-text index only

SysPIMP is a web-based platform integrating disease mutation databases with X!Tandem and BLAST to identify disease-related mutated proteins from MS results

omim pmd swissprot msipi database sequence tandem
A mouse plasma peptide atlas as a resource for disease proteomics.

PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

Full-text index only

A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

plasma peptides fully tissues lc-ms anion database
Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 8 setups

Has reproduction · 49

S100A3 is a robust candidate biomarker showing consistent discriminatory performance across the acute sleep deprivation training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort.

peripheral blood normal integrated bulk interpretable immune
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

Full-text index only

FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription

Experiments

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

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

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

Characterization of a natural mutator variant of human DNA polymerase lambda which promotes chromosomal instability by compromising NHEJ.

Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

Protein expression patterns in primary carcinoma of the vagina.

Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

p53 mutations in cervical carcinogenesis--low frequency and lack of correlation with human papillomavirus status.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.

A mouse plasma peptide atlas as a resource for disease proteomics.

Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.