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 19

System / cell line: qpcr ✕ Assay: selection ✕ Clear

Directing stem cell differentiation by chromatin state approximation.

PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

Full-text index only

Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr
KRT15 identified by scRNA-Seq and machine learning as stemness regulator and prognostic biomarker in ESCC.

PMID 41907411 · PMC13018899 · iScience · 2026 · 8 claims · 8 setups

Full-text index only

A malignant epithelial subpopulation (Cluster 0) with the highest CytoTRACE stemness potential and highest EMT activity exists in ESCC scRNA-seq data

escc degs eca109 kyse180 scrna-seq machine immunohistochemistry
Single point mutations in global regulatory genes restore cephalosporin resistance in a low-MIC Enterococcus faecium natural isolate.

PMID 41870094 · PMC13148053 · Antimicrobial agents and chemotherapy · 2026 · 8 claims · 8 setups

Full-text index only

E. faecium isolates with low MICs to cephalosporins can arise in clinical settings without laboratory manipulation

faecium efm5 antibiotic selection whole-genome
Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.

PMID 41484656 · PMC12857045 · Genome biology · 2026 · 8 claims · 8 setups

Full-text index only

pRIC-seq, an adaptation of RIC-seq for plants, enables genome-wide mapping of RNA-RNA spatial interactions in diploid and tetraploid cotton

diploid tetraploid cotton nicotiana pric-seq gro-cap chip-seq
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

Has reproduction · 55

352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

endometrial degs hub decidua microarray wgcna machine
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 80

WGCNA identified 214 key genes in the blue module most correlated with LUAD

tcga-luad merged tedc2-associated a549 wgcna differential machine
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups

Has reproduction · 49

ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

ptc degs key bulk kegg weighted
Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.

PMID 34090257 · PMC8182229 · EBioMedicine · 2021 · 8 claims · 6 setups

Has reproduction · 53

1,613 genes were differentially expressed in leprosy progressors before diagnosis (t=1) compared to household contacts.

blood rna-seq rt-qpcr differentially rna-seq rt-qpcr random
RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

Full-text index only

RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq
Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

PMID 41501725 · PMC12870398 · Cancer cell international · 2026 · 7 claims · 8 setups

Full-text index only

MEST is a key oncogenic GLD-related gene and a novel therapeutic target in glioma, identified via a machine learning feature selection framework

bulk single-cell tcga glioma gsva aucell machine
Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells.

PMID 41554880 · PMC12901986 · Communications biology · 2026 · 8 claims · 8 setups

Full-text index only

LbuCas13a delivered as ribonucleoprotein (RNP) exhibits strong collateral RNA cleavage in human cells, independent of cell line, and targeting both exogenous and endogenous transcripts

hap1 recombinant hap1-egfp lbucas13a bioanalyzer rnasealert rt-qpcr
Identification and validation of prognostic genes related to glycolysis and M2 macrophage in hepatocellular carcinoma: an integrated analysis of bulk RNA sequencing and single-cell RNA sequencing.

PMID 41766871 · PMC12935947 · Frontiers in immunology · 2026 · 8 claims · 8 setups

Full-text index only

52 candidate genes were identified at the intersection of glycolysis-related genes (GRGs), M2 macrophage-related genes (MRGs), and HCC-vs-control DEGs (DEGs2).

tcga-lihc gse149614 key hcc bulk immune cox
HIF3A-mediated aberrant activation of TXNIP promotes Alzheimer's disease progression.

PMID 41807716 · PMC13096512 · Scientific reports · 2026 · 8 claims · 8 setups

Full-text index only

OS activity is significantly elevated in AD and shows pronounced heterogeneity across brain cell types

entorhinal brain middle c57bl scrna-seq bulk animal
Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

PMID 41939867 · PMC13043422 · Frontiers in immunology · 2026 · 7 claims · 8 setups

Full-text index only

CXCL13, IL33, TLR4, and IGF1 are core IPF genes consistently linked to immune infiltration and fibrotic remodeling across bulk, single-cell, spatial, and blood multi-omics data

lung candidate bulk normalized bulk ppi machine
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 71

Mitophagy-related genes associated with immune infiltration have diagnostic/prognostic significance in ALS

blood als microarray spearman univariate
Identification of new ETV6 modulators through a high-throughput functional screening.

PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

Has reproduction · 68

A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

reh genome-wide qrt-pcr chip-seq
Comprehensive analysis for the role of macrophage-driven genes in abdominal aortic aneurysm.

PMID 41815567 · PMC12973086 · Cardiovascular diagnosis and therapy · 2026 · 8 claims · 8 setups

Full-text index only

SMU1 is identified as a novel macrophage-related gene associated with AAA development, serving as a potential diagnostic biomarker and therapeutic target

aaa macrophage-related merged gwas single-cell bulk rt-qpcr
Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.

PMID 42112332 · PMC13149443 · Frontiers in immunology · 2026 · 7 claims · 8 setups

Full-text index only

A 6-gene (RGS20, ADA, AICDA, SLC12A5, RUFY4, CDK5RAP3) prognostic risk model was constructed for ccRCC from ammonia death-related genes

tcga-kirc gse159115 clinical bulk univariate gsea
Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.

PMID 41327045 · PMC12763953 · BMC plant biology · 2025 · 8 claims · 7 setups

Has reproduction · 58

Genome-wide identification revealed 102 GLPs in B. juncea, 51 in B. nigra, and 48 in B. rapa

juncea promoter duplicated super genome-wide phylogenetic synteny

Experiments

Directing stem cell differentiation by chromatin state approximation.

KRT15 identified by scRNA-Seq and machine learning as stemness regulator and prognostic biomarker in ESCC.

Single point mutations in global regulatory genes restore cephalosporin resistance in a low-MIC Enterococcus faecium natural isolate.

Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.

Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.

RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells.

Identification and validation of prognostic genes related to glycolysis and M2 macrophage in hepatocellular carcinoma: an integrated analysis of bulk RNA sequencing and single-cell RNA sequencing.

HIF3A-mediated aberrant activation of TXNIP promotes Alzheimer's disease progression.

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

Identification of new ETV6 modulators through a high-throughput functional screening.

Comprehensive analysis for the role of macrophage-driven genes in abdominal aortic aneurysm.

Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.

Genome-wide identification and characterization of germin-like protein family in Brassica juncea reveals their role against biotic stress.