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).

• A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

  PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC

  urinary tcga paired urine sequencing lncrna qrt-pcr

• Genome-wide reprogramming of sRNA and lncRNA in the epigenetic regulation following interspecific hybridization in the Brassica species.

  PMID 41668146 · PMC12892563 · Molecular horticulture · 2026 · 6 claims · 5 setups

  Full-text index only

  Regulatory differences in sRNAs between the two F1 hybrids are mainly driven by maternal inheritance, with Hybrid-sh showing more maternal influence and Hybrid-yh showing transgressive regulation

  brassica s70 small strand-specific atac-seq

• Integrated transcriptome and single-cell sequencing analysis identify blood-pancreas shared lncRNA biomarkers in new-onset T2DM.

  PMID 41915667 · PMC13037964 · PloS one · 2026 · 8 claims · 6 setups

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  1,709 lncRNAs are differentially expressed in peripheral blood of new-onset T2DM patients vs controls

  peripheral pancreatic predicted bulk weighted single-cell

• Identification of a novel lncRNA prognostic signature and analysis of functional lncRNA AC115619.1 in hepatocellular carcinoma.

  PMID 37614318 · PMC10442647 · Frontiers in pharmacology · 2023 · 8 claims · 8 setups

  Has reproduction · 87

  A six-lncRNA prognostic signature (LINC02428, LINC02163, AC008549.1, AC115619.1, CASC9, LINC02362) predicts overall survival in HCC patients

  hcc tcga paired snu-449 lncrna sequencing univariate

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid

• Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

  PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

  PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups

  Has reproduction · 64

  A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs

  peripheral genome blood bulk illumina ion

• FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs in Drosophila melanogaster.

  PMID 41551930 · PMC12805895 · NAR genomics and bioinformatics · 2026 · 7 claims · 8 setups

  Full-text index only

  FLYNC, an explainable boosting machine (EBM) model, accurately predicts the probability that a newly identified RNA transcript in D. melanogaster is a lncRNA

  melanogaster drosophila automated ebm hyperparameter

• Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

  PMID 41807385 · PMC12979833 · Nature communications · 2026 · 8 claims · 8 setups

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  Integration of CAD GWAS summary statistics with epigenetic data from 45 cell types identifies 1580 candidate CAD genes

  cad-associated disease-relevant types cad variant epigenetic tf-snv

• Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions.

  PMID 42258536 · PMC13244158 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  RADIAnT is a reads-to-interactions computational pipeline for analyzing RNA–DNA ligation data

  embryonic k562 mesc endothelial grid-seq radicl-seq red-c

• Pervasive enhanced transcription in inflammatory breast cancer tumors and PBMCs impacts RNA splicing and intronic RNAs in plasma.

  PMID 42066072 · PMC13134590 · Science advances · 2026 · 8 claims · 7 setups

  Full-text index only

  TGIRT-seq of tumors, PBMCs, and plasma reveals widespread differences that distinguish IBC patients from non-IBC patients and healthy donors across breast cancer subtypes.

  ffpe pbmcs plasma frozen tgirt-seq differential principal