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).

• Gpc3 selectively suppresses subcutaneous adipogenesis in diet-induced obesity.

  PMID 41779769 · PMC12978566 · PLoS biology · 2026 · 8 claims · 8 setups

  Full-text index only

  Gpc3 is an obesity-responsive gene exhibiting reciprocal expression patterns between subcutaneous and visceral adipose depots in mice and humans

  paired iwat asat subcutaneous dia single-cell qpcr

• SARS-CoV-2 infection during the first trimester leads to profound immune dysregulation at the maternal-fetal interface despite limited virus detection in placental tissues.

  PMID 41974725 · PMC13249863 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  SARS-CoV-2 rarely infects villous and decidual placental tissues in the first trimester despite maternal infection

  villous maternal rt-qpcr fluorescence indirect

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr

• SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.

  PMID 41691474 · PMC13042402 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  SiCmiR, a two-layer neural network, predicts mature miRNA expression profiles from only 977 LINCS L1000 landmark genes

  tcga k562 pancreatic acth-secreting paired bulk scrna-seq-based

• HIF sustain a transcriptional regulatory circuit of EPAS1 expression in renal clear cell carcinoma.

  PMID 41714613 · PMC12921326 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  HIF-2α mRNA is specifically overexpressed in ccRCC tumor tissue/cells compared to normal kidney, while it is reduced in papillary and chromophobe RCC

  erlangen tcga ccrcc tubule qpcr rna-seq rnascope

• Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

  PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

  Has reproduction

  m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

  paired hl-60 gene aml nanopore functional kaplan-meier

• CCAAT-enhancer binding protein delta functions as a tumor suppressor gene in acute myeloid leukemia.

  PMID 41844049 · PMC13010944 · Neoplasia (New York, N.Y.) · 2026 · 8 claims · 8 setups

  Full-text index only

  CEBPD is identified as a novel tumor suppressor gene in AML

  paired aml tcga oci-aml5 bulk bart kaplan-meier

• Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.

  PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  KCTD16, CD3D, and GSDMB were identified as prognostic succinylation-related genes in BLCA

  soochow-blca tcga-blca gse13507 gse135337 bulk scrna-seq somatic

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

  PMID 41699006 · PMC13002898 · Scientific reports · 2026 · 8 claims · 8 setups

  Full-text index only

  CDC20, PLK1, BUB1, CDC45, and CDCA5 are concordantly identified as hub genes across seven NCBI-GEO datasets and the Pakistani RNA-seq dataset

  pakistani pdac overlapping tcga-paad bulk functional protein-protein

• 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

• ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

  PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

  Full-text index only

  Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

  ductal same sporadic paired cdna quantitative genotyping

• An epigenomic investigation of atrial fibrillation in a matched left and right atrial human cohort.

  PMID 41906156 · PMC13045105 · Clinical epigenetics · 2026 · 8 claims · 6 setups

  Full-text index only

  H3K27ac epigenomic profiles differ more strongly by anatomical side (left vs right atrium) than by disease status (AF vs SR)

  left independent paired ipsc-derived h3k27ac bulk rt-qpcr

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

  meta-geo tcga-blca bca genomics unsupervised lasso weighted

• Tet2 modulates ER stress responses related to β-cell death and autoimmunity in diabetes.

  PMID 41782826 · PMC12955150 · iScience · 2026 · 8 claims · 6 setups

  Full-text index only

  Tet2-deficient NOD mice transplanted with WT bone marrow show fewer islet-infiltrating lymphocytes beginning 8–10 weeks post-transplant, primarily among CD4+ T cells

  islets islet islet-infiltrating cadaveric flow single-cell single-nucleus

• Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

  PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

  Full-text index only

  A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

  tcga-blca blca paired wgcna differential machine

• Decoding the circRNA-miRNA-mRNA regulatory network in hepatitis B virus-driven hepatocellular carcinoma.

  PMID 41845440 · PMC13107627 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

  Full-text index only

  A bioinformatic pipeline combining RNA-seq, circRNA calling, ECDF analysis, PPI, and survival analysis identifies a circRNA-miRNA-mRNA ceRNA network in HBV-integrated HCC cells

  hep3b qpcr dysregulated target bulk circrna rt-qpcr

• Spatial transcriptomics identifies differentiation, lipid metabolism, and retinoid pathway alterations in acne vulgaris.

  PMID 41657309 · PMC12892907 · JCI insight · 2026 · 8 claims · 6 setups

  Full-text index only

  A custom KRT5-directed segmentation pipeline improves transcript assignment accuracy in the spatially complex sebaceous gland compared with standard multimodal or nuclei-expansion segmentation

  skin inflammatory tert gtrd spatial immunohistochemistry reanalysis