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).

• Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.

  PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 61

  Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC

  hct116 crc tumor chip-seq bulk single

• Pre-implantation embryo metabolism identified by PEMA reveals endogenous lactate insufficiency contributes to pre-implantation development arrest.

  PMID 42272466 · PMC13247451 · Fundamental research · 2026 · 6 claims · 7 setups

  Has reproduction

  PEMA, a computational tool that weights metabolic reactions using Ribo-seq data combined with RNA-seq-derived flux balance analysis, can characterize metabolic states of human and mouse pre-implantation embryos more precisely than existing methods like Compass.

  embryos pre-implantation ch3pn single-embryo immunofluorescence single-cell

• Gene Regulatory Interactions at Lamina-Associated Domains.

  PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

  Has reproduction · 31

  Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

  adipose ascs mesenchymal chip-seq rna-seq atac-seq

• ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

  PMID 41820617 · PMC13084044 · The EMBO journal · 2026 · 8 claims · 7 setups

  Has reproduction · 50

  ZAP (ZC3HAV1/PARP13) is a key component of the RAPP quality control pathway

  k562 zap-s rt-qpcr western immunofluorescence

• Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).

  PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups

  Has reproduction · 58

  A cheetah-specific epigenetic clock (CheetahClock) built from 52 CpG sites predicts age across blood and liver samples with r=0.97 and MAE=0.86 years

  cheetah genes methylation elastic epigenome-wide

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

  PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

  Has reproduction · 54

  In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

  analysis microarray rna-seq quantitative

• Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

  PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups

  Has reproduction · 67

  Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines

  brain tumour gbm retrotransposon empty qrt-pcr

• Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling.

  PMID 32927917 · PMC7570247 · Plants (Basel, Switzerland) · 2020 · 8 claims · 6 setups

  Has reproduction

  Pba infection of tobacco causes massive transcriptomic reprogramming, with 8636 differentially expressed genes (DEGs) split between up- and downregulated genes.

  tobacco potato rna-seq qpcr enzyme

• Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

  PMID 33690630 · PMC7978347 · PLoS genetics · 2021 · 8 claims · 4 setups

  Has reproduction · 97

  Paramutation between R and S HPT epialleles occurs only in tetraploid (RRSS) F2 progeny, not in diploid (RS) F2 progeny, reducing the ratio of hygromycin-resistant plants below Mendelian expectation.

  diploid 14-day-old tetraploid type hygromycin small crispr-cas9

• Essential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.

  PMID 34745063 · PMC8564382 · Frontiers in microbiology · 2021 · 7 claims · 7 setups

  Has reproduction · 67

  Tn-seq using the TnSC189 mariner transposon identified 329 essential genes in V. anguillarum NB10Sm from a library of 52,662 insertion mutants.

  vibrio coli anguillarum transposon-insertion conjugative functional

• Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

  PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

  Has reproduction · 55

  RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

  amir-sul col 14-day-old arabidopsis small rna-seq gel

• Base editing in human cells with monomeric DddA-TALE fusion deaminases.

  PMID 35821233 · PMC9276701 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  mDdCBEs built from non-toxic full-length DddA_tox variants enable mitochondrial DNA base editing with efficiencies of up to 50% upon transient expression in human cells

  hek293t nih3t3 targeted clonal aav2

• Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

  PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

  preimplantation single uniparental embryos rna-seq paired gene

• β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia.

  PMID 36597789 · PMC9906382 · EMBO molecular medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  β-catenin binds directly to promoters of RNA processing, splicing, and ribosomal biogenesis genes in T-ALL cells

  rpmi8402 chipseq chip-qpcr sequencing

• The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.

  PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se

  sez-derived computational nsc npc atac-seq bulk lisa

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.

  PMID 35806266 · PMC9267015 · International journal of molecular sciences · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  mCCD cl1 cells mount a broad transcriptional response to 24 h hypoxia (0.2% O2), with 3086 genes differentially expressed

  mccd lines bulk rt-qpcr western

• Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

  PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

  agaricia agaricites coral sites 2brad population hierarchical