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).

• 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

• Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.

  PMID 36591261 · PMC9797520 · Frontiers in immunology · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  CCR2hi and CCR2lo periarticular bone marrow OCP subsets show a disparate transcriptome (863 differentially expressed genes)

  sorted rna-seq periarticular bulk gene flow

• Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.

  PMID 34498920 · PMC8428255 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

  Has reproduction · 78

  The complete genome sequence of Leishmania (Mundinia) orientalis, isolate LSCM4, strain LV768, was determined using combined short-read and long-read sequencing.

  leishmania orientalis culture extraction short-read

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.

  v6.5 mes icshape rt-qpcr western

• Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104).

  PMID 38897205 · PMC11293361 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 72

  Neoadjuvant sintilimab plus carboplatin/nab-paclitaxel is clinically feasible and tolerable in resectable EGFR-mutant NSCLC, with all 18 patients completing treatment and undergoing radical surgery.

  pre resected tumor serial whole-exome bulk single-cell

• Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

  PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 100

  TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

  hesc hescs long-read short-read rt-pcr

• The genomics of probiotic intestinal microorganisms.

  PMID 15998456 · PMC1175979 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  Genomic characterization of probiotic and commensal intestinal bacteria will deepen understanding of their beneficial effects on host health

  lactobacillus bacteroides bifidobacterium host whole-genome inflammation microarray

• Better smelling through genetics: mammalian odor perception.

  PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

  Full-text index only

  Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

  mammals subjects v1r trpc2 comparative genetic targeted

• TB database: an integrated platform for tuberculosis research.

  PMID 18835847 · PMC2686437 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  TBDB is an integrated database providing access to TB genomic data and resources relevant to discovery/development of TB drugs, vaccines and biomarkers.

  tuberculosis streptomyces tb-infected whole-genome sequence trna

• GSDME-mediated pyroptosis promotes the progression and associated inflammation of atherosclerosis.

  PMID 36807553 · PMC9938904 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  GSDME-mediated pyroptosis promotes atherosclerosis progression and its associated inflammation

  carotid macrophages gsdme− apoe− single-cell transmission immunohistochemistry

• 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 are succinylation-related prognostic genes in BLCA

  paired tcga-blca geo gse135337 bulk single-cell rt-qpcr

• A common polymorphism in the oxygen-dependent degradation (ODD) domain of hypoxia inducible factor-1alpha (HIF-1alpha) does not impair Pro-564 hydroxylation.

  PMID 14521712 · PMC212228 · Molecular cancer · 2003 · 6 claims · 5 setups

  Full-text index only

  Pro582Ser is a common HIF-1α ODD-domain polymorphism occurring at similar frequency in idiopathic erythrocytosis patients (0.109) and normal controls (0.073)

  genomic recombinant 35s-labeled sanger pcr-rflp gst

• MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia.

  PMID 16834459 · PMC1502153 · PLoS medicine · 2006 · 8 claims · 8 setups

  Full-text index only

  A somatic activating mutation in MPL (W515L, transmembrane domain) is present in 9% (4/45) of JAK2V617F-negative myelofibrosis (MF) patients

  granulocyte hapmap 32d balb sequencing genotyping proliferation

• Novel causative mutations in patients with Nance-Horan syndrome and altered localization of the mutant NHS-A protein isoform.

  PMID 18949062 · PMC2571945 · Molecular vision · 2008 · 8 claims · 5 setups

  Full-text index only

  Truncating (nonsense/frameshift) mutations in NHS cause Nance-Horan syndrome by prematurely terminating the protein

  genomic nhs-a hek mdck pcr pcr-based western

• mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice.

  PMID 19763141 · PMC2909846 · Journal of human genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  The G10398A cybrid shows slower proliferation and delayed cell cycle progression (G1 accumulation, decreased G2/M) compared to wild-type G10398 cybrid

  blood mitochondria g10398a cybrid pcr cybrid spectrophotometric

• Molecular helminthology in the Rockies. Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005.

  PMID 15998458 · PMC1175981 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  The Schistosoma mansoni genome (~300 Mb) is nearing completion via whole-genome shotgun sequencing at ninefold coverage, with an estimated 15,000-20,000 protein-coding genes

  schistosoma brugia ancylostoma echinococcus whole-genome interference transgenesis

• Single-Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression.

  PMID 34825784 · PMC8787427 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022 · 8 claims · 6 setups

  Has reproduction · 59

  Human NP contains six transcriptionally distinct NPC subpopulations: HT-CLNPs, effector NPCs, homeostatic NPCs, regulatory NPCs, fibroNPCs, and adhesion NPCs

  npcs scrna-seq-derived ht-clnp-i g-mdscs single-cell rt-qpcr immunohistochemistry

• MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.

  PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 70

  MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling

  bat stromal paraffin-embedded aortic bulk proteomics scrnaseq

• A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

  PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups

  Full-text index only

  Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)

  genomic hek293 hepg2 microsomes pcr site-directed luciferase

• The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.

  PMID 38537644 · PMC11063626 · Cell reports · 2024 · 8 claims · 8 setups

  Has reproduction · 62

  The natural soil microbiome reduces Striga attachment to sorghum roots at the post-germination stage by interfering with haustorium initiation rather than seed germination

  clue sorghum striga sqr 16s striga haustorium