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).

• 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

• Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

  PMID 37223250 · PMC10117727 · microLife · 2021 · 8 claims · 9 setups

  Has reproduction · 50

  Grad-seq resolves in-gradient sedimentation profiles for ~87-88% of annotated C. difficile transcripts and ~50% of annotated proteins, providing a comprehensive RNA-protein complexome resource

  difficile grad-seq rna-seq lc-ms

• Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

  PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups

  Has reproduction · 89

  Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM

  european cis-pqtl myocardial geo mendelian bayesian differential

• Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

  PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

  interscapular ibat bat single-nucleus qpcr western

• Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.

  PMID 40629142 · PMC12321585 · Nature neuroscience · 2025 · 8 claims · 8 setups

  Has reproduction · 82

  Ganglionic eminence (ventral) progenitors maintain stable differentiation competence throughout neurogenesis, generating a consistent set of postmitotic precursor states at all stages, unlike dorsal cortical progenitors whose differentiation competence changes gradually.

  dlx5 progenitors sections cortical scrna-seq trackerseq flashtag

• Discovery and characterization of Alu repeat sequences via precise local read assembly.

  PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups

  Has reproduction · 69

  Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads

  hgdp insertion-supporting candidate assembled genome discordant novo

• Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.

  PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.

  rhizosphere nematode wtex wolbachia metagenomic pcr comparative

• GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

  PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 96

  gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

  avian comparative correlation robustness

• A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.

  PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids

  coli st58 novo draft whole-genome pan-genome-wide plasmid

• Potentially bioavailable iron produced through benthic cycling in glaciated Arctic fjords of Svalbard.

  PMID 33649339 · PMC7921405 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 89

  Benthic biogeochemical cycling in Arctic fjord sediments converts glacially-derived iron into more labile phases, generating up to a 9-fold increase in potentially bioavailable iron with distance from the fjord head

  glacial fjord sediment ascorbate microbial sequential

• Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens.

  PMID 34438997 · PMC8388888 · Antibiotics (Basel, Switzerland) · 2021 · 8 claims · 5 setups

  Has reproduction · 49

  The S. ambofaciens ATCC 23877 transcriptome was redefined from RNAseq data into 5587 transcriptional units (4433 monocistronic, 1154 polycistronic) covering 90.8% of the linear chromosome

  streptomyces ambofaciens bulk rna-seq target

• Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

  PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

  Full-text index only

  Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

  falciparum cdna c18 genomic rt-pcr southern genomic

• Loss of heterozygosity at the 5,10-methylenetetrahydrofolate reductase locus in human ovarian carcinomas.

  PMID 9099956 · PMC2222800 · British journal of cancer · 1997 · 8 claims · 7 setups

  Full-text index only

  No sequence mutations were found in the MTHFR gene in ovarian tumors and cell lines despite extensive SSCP screening

  ovarian non-mucinous informative rt-pcr immunohistochemistry pcr-rflp

• Therapy effect of either paclitaxel or cyclophosphamide combination treatment in patients with epithelial ovarian cancer and relation to TP53 gene status.

  PMID 9703286 · PMC2063030 · British journal of cancer · 1998 · 6 claims · 4 setups

  Full-text index only

  Paclitaxel/cisplatin therapy produces a higher positive response rate than cyclophosphamide/cisplatin therapy in advanced ovarian cancer

  patients frozen genomic clinically randomized rt-pcr temporal

• Extent of laminin-5 assembly and secretion effect junctional epidermolysis bullosa phenotype.

  PMID 9547338 · PMC2212220 · The Journal of experimental medicine · 1998 · 6 claims · 6 setups

  Full-text index only

  The most severe (Herlitz) form of JEB correlates best with mutations causing premature termination codons (PTCs), not with mutation location in a particular protein domain

  keratinocytes keratinocyte genomic pcr biosynthetic northern pcr

• Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

  PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

  Full-text index only

  Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

  sporadic msi-positive tumour unstable microsatellite denaturing sequencing

• BRCA1 and BRCA2 mutations in central and southern Italian patients.

  PMID 11056688 · PMC13918 · Breast cancer research : BCR · 2000 · 8 claims · 4 setups

  Full-text index only

  Deleterious germline BRCA1/BRCA2 mutations were detected in 11 of 136 (8%) unrelated Italian breast/ovarian cancer probands.

  genomic peripheral truncation single-strand direct

• Using DNA microarrays to study host-microbe interactions.

  PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

  Full-text index only

  DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

  streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene

• Analysis of the TGF beta functional pathway in epithelial ovarian carcinoma.

  PMID 11531253 · PMC2364123 · British journal of cancer · 2001 · 6 claims · 6 setups

  Full-text index only

  IGFIIR, TGFβ1 and TGFβRII are proposed to function as a unit in the TGFβ growth inhibitory pathway

  epithelial tumor genomic ovarian sscp sequencing pcr

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

  Full-text index only

  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage