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).

• Microbial Community Shifts Associated With the Ongoing Stony Coral Tissue Loss Disease Outbreak on the Florida Reef Tract.

  PMID 31608047 · PMC6769089 · Frontiers in microbiology · 2019 · 7 claims · 5 setups

  Has reproduction · 93

  Five amplicon sequence variants (unclassified Flavobacteriales, Fusibacter, Planktotalea, Algicola, and Vibrio) were consistently enriched in disease lesions across three coral species (M. cavernosa, D. labyrinthiformis, D. stokesii)

  coral cavernosa 16s differential principal

• Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

  PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

  macrophage hela vaccinia bacillus gene protein-protein comparative

• Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

  PMID 37948380 · PMC10637681 · PloS one · 2023 · 6 claims · 7 setups

  Has reproduction · 90

  Three stem cell-related genes (ORC1L, KIF20A, DLGAP5) are differentially expressed in LUAD and correlate with altered immune infiltration and reduced patient survival.

  luad differentially bulk mirna-seq microarray

• Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

  PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

  Has reproduction · 98

  Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

  clinical dnaa isogenic h37rv genome-wide structural deep-sequencing

• Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

  PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

  Full-text index only

  Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

  imr-32 subtracted mycn-amplified suppression differential array

• Alzheimer's disease biomarker discovery in symptomatic and asymptomatic patients: experimental approaches and future clinical applications.

  PMID 19796674 · PMC2840994 · Experimental gerontology · 2010 · 8 claims · 4 setups

  Full-text index only

  cDNA microarray screening of 6794 genes identified 32 genes aberrantly expressed (>1.8-fold) in the superior temporal gyrus of moderate dementia cases versus cognitively normal controls

  post-mortem cortico-hippocampal cdna western culture

• Application of proteomics methods for pathogen discovery.

  PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

  Full-text index only

  Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

  hlf sequences synthetic conventional 2d-dige gelc-ms

• IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.

  PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 8 claims · 2 setups

  Has reproduction · 78

  IsomiR Window is an integrated, user-friendly platform that systematically identifies, quantifies, and functionally explores isomiR expression in small-RNA-seq datasets without requiring computational skills

  simulated basal small-rna-seq

• Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

  PMID 27655631 · PMC5175363 · Nucleic acids research · 2016 · 8 claims · 8 setups

  Has reproduction · 10

  Embryonic ATZ exposure affects meiosis, spermiogenesis and reduces spermatozoa number in F3 generation male mice

  testis dissociated epididymis chip-seq strand-specific h&e

• EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

  PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 54

  EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology

  populus nigra genome variant clustering

• Genetics and functional genomics of type 2 diabetes mellitus.

  PMID 14659011 · PMC329413 · Genome biology · 2003 · 7 claims · 5 setups

  Full-text index only

  Genome-wide transcription profiling of diabetic skeletal muscle reveals coordinated downregulation of oxidative phosphorylation genes, converging on PGC1α as a central regulator.

  skeletal population microarray real-time genetic

• Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

  PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

  Full-text index only

  A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

  cdna image hbs1l ahi1 rt-pcr est northern

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• 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

• Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

  PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

  Has reproduction · 80

  AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

  b.g parental nicotiana benthamiana qtl comparative rna-sequencing

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr

• The cancer secretome: a reservoir of biomarkers.

  PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

  Full-text index only

  Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

  a549 m-be sw480 neoplastic 2-de dige icat