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).

Publications 1.3k Datasets 392.5k Experiments 13

System / cell line: cdna ✕ Assay: extraction ✕ Clear

Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

PMID 16916263 · PMC7121524 · Methods in molecular biology (Clifton, N.J.) · 2006 · 7 claims · 7 setups

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PCR-based amplification and direct sequencing of SARS-CoV genome fragments is feasible from uncultured clinical specimens (serum, nasopharyngeal aspirate, stool), avoiding culture-derived artifacts and biohazard risk.

sars-cov extracted cdna pcr viral reverse real-time
Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

PMID 15115540 · PMC420239 · BMC genomics · 2004 · 6 claims · 3 setups

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Bioinformatic sequence comparison of 60,770 RIKEN FANTOM2 mouse cDNA clones identified 2,578 sequences with 70-85% identity to known human disease genes/proteins

riken medline sequence manual semi-automated
Molecular epidemiology of measles viruses in the United States, 1997-2001.

PMID 12194764 · PMC2732556 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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The diversity of measles virus genotypes observed in the US from 1997–2001 reflects multiple imported sources of virus, indicating no strain of measles is endemic in the United States.

b95a clinical pcr measles viral extraction rt-pcr
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups

Has reproduction · 97

The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)

duvernoy's nigriceps rna-seq differential extraction
Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions.

PMID 31681245 · PMC6813237 · Frontiers in microbiology · 2019 · 8 claims · 5 setups

Has reproduction · 73

S. aureus COL (MRSA) can survive and grow under acidic (pH5) and alkaline (pH9) conditions both planktonically and as a biofilm.

aureus growth microarray extraction
Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

PMID 19757078 · PMC2843092 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2009 · 7 claims · 8 setups

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Human B cells express one CB2 transcript while mouse B cells express three CB2 transcripts

splenocytes pbmc-derived splenic genbank race pcr quantitative
DNA sequence and analysis of human chromosome 9.

PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

bac chromosome fibres chimpanzee clone-based restriction computational
Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

saliva amplified extracted differentially genome quality extraction
p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

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p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

frozen plasmids single extracted p53 sanger laser
Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

umbilical ucb zebrafish microarray fluorescence-activated quantitative
Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

hapmap combined coriell ceu allele-specific linear one-sample
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 41

Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative

Experiments

Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

Molecular epidemiology of measles viruses in the United States, 1997-2001.

Genome assembly comparison identifies structural variants in the human genome.

Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions.

Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

DNA sequence and analysis of human chromosome 9.

Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.