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 937

System / cell line: presence ✕ Clear

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

Full-text index only

FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

chimpanzee hepg2 promoters liver quantitative western sirna
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

PMID 18281699 · PMC2367731 · Nucleic acids research · 2008 · 8 claims · 7 setups

Full-text index only

H3t/H4 forms nucleosomes with H2A/H2B via the salt-dialysis method, similar to conventional H3.1/H4

recombinant reconstituted his6-tagged hnap1 salt-dialysis micrococcal chaperone-mediated
Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

PMID 18281252 · PMC2443276 · Carcinogenesis · 2008 · 7 claims · 4 setups

Full-text index only

Cigarette smoking is associated with a higher frequency of somatic mtDNA mutations in buccal cells

buccal subject ttge real-time pcr-based
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

Full-text index only

BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence
HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.

PMID 18215327 · PMC2265691 · Virology journal · 2008 · 8 claims · 6 setups

Full-text index only

N-linked glycosylation of HIV-1 gp120 differs between plasma and leukocyte compartments

plasma hiv-1 nlg presence env phylogenetic signature
Analysis of Parkinson disease patients from Portugal for mutations in SNCA, PRKN, PINK1 and LRRK2.

PMID 18211709 · PMC2248204 · BMC neurology · 2008 · 6 claims · 4 setups

Full-text index only

Pathogenic mutations in PRKN and LRRK2, but not SNCA or PINK1, are found in a Portuguese cohort of early-onset/familial PD patients

genomic cohort bidirectional targeted gene
Genome-wide analysis of antisense transcription with Affymetrix exon array.

PMID 18211689 · PMC2257944 · BMC genomics · 2008 · 8 claims · 4 setups

Full-text index only

A modified cDNA synthesis protocol (ATE: Antisense Transcriptome analysis using Exon array), which skips the first-cycle cDNA synthesis and IVT amplification step, labels cDNA in reverse orientation, enabling Exon arrays to detect antisense transcripts

jurkat exon orientation-specific
Approaching the genomics of risk-taking behavior.

PMID 20109660 · PMC3961474 · Advances in genetics · 2009 · 8 claims · 8 setups

Full-text index only

Candidate genes (e.g., DRD4, SERT, MAOA) explain only a small fraction of total genetic variation in risk-taking-related behaviors, motivating a whole-genome approach.

wild-caught three-spined sticklebacks open-field-like predator repeated-measures
Proteomic studies of cholangiocarcinoma and hepatocellular carcinoma cell secretomes.

PMID 20069059 · PMC2801507 · Journal of biomedicine & biotechnology · 2010 · 7 claims · 5 setups

Full-text index only

The secretomes of cholangiocarcinoma (HuCCA-1) and four hepatocellular carcinoma cell lines show distinct, differing protein profiles.

hucca-1 same conditioned paired sds-page trypan 1-de
Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma.

PMID 20057906 · PMC2802294 · Molecular vision · 2009 · 7 claims · 4 setups

Full-text index only

Screening of 32 Chinese patients with microphthalmia and/or coloboma across ten candidate genes revealed no clearly causative mutation.

genomic unrelated bmp4 sanger restriction heteroduplex-single
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

Full-text index only

BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

PMID 20044523 · PMC2923092 · Stroke · 2010 · 8 claims · 6 setups

Full-text index only

SNP rs2208454 in intron 3 of MACROD2 (near FLRT3, chr20p12) is associated with lower risk of covert MRI-infarcts (OR=0.76, p=4.64x10-7)

stroke-free elderly african-american cardiovascular genome-wide direct expression
Skittle: a 2-dimensional genome visualization tool.

PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups

Full-text index only

Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales

chromosome random alpha genome nucleotide repeat alignment
A novel recessive Nefl mutation causes a severe, early-onset axonal neuropathy.

PMID 20039262 · PMC4439312 · Annals of neurology · 2009 · 8 claims · 8 setups

Full-text index only

A homozygous NEFL nonsense mutation (E210X) causes a severe, early-onset recessive axonal neuropathy in four siblings of a consanguineous family

family sural nefl-null sw-13 clinical genetic immunohistochemistry
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

Full-text index only

A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

personal genomic pcr-validated unrelated short-read pcr sanger
Complex landscapes of somatic rearrangement in human breast cancer genomes.

PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

Full-text index only

There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

breast subset confirmed paired-end fish exon-exon
A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

Full-text index only

A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.

hct116 silac silac-based immunofluorescence
Mutation analysis of the AATF gene in breast cancer families.

PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

Full-text index only

No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

genomic showing aatf case conformation direct pathogenicity

Experiments

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro.

Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments.

Analysis of Parkinson disease patients from Portugal for mutations in SNCA, PRKN, PINK1 and LRRK2.

Genome-wide analysis of antisense transcription with Affymetrix exon array.

Approaching the genomics of risk-taking behavior.

Proteomic studies of cholangiocarcinoma and hepatocellular carcinoma cell secretomes.

Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

Skittle: a 2-dimensional genome visualization tool.

A novel recessive Nefl mutation causes a severe, early-onset axonal neuropathy.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

Mutation analysis of the AATF gene in breast cancer families.