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 210

Assay: profile ✕ Clear

Long-term survival and transmission of INI1-mutation via nonpenetrant males in a family with rhabdoid tumour predisposition syndrome.

PMID 18087273 · PMC2361463 · British journal of cancer · 2008 · 8 claims · 5 setups

Full-text index only

The malignant brain tumours in patients III-1, III-3, and III-4, originally classified as anaplastic ependymomas, are in fact atypical teratoid/rhabdoid tumours (AT/RT)

constitutional formalin-fixed tumour blood sanger denaturing immunohistochemistry
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

Full-text index only

A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

PMID 18074030 · PMC2111048 · PloS one · 2007 · 8 claims · 7 setups

Full-text index only

MDA-based single-cell whole-genome amplification (S-WGA) products show large variability in amplification bias, including allele dropout and preferential amplification.

lymphoblastoid lcl cmk11-5 gel taqman oligonucleotide
Characterisation and protein expression profiling of annexins in colorectal cancer.

PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

Full-text index only

Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

dukes colorectal immunised whole-cell gel immunohistochemistry elisa
Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

PMID 17949499 · PMC2148065 · BMC genomics · 2007 · 8 claims · 8 setups

Full-text index only

ECM-stimulated hMSC and OS-media-stimulated hMSC represent two distinct intermediate/transitional phenotypes en route to becoming osteoblasts

naive hmsc osteoblasts proteomic lc-ms gene computational
The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

PMID 17932789 · PMC2140095 · Journal of structural and functional genomics · 2007 · 8 claims · 6 setups

Full-text index only

A family-based target selection approach (rather than genome-wide or fold-novelty based selection) maximizes cross-member methodological transfer and biological insight

recombinant target coli x-ray differential analytical
High resolution melting for mutation scanning of TP53 exons 5-8.

PMID 17764544 · PMC2025602 · BMC cancer · 2007 · 7 claims · 5 setups

Full-text index only

HRM is an effective technique for rapid scanning of TP53 mutations that can markedly reduce required sequencing

tp53-mutant ovarian breast high hrm dideoxy
Genomic expression during human myelopoiesis.

PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

Full-text index only

An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

myeloid same cd34+ gene microarray unsupervised sam
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

Full-text index only

Current syndromic disease classification lacks specificity despite historically serving clinicians well

prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene
Nucleosome regulatory dynamics in response to TGFβ.

PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

Has reproduction · 59

SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

hepatocellular hepg2 130-bp mnase strand-specific taqman
Proteolysis of the endothelial cell protein C receptor by neutrophil proteinase 3.

PMID 17459006 · PMC1890847 · Journal of thrombosis and haemostasis : JTH · 2007 · 8 claims · 8 setups

Full-text index only

Activated neutrophils decrease EPCR surface expression on endothelial cells over time

ea.hy926 peripheral neutrophils recombinant flow luminol-dependent sds-page
Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 77

Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.

fresh-frozen ffpe breast unc microarray mrna-seq ribo-zero-seq
Tissue microarrays characterise the clinical significance of a VEGF-A protein expression signature in gastrointestinal stromal tumours.

PMID 17299397 · PMC2360083 · British journal of cancer · 2007 · 8 claims · 5 setups

Full-text index only

A combined VEGF-A ligand and flt-1 receptor protein expression signature discriminates malignant from benign GIST

archival tma genomic pcr immunohistochemistry unsupervised pcr-dhplc
The field of tissue injury in the lung and airway.

PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

Full-text index only

Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific
Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

PMID 19126968 · PMC3827814 · Disease markers · 2008 · 8 claims · 5 setups

Full-text index only

Glycomic profiling of N-linked glycans in serum can reveal potential biomarkers distinguishing prostate cancer patients from controls

serum prns-1-1 n-linked maldi solid tandem
Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein.

PMID 19028452 · PMC2633355 · Biochemical and biophysical research communications · 2009 · 7 claims · 6 setups

Full-text index only

Developed a multi-step fractionation scheme (gel exclusion chromatography, rate zonal sucrose gradient centrifugation, high-speed centrifugation) to purify exosomes from human plasma

plasma-derived plasma lc-ms sds-page western
Mercury immune toxicity in harbour seals: links to in vitro toxicity.

PMID 18959786 · PMC2600635 · Environmental health : a global access science source · 2008 · 8 claims · 6 setups

Full-text index only

In vitro MeHg exposure reduces seal lymphocyte number, viability, metabolic activity, and DNA/RNA synthesis

blood pha-stimulated cytoplasmic cold trypan mts
Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells.

PMID 18847511 · PMC2571112 · BMC genomics · 2008 · 8 claims · 8 setups

Full-text index only

[BF/S+L/Ep] butanol fraction from E. purpurea enhances maturation of human immature dendritic cells (increased CD83 expression)

immature idcs [bf phytocompounds flow mtt lal
Collagen VI glycine mutations: perturbed assembly and a spectrum of clinical severity.

PMID 18825676 · PMC2743946 · Annals of neurology · 2008 · 8 claims · 6 setups

Full-text index only

All eight new patients had heterozygous glycine substitution mutations toward the N-terminal end of the collagen VI triple helix

dermal skeletal fibroblast confluent rt-pcr immunohistochemistry biosynthetic
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

Full-text index only

A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine

Experiments

Long-term survival and transmission of INI1-mutation via nonpenetrant males in a family with rhabdoid tumour predisposition syndrome.

Comparative genomics search for losses of long-established genes on the human lineage.

Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

Characterisation and protein expression profiling of annexins in colorectal cancer.

Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

High resolution melting for mutation scanning of TP53 exons 5-8.

Genomic expression during human myelopoiesis.

Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

Nucleosome regulatory dynamics in response to TGFβ.

Proteolysis of the endothelial cell protein C receptor by neutrophil proteinase 3.

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

Tissue microarrays characterise the clinical significance of a VEGF-A protein expression signature in gastrointestinal stromal tumours.

The field of tissue injury in the lung and airway.

Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein.

Mercury immune toxicity in harbour seals: links to in vitro toxicity.

Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells.

Collagen VI glycine mutations: perturbed assembly and a spectrum of clinical severity.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.