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 363

System / cell line: cdna ✕ Clear

The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

PMID 12036445 · PMC5927037 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 5 setups

Full-text index only

SNI (elevated spontaneous point mutation rate without microsatellite instability) is present in rat mammary carcinoma cell lines and human breast cancer cell lines

mammary same normal pcr-sscp direct quantitative
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

Full-text index only

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

frozen plasmids single extracted p53 sanger laser
Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

PMID 11870543 · PMC2375272 · British journal of cancer · 2002 · 8 claims · 5 setups

Full-text index only

DFFA is localized within the 1p36.2-3 smallest region of overlap (SRO) of deletions defined in Scandinavian neuroblastoma tumours, distal to marker D1S244

scandinavian chromosome unfinished neuroblastoma pcr bac-library in-silico
Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

PMID 12615897 · PMC2193825 · The Journal of experimental medicine · 2003 · 8 claims · 8 setups

Full-text index only

Artemis-deficient ES cells are severely impaired in VDJ coding joining but retain relatively normal RS (signal) joining

recombined southern rt-pcr colony
CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

Full-text index only

RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite
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
Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

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

Full-text index only

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
Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

Full-text index only

B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

paraffin-embedded cloned same predicted pcr cloning blastx
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

Full-text index only

Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

otx sea elegans endo16 windowed reporter comparative
Thirty years into the genomics era: tumor viruses led the way.

PMID 17940630 · PMC1994808 · The Yale journal of biology and medicine · 2006 · 8 claims · 8 setups

Full-text index only

Restriction endonuclease-based analysis and sequencing of small tumor virus genomes (SV40, phiX174) established the technical framework later used to sequence bacterial and human genomes

sv40 bacteriophage epstein-barr aids-associated restriction recombinant sequencing
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

Full-text index only

A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

Full-text index only

GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

Full-text index only

Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

Full-text index only

MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

genomic domestic pooled colorectal snp pooling microsatellite
Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

PMID 16840528 · PMC1524903 · Nucleic acids research · 2006 · 7 claims · 5 setups

Full-text index only

MS-PET, which dimerizes PETs prior to 454 multiplex sequencing, achieves an approximate 100-fold efficiency increase over standard Sanger-based PET analysis

mcf7 hct116 flcdna gis-pet chip-pet quantitative
PRKCA and multiple sclerosis: association in two independent populations.

PMID 16596167 · PMC1420678 · PLoS genetics · 2006 · 8 claims · 8 setups

Full-text index only

PRKCA (protein kinase C alpha) on 17q24 is associated with MS in Finnish families

finnish canadian unrelated blood snp dense multipoint
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

Full-text index only

The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

PMID 16430766 · PMC1434729 · BMC medical genetics · 2006 · 7 claims · 8 setups

Full-text index only

Linkage analysis can pre-select which gene (PKD1 or PKD2) to screen for mutations in ADPKD families with sufficient samples

genomic pcr additional cat linkage direct heteroduplex
Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

Full-text index only

Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

peripheral genomic ebv-transformed conformation pira-pcr rt-pcr
miRBase: tools for microRNA genomics.

PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

Full-text index only

miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

species utrs genomic chromosome genome-wide target transcription

Experiments

The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

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.

Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

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

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

Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Thirty years into the genomics era: tumor viruses led the way.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

GENCODE: producing a reference annotation for ENCODE.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

PRKCA and multiple sclerosis: association in two independent populations.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

miRBase: tools for microRNA genomics.