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 21

System / cell line: clone ✕ Assay: cloning ✕ Clear

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

mgc cloned orfs genome gateway orf blat
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

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Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

individuals e.coli cerevisiae yeast pcr plasmid phi-29
Shotgun haplotyping: a novel method for surveying allelic sequence variation.

PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

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A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

genomic long pcr ampicillin-resistant long cloning short
Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

PMID 18832376 · PMC2577333 · Nucleic acids research · 2008 · 8 claims · 6 setups

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A novel enhancer trap method retrofitting BACs with Tn10-based transposons enables nontargeted, functional mapping of noncontiguous cis-regulatory elements as zebrafish transgenes.

zebrafish bac genomic transgenic field bac
Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

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Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

synovial ss-derived normal liver rt-pcr cloning densitometric
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

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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
A high throughput method for genome-wide analysis of retroviral integration.

PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

hela ht3 genome chromosomes isf vita sanger
A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

falciparum cloned pyrosequencing pcr
DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

PMID 18628296 · PMC2504308 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Digital PCR compartmentalizes individual bisulfite-converted DNA template molecules into separate wells, enabling single-molecule DNA methylation analysis

fresh-frozen same sssi-methylated mixture digital conventional classic
A biomedically enriched collection of 7000 human ORF clones.

PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

genes mgc plasmid literature pcr sequence
Mutation patterns of mtDNA: empirical inferences for the coding region.

PMID 18518963 · PMC2438339 · BMC evolutionary biology · 2008 · 5 claims · 3 setups

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Heteroplasmy was detected in 6.5% (3/46) of Azorean families analyzed, all caused by new point mutations with no insertions/deletions.

extended-family same direct electropherogram molecular
Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

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Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

falciparum cdna c18 genomic rt-pcr southern genomic
New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

PMID 19948351 · PMC2813930 · Virology · 2010 · 8 claims · 8 setups

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The new CUT primer system detects a broader range of HPV genera/species and novel putative types than the FAP primer system (p<0.01)

skin cloned mixed-type gene nested sequencing molecular
Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX.

PMID 19864251 · PMC2811011 · Nucleic acids research · 2010 · 7 claims · 8 setups

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SPEX-type approaches preferentially access genetic information from damaged, degraded endogenous ancient DNA templates over modern human contaminant DNA

iceman hb50 pe168 lq4 relative pcr spex
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip

Experiments

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

Molecular analysis of Plasmodium ovale variants.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

Shotgun haplotyping: a novel method for surveying allelic sequence variation.

Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish.

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

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

A high throughput method for genome-wide analysis of retroviral integration.

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

A biomedically enriched collection of 7000 human ORF clones.

Mutation patterns of mtDNA: empirical inferences for the coding region.

Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX.

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.