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 152

System / cell line: mutant ✕ Assay: sequence ✕ Clear

EGenBio: a data management system for evolutionary genomics and biodiversity.

PMID 17118150 · PMC1683573 · BMC bioinformatics · 2006 · 7 claims · 7 setups

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EGenBio is a web-based system for integrated management, filtering, curation, and visualization of large-scale genomic sequences, alignments, and phylogenetic trees for evolutionary genomics and biodiversity research.

vertebrate sequence mutant phylogenetic sequence coevolution saturation
Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

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A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

genomic lca5 lymphocyte affected snp sanger splice
A novel GJA8 mutation causing a recessive triangular cataract.

PMID 18483562 · PMC2375854 · Molecular vision · 2008 · 8 claims · 6 setups

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A homozygous single base-pair insertion (c.776insG) in GJA8 causes a recessive triangular nuclear cataract in two affected siblings.

proband's blood-derived genomic family rt-pcr pcr restriction
Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

armd dutch fibulin pef6-ssflag mutation computational site-directed
Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups

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ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable

pfm selected point-mutation-negative family dhplc bidirectional multiplex
Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

PMID 18616530 · PMC4732719 · Clinical genetics · 2008 · 8 claims · 8 setups

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TMC1 mutations were identified in seven of the families/patients segregating hearing loss linked to DFNA36/DFNB7-11

families affected tmc1 tjp2 genetic sequencing multiplex
Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants.

PMID 17895983 · PMC1976591 · PloS one · 2007 · 8 claims · 5 setups

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Sequencing of complete mtDNA genomes in 23 pediatric patients identified 27 significant variants (12 novel, 15 known) associated with mitochondrial encephalomyopathies.

blood-derived lymphocytes maternal wild-type complete respiratory pcr-rflp
A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese family.

PMID 20019893 · PMC2794658 · Molecular vision · 2009 · 7 claims · 7 setups

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A novel missense mutation c.92T>C (p.I31T) in GJA8 causes autosomal dominant congenital nuclear cataract in this Chinese family

family genomic unrelated gja8 clinical microsatellite sequencing
Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

PMID 17697348 · PMC2042502 · BMC genetics · 2007 · 8 claims · 5 setups

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CTCE eliminates the need for laboratory optimization of separation conditions for each exonic target sequence.

pcr-amplified target exonic cycling ctce
Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

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Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

family additional unrelated mutant direct linkage targeted
Biased exon/intron distribution of cryptic and de novo 3' splice sites.

PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

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Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

disease authentic hek293t nuclear literature shapiro-senapathy splicing
A novel missense mutation in DAX-1 with an unusual presentation of X-linked adrenal hypoplasia congenita.

PMID 17308433 · PMC3479083 · Hormone research · 2007 · 7 claims · 6 setups

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A novel C794G transversion causing missense mutation T265R in DAX1 (NR0B1) is responsible for X-linked adrenal hypoplasia congenita in this kindred

genomic tsa201 unspecified proband sequence modified full-length
Familial hypercholesterolemia in St-Petersburg: the known and novel mutations found in the low density lipoprotein receptor gene in Russia.

PMID 15701167 · PMC551615 · BMC medical genetics · 2005 · 8 claims · 6 setups

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21 rare sequence variations of the LDL receptor gene were identified in St.-Petersburg FH patients, 19 of which are probably pathogenic and 2 (P518P, T705I) neutral.

genomic pcr proband restriction sscp automated
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Use of modified U1 snRNAs to inhibit HIV-1 replication.

PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

hiv-1 293t hela bioinformatic western reporter
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 68

LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

schizosaccharomyces pombe rna-seq lasso lariat-specific
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
MutDB: update on development of tools for the biochemical analysis of genetic variation.

PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

proteins mutdb nonsynonymous genes sequence web functional
Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

PMID 18719945 · PMC2716558 · Human genetics · 2008 · 8 claims · 6 setups

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PCDH15 has an updated gene structure with four additional exons beyond the previously reported 35, producing isoforms in four classes with three alternative cytoplasmic domains (CD1, CD2, CD3).

genomic retina cdna protocadherin str pcr rt-pcr
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow

Experiments

EGenBio: a data management system for evolutionary genomics and biodiversity.

Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

A novel GJA8 mutation causing a recessive triangular cataract.

Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants.

A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese family.

Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

Biased exon/intron distribution of cryptic and de novo 3' splice sites.

A novel missense mutation in DAX-1 with an unusual presentation of X-linked adrenal hypoplasia congenita.

Familial hypercholesterolemia in St-Petersburg: the known and novel mutations found in the low density lipoprotein receptor gene in Russia.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Use of modified U1 snRNAs to inhibit HIV-1 replication.

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

MutDB: update on development of tools for the biochemical analysis of genetic variation.

Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.