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 70

System / cell line: normalized ✕ Assay: number ✕ Clear

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

normalized individuals subset same affymetrix fluorescent snp
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

Has reproduction · 57

Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

cast inbred gfp mescs single-cell smfish flow
Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

normalized rainbow salmonids microsatellite sanger pcr
Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

Has reproduction · 94

Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

user-submitted string pubmed protein-coding gene hierarchical text-mining
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide
Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

PMID 15842735 · PMC1087844 · BMC medical genetics · 2005 · 7 claims · 3 setups

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MLPA was cheaper, more accurate and more precise than Real-Time PCR for detecting LDL receptor gene deletions

genomic real-time multiplex long-range
SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

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SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

chromosome 16p array probe-by-probe sw-array
MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

pooled genomic aneuploid dog mlga
Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

PMID 19969118 · PMC2821965 · Vaccine · 2010 · 7 claims · 8 setups

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rMVA expressing multiple antigens under the mH5 promoter exhibit remarkable genetic stability and maintain potent immunogenicity after serial passage

rmva-infected individually bhk-21 pbmc qpcr western southern
Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay.

PMID 16507671 · PMC1385994 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Gamma radiation increases L1 retrotransposition frequency in cultured cells

143b cho-k1 retrotransposition immunofluorescence quantitative
Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

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

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

buccal subject ttge real-time pcr-based
Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups

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Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.

peripheral array custom snp
Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

Has reproduction · 93

An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

hff mrc5 chip-qpcr rt-qpcr chipseq
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

Has reproduction · 93

Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based
Wiggle-predicting functionally flexible regions from primary sequence.

PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups

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A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).

hiv bovine calmodulin nonredundant gaussian gnm support
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

PMID 18980691 · PMC2612029 · BMC genomics · 2008 · 8 claims · 8 setups

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mtDNA depletion confers specific, shared gene expression profiles in A549 cells grown in culture and as xenografts

a549 growth oxygen mtdna
Optimizing sample handling for urinary proteomics.

PMID 18662026 · PMC5451898 · Journal of proteome research · 2008 · 7 claims · 4 setups

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The method of protein extraction (lyophilization, ethanol precipitation, ultrafiltration, reverse-phase trapping column) does not alter the urinary proteome at the protein or peptide level

urine bradford sds-page
Stabilizing mutation of CTNNB1/beta-catenin and protein accumulation analyzed in a large series of parathyroid tumors of Swedish patients.

PMID 18541010 · PMC2435117 · Molecular cancer · 2008 · 8 claims · 5 setups

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The CTNNB1 stabilizing mutation S37A was detected in 6 of 104 (5.8%) sporadic parathyroid adenomas by direct DNA sequencing.

sporadic ctnnb1 paired frozen direct restriction snp
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

Experiments

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay.

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

Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

Wiggle-predicting functionally flexible regions from primary sequence.

mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

Optimizing sample handling for urinary proteomics.

Stabilizing mutation of CTNNB1/beta-catenin and protein accumulation analyzed in a large series of parathyroid tumors of Swedish patients.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.