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 144

System / cell line: pcr ✕ Assay: electrophoresis ✕ Clear

Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish
High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer.

PMID 11207044 · PMC2363776 · British journal of cancer · 2001 · 8 claims · 4 setups

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The SAFB locus region on chromosome 19p13.2-3 shows a very high rate of loss of heterozygosity (LOH) in primary breast cancer, indicating presence of a breast tumour-suppressor gene locus

breast microdissected loh rt-pcr pcr
PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.

PMID 16845094 · PMC1538814 · Nucleic acids research · 2006 · 7 claims · 2 setups

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Selecting primers using the stringent hybridization ratio (requiring an 'executable temperature' where target hybridization ratio >0.99 and off-target ratio <0.05) yields more specific genomic primers than the conventional melting-temperature-based approach, which only guarantees >0.5 vs <0.5

chrx entire multiplex computational
Genomic variability within an organism exposes its cell lineage tree.

PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

robinia arabidopsis randomly genotyping multiplex computer
Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

PMID 19656662 · PMC2744841 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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Pyrosequencing™ can substitute for traditional sequencing methods, providing rapid (<1 h) and reliable detection of antibiotic resistance mutations in P. aeruginosa

clinical extracted pcr fluoroquinolone-resistant kirby–bauer multiplex sanger
A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

PMID 17440616 · PMC1847701 · PloS one · 2007 · 8 claims · 6 setups

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PAMP enriches deletion-breakpoint-spanning DNA because shorter mutant amplicons are preferentially amplified over much longer wild-type sequences when using approximated flanking primer pairs.

detroit serial hs578t pamp individual nested
Genomic and epigenetic instability in colorectal cancer pathogenesis.

PMID 18773902 · PMC2866182 · Gastroenterology · 2008 · 8 claims · 7 setups

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Genomic instability (CIN or MSI) is a key early molecular step in colorectal tumorigenesis that may initiate rather than merely accompany the adenoma-carcinoma sequence

colon embryonic colorectal inter immunohistochemistry karyotype
Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM.

PMID 18565236 · PMC2442058 · BMC medical genetics · 2008 · 7 claims · 6 setups

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The combined LD-PCR/DHPLC diagnostic strategy achieved a 100% mutation detection rate across 122 Taiwanese hemophilia A families.

genomic pcr long-distance pcr sanger
Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

e2348 hep-2 blast colony transformation
RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.

PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups

Has reproduction · 79

RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report

wgs single whole-genome nested capillary
Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology

tigr xanthomonas xcc ann wu-blast whole-genome
MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

PMID 17480217 · PMC1868705 · BMC medical genetics · 2007 · 8 claims · 7 setups

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The MRX87 disease locus maps to the Xp22-p21 interval, a known hot spot region for mental handicap

peripheral genomic pcr leukocytes two-point direct pcr
Differences in the histological findings, phenotypic marker expressions and genetic alterations between adenocarcinoma of the gastric cardia and distal stomach.

PMID 17262083 · PMC2360051 · British journal of cancer · 2007 · 8 claims · 6 setups

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C-Ca is associated with a significantly higher incidence of differentiated-type tumours and lymphatic vessel invasion (LVI) compared with D-Ca

resected c-ca microdissected formalin-fixed histopathological immunohistochemistry pcr-single-strand
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device.

PMID 19053073 · PMC3010182 · Electrophoresis · 2008 · 8 claims · 7 setups

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LDR-FSCE (combining LDR with free-solution conjugate electrophoresis) enables single-base resolution separation of LDR products without a polymer sieving matrix

genomic synthetic k-ras ldr-dt pcr solid-phase ligase
Prognostic significance of p53 and ras gene abnormalities in lung adenocarcinoma patients with stage I disease after curative resection.

PMID 7852188 · PMC5919395 · Japanese journal of cancer research : Gann · 1994 · 6 claims · 5 setups

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Presence of p53 gene abnormalities is associated with shorter disease-free survival in stage I lung adenocarcinoma

formalin-fixed stage pcr-dgge immunohistochemistry pcr-rflp
TP53 mutation analyses on breast carcinomas: a study of paraffin-embedded archival material.

PMID 8761369 · PMC2074687 · British journal of cancer · 1996 · 8 claims · 8 setups

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CDGE can be used to successfully detect TP53 mutations (exons 5-8) in DNA extracted from archival paraffin-embedded breast carcinoma tissue

archival pcr breast tumour pcr-cdge direct restriction
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

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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
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
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer.

PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.

Genomic variability within an organism exposes its cell lineage tree.

Detection of point mutations associated with antibiotic resistance in Pseudomonas aeruginosa.

A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

Genomic and epigenetic instability in colorectal cancer pathogenesis.

Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM.

Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.

Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

Differences in the histological findings, phenotypic marker expressions and genetic alterations between adenocarcinoma of the gastric cardia and distal stomach.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

Ligase detection reaction for the analysis of point mutations using free-solution conjugate electrophoresis in a polymer microfluidic device.

Prognostic significance of p53 and ras gene abnormalities in lung adenocarcinoma patients with stage I disease after curative resection.

TP53 mutation analyses on breast carcinomas: a study of paraffin-embedded archival material.

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

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

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.