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 24

System / cell line: products ✕ Assay: derived ✕ Clear

Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

Has reproduction · 100

iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein
Ontological visualization of protein-protein interactions.

PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

gene interacting interaction annotation yeast co-immunoprecipitation
Minisequencing mitochondrial DNA pathogenic mutations.

PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

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A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

blood-derived same genomic pcr minisequencing automatic multiplex
A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

PMID 18629826 · PMC2697596 · Human mutation · 2008 · 8 claims · 5 setups

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A novel 154-bp mtDNA control region deletion (m.16154_16307del154) was identified in a healthy family

blood-derived mtdna pcr fragment mtdna
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant
V-MitoSNP: visualization of human mitochondrial SNPs.

PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface

blood blood-derived mtdna standard agarose rflp
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational
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
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
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

PMID 17299583 · PMC1797623 · PloS one · 2007 · 6 claims · 4 setups

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5′-tagged PCR primers enable pooling of homologous PCR products from multiple sources into a single GS20 run with accurate post-hoc assignment of sequences to source

extracts pooled same non-assigned pcr parallel conventional
The use of multiple displacement amplification to amplify complex DNA libraries.

PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

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MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

hes3 hes3-derived coli plasmids isolation flcdna gis-pet
Genetic variation of SARS coronavirus in Beijing Hospital.

PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

clinical extracted rna-derived cloned nested screening direct
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

dog hamster pcr primer pcr blast sequence
Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy.

PMID 17428346 · PMC1855920 · BMC medical genetics · 2007 · 7 claims · 5 setups

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Two novel missense mutations in the myostatin gene (p.95D>H and p.156L>I) were identified in Japanese DMD patients

genomic pcr elbow peripheral pcr subcloning gel
Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

PMID 18974839 · PMC2572839 · PloS one · 2008 · 7 claims · 6 setups

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Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients

ileal p16s otu pseudomonas nested cloning
Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

PMID 10551321 · PMC5926156 · Japanese journal of cancer research : Gann · 1999 · 8 claims · 6 setups

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6 of 10 glioma cell lines examined showed MMAC1 mutations with presumed loss of heterozygosity (LOH)

glioma pcr northern rt-pcr sscp
Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

PMID 15496254 · PMC3320417 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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SFG Rickettsia infection prevalence in Maryland D. variabilis was 3.8% (15/392)

dermacentor tick-derived glta field pcr single sequencing
Continued colonization of the human genome by mitochondrial DNA.

PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

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NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

homo genomic chimpanzee genome genome-wide pcr sanger
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
Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

coli plasmids plasmid white plasmid sequencing non-b

Experiments

Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

Ontological visualization of protein-protein interactions.

Minisequencing mitochondrial DNA pathogenic mutations.

A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

Predicting failure rate of PCR in large genomes.

V-MitoSNP: visualization of human mitochondrial SNPs.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

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

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

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

The use of multiple displacement amplification to amplify complex DNA libraries.

Genetic variation of SARS coronavirus in Beijing Hospital.

Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy.

Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

Continued colonization of the human genome by mitochondrial DNA.

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

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.