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 45

System / cell line: expression ✕ Assay: fragment ✕ Clear

Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

PMID 15138480 · PMC2410281 · British journal of cancer · 2004 · 7 claims · 5 setups

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MBD3 is not a major target of genetic or epigenetic alteration in colon and lung cancer

colon normal pcr-sscp rt-pcr northern
Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

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None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

breast quantitative fragment gene-expression
An integrative genomic and epigenomic approach for the study of transcriptional regulation.

PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups

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Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone

aml computational help chip-chip gene
MDM2 overexpression with alteration of the p53 protein and gene status in oral carcinogenesis.

PMID 10835493 · PMC5926374 · Japanese journal of cancer research : Gann · 2000 · 7 claims · 4 setups

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MDM2 and p53 protein expression significantly increase in accordance with histological progression from normal mucosa to dysplasia to SCC.

oral paraffin-embedded rt-pcr-sscp direct restriction
Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

PMID 18433472 · PMC2386800 · BMC molecular biology · 2008 · 7 claims · 6 setups

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Co-agroinfiltration of ENDO1 and p19 constructs into N. benthamiana leaves gives high-level transient expression of active, mismatch-specific ENDO1 via a simple purification protocol

benthamiana test genomic hiv-1 transient heteroduplex mutation
p53 mutations in cervical carcinogenesis--low frequency and lack of correlation with human papillomavirus status.

PMID 8142262 · PMC1968818 · British journal of cancer · 1994 · 7 claims · 6 setups

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Somatic mutation in the p53 gene hotspot regions occurs infrequently in cervical carcinomas

cervical tumour paired hpv-positive immunocytochemistry pcr sequencing
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide
A distinct epigenetic signature at targets of a leukemia protein.

PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

32d sequence gene bioinformatic real-time
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 ERGIC-53 as an intracellular transport receptor of alpha1-antitrypsin.

PMID 18283111 · PMC2265576 · The Journal of cell biology · 2008 · 8 claims · 6 setups

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α1-antitrypsin is a novel ERGIC-53 cargo protein identified via a YFP protein-fragment complementation assay (PCA) cDNA library screen

cos-1 hela hepg2 ergic-53 yfp sirna [35s]methionine
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

msi-h computational rb1cc1 normal pcr nonlinear real-time
Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

PMID 17442112 · PMC1863428 · BMC cancer · 2007 · 7 claims · 5 setups

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CYYR1 mRNA undergoes a 'subtle' alternative splicing event generating two isoforms (CAG- and CAG+) differing by a single alanine codon at the exon3/exon4 junction

neuroendocrine tumors normal cyyr1 rt-pcr quantitative psti
Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

pooled hcec-dm corneal 2-d western real-time
A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 6 claims · 8 setups

Has reproduction · 76

Hnf4a is a major transcriptional regulator of Dnajc22.

mus tissues liver-specific kidney bulk microarray chip-seq
Complex landscapes of somatic rearrangement in human breast cancer genomes.

PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

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There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

breast subset confirmed paired-end fish exon-exon
Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

PMID 19698114 · PMC2749045 · BMC infectious diseases · 2009 · 8 claims · 7 setups

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Three PRNP mutations—D178N, E200K, and M232R—were identified in heterozygosity in Korean probable CJD patients, marking their first report in this population.

csf 293t genomic pcr western recombinant sequencing
Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups

Has reproduction · 97

The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)

duvernoy's nigriceps rna-seq differential extraction
HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

Has reproduction · 66

HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq
p53 mutations occur in clinical, but not latent, human prostate carcinoma.

PMID 7737911 · PMC5920585 · Japanese journal of cancer research : Gann · 1995 · 5 claims · 4 setups

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p53 point mutations occur in clinical prostate cancer but not in latent (subclinical) prostate carcinoma

prostate sscp rflp direct
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping

Experiments

Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

An integrative genomic and epigenomic approach for the study of transcriptional regulation.

MDM2 overexpression with alteration of the p53 protein and gene status in oral carcinogenesis.

Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

p53 mutations in cervical carcinogenesis--low frequency and lack of correlation with human papillomavirus status.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

A distinct epigenetic signature at targets of a leukemia protein.

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

Identification of ERGIC-53 as an intracellular transport receptor of alpha1-antitrypsin.

Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

p53 mutations occur in clinical, but not latent, human prostate carcinoma.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.