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 23

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

Alteration of the p53 tumor suppressor gene occurs independently of K-ras activation and more frequently in serous adenocarcinomas than in other common epithelial tumors of the human ovary.

PMID 7852189 · PMC5919385 · Japanese journal of cancer research : Gann · 1994 · 7 claims · 4 setups

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p53 gene mutations occur more frequently in serous adenocarcinomas than in other common epithelial ovarian tumors combined

common ovarian restriction sscp direct
Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain.

PMID 15737014 · PMC549606 · PLoS medicine · 2005 · 7 claims · 6 setups

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A secondary EGFR exon 20 mutation (T790M) is found in tumors from patients with acquired resistance to gefitinib or erlotinib

tumor 293t nsclc direct fluorescent rt-pcr
Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.

PMID 19000305 · PMC2586028 · BMC cancer · 2008 · 7 claims · 6 setups

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16 PTP candidate genes containing coding mononucleotide repeats (cMNR) of at least 7 units were identified via bioinformatic analysis and screened in MSI-H cell lines, cancers, and adenomas

msi-h genome colorectal fragment bioinformatic sequencing
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
Mitochondrial DNA mutations in renal cell carcinomas revealed no general impact on energy metabolism.

PMID 16404428 · PMC2361126 · British journal of cancer · 2006 · 6 claims · 5 setups

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Somatic mtDNA mutations occur in renal cell carcinoma but are infrequent and frequently present at low (below 25%) heteroplasmy levels

renal dhplc direct pcr-restriction
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
Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

PMID 34927097 · PMC8649395 · STAR protocols · 2021 · 6 claims · 7 setups

Has reproduction · 50

A combined mechanical and enzymatic dissociation protocol using the gentleMACS Dissociator yields a single-cell suspension from mouse pancreatic tumor tissue suitable for scRNA-seq while preserving cell characteristics

pancreatic dissociated single-cell scrna-seq tumor dead red
Large-scale analysis of mutations in RET exon 16 in sporadic medullary thyroid carcinomas in Japan.

PMID 11429053 · PMC5926749 · Japanese journal of cancer research : Gann · 2001 · 5 claims · 4 setups

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RET exon 16 (codon 918) somatic mutations are rare in sporadic MTC among Japanese patients

paraffin-embedded genomic direct pcr-rflp nested
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
Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

PMID 11429044 · PMC5926751 · Japanese journal of cancer research : Gann · 2001 · 6 claims · 3 setups

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RAD50 (A)9 mononucleotide repeat is frequently frameshift-mutated in MSI-H colorectal cancer cell lines and primary tumors

colorectal same pcr-based msi
A critical reassessment of the role of mitochondria in tumorigenesis.

PMID 16187796 · PMC1240051 · PLoS medicine · 2005 · 8 claims · 8 setups

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A significant number of published medical mtDNA cancer studies are based on obviously flawed sequencing results.

hepatocellular papillary prostate tissues mtdna mutational
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
Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

PMID 16545110 · PMC1475604 · BMC cancer · 2006 · 8 claims · 4 setups

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Smoking is associated with adenoma and CRC development, with the association strongest in tumors lacking APC truncation mutations

formalin-fixed ffpe paired study direct pcr restriction
Methods for genome-wide analysis of DNA methylation in intestinal tumors.

PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

cd19+ lung gpx1 tumor mira medip goldengate
Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples.

PMID 19663459 · PMC2756321 · Journal of proteome research · 2009 · 8 claims · 4 setups

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In ECD MS/MS, isoaspartyl (but not aspartyl) residues produce specific fragments c_n•+58.0054 (C2H2O2) and z_(l-n)-56.9976 (C2HO2), which serve as markers for Asp isomerization

a431 brain ecd cad label-free
Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

Has reproduction

Transposable elements make up nearly 45% of the human genome, vastly exceeding the ~1.5% that is protein-coding.

genome normal drosophila long short-read whole-genome synthetic
Proteomics as a tool for biomarker discovery.

PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

serum laser ovarian seldi-tof two-dimensional gene
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

tumors cancer tumor lung direct database quantitative
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

inhbb cloned same fresh-frozen rnase masscleave clonal
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

Alteration of the p53 tumor suppressor gene occurs independently of K-ras activation and more frequently in serous adenocarcinomas than in other common epithelial tumors of the human ovary.

Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain.

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.

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

Mitochondrial DNA mutations in renal cell carcinomas revealed no general impact on energy metabolism.

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

Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

Large-scale analysis of mutations in RET exon 16 in sporadic medullary thyroid carcinomas in Japan.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

Frameshift mutations at mononucleotide repeats in RAD50 recombinational DNA repair gene in colorectal cancers with microsatellite instability.

A critical reassessment of the role of mitochondria in tumorigenesis.

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

Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

Methods for genome-wide analysis of DNA methylation in intestinal tumors.

Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples.

Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

Proteomics as a tool for biomarker discovery.

Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

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.