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 17

System / cell line: fresh-frozen ✕ Clear

Protein expression patterns in primary carcinoma of the vagina.

PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical
Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 77

Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.

fresh-frozen ffpe breast unc microarray mrna-seq ribo-zero-seq
DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

PMID 18628296 · PMC2504308 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Digital PCR compartmentalizes individual bisulfite-converted DNA template molecules into separate wells, enabling single-molecule DNA methylation analysis

fresh-frozen same sssi-methylated mixture digital conventional classic
Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

fresh-frozen same banked resected array mutational pcr
Rapid detection of allele loss in colorectal tumours using microsatellites and fluorescent DNA technology.

PMID 8512811 · PMC1968523 · British journal of cancer · 1993 · 6 claims · 3 setups

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Fluorescently labelled microsatellite PCR products analysed on an automated DNA sequencer allow rapid, automated quantitation (peak size, height, area) of allele loss, avoiding drawbacks of radioactive RFLP analysis.

fresh-frozen paired pcr genomic fluorescent automated
Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 73

Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

fresh tcga gbm bulk rna-seq consensus
Profiling critical cancer gene mutations in clinical tumor samples.

PMID 19924296 · PMC2774511 · PloS one · 2009 · 7 claims · 4 setups

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OncoMap, a panel of ~400 mass-spectrometric genotyping assays targeting 33 cancer genes, enables robust mutation profiling of clinical fresh-frozen and FFPE tumor DNA.

clinical fresh same pediatric mass sanger barcoded
Rapid detection of SMARCB1 sequence variation using high resolution melting.

PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

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HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

genomic same tumor rhabdoid high direct hrm
Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

PMID 19856998 · PMC2924679 · Journal of proteome research · 2009 · 7 claims · 4 setups

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RCL2/CS100-fixed tissues yield peptide and protein identifications by nanoRPLC-MS/MS comparable to matched fresh-frozen tissues, with proteome coverage not obviously compromised by fixation.

colonic rcl2 colon nanorplc-ms extraction laser
Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

PMID 7577492 · PMC2033953 · British journal of cancer · 1995 · 7 claims · 4 setups

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LOH analysis has higher sensitivity than DNA flow cytometry for detecting unifocal origin of bilateral ovarian tumors

bilateral paraffin-embedded ovarian peripheral loh flow isolation
c-Ki-ras mutations in colorectal adenocarcinomas from a country with a rapidly changing colorectal cancer incidence.

PMID 10496348 · PMC2362864 · British journal of cancer · 1999 · 7 claims · 4 setups

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c-Ki-ras codon 12/13 mutations were found in 28% (14/50) of contemporary (1994-1996) colorectal adenocarcinomas but 0% (0/18) of archival (1962-1966) tumours

archival fresh genomic pcr mismatch-specific pcr sequencing
TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups

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Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)

ovarian sporadic paraffin-embedded mutation survival extraction
Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

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BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

serum-derived tumour serum ht29 arms sanger topo
Mutational spectrum of p53 gene in arsenic-related skin cancers from the blackfoot disease endemic area of Taiwan.

PMID 10362120 · PMC2363055 · British journal of cancer · 1999 · 7 claims · 4 setups

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p53 gene mutation rate is high in arsenic-related skin cancers (39% Bowen's disease, 28.6% BCC, 55.6% SCC)

skin fresh-frozen pcr-sscp direct immunohistochemistry
The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.

PMID 16573809 · PMC1450280 · BMC genomics · 2006 · 7 claims · 8 setups

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MDA-amplified DNA does not introduce major distortion of copy number imbalance assignments compared to unamplified DNA in control CGH experiments.

laser-capture-microdissected normal cancer fresh-frozen array gacgh laser
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
The field of tissue injury in the lung and airway.

PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

Experiments

Protein expression patterns in primary carcinoma of the vagina.

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

Rapid detection of allele loss in colorectal tumours using microsatellites and fluorescent DNA technology.

Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

Profiling critical cancer gene mutations in clinical tumor samples.

Rapid detection of SMARCB1 sequence variation using high resolution melting.

Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

c-Ki-ras mutations in colorectal adenocarcinomas from a country with a rapidly changing colorectal cancer incidence.

TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

Mutational spectrum of p53 gene in arsenic-related skin cancers from the blackfoot disease endemic area of Taiwan.

The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.

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

The field of tissue injury in the lung and airway.