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 30

System / cell line: fixed ✕ Assay: comparison ✕ Clear

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

Full-text index only

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
Most microsatellite unstable sporadic colorectal carcinomas carry MBD4 mutations.

PMID 11104560 · PMC2363466 · British journal of cancer · 2000 · 8 claims · 2 setups

Full-text index only

MBD4 mutations occur in 89% (17/19) of RER+ sporadic colorectal carcinomas when microdissected tumor sites are analyzed

microdissected frozen pcr comparison
Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

PMID 18416831 · PMC2377273 · BMC cancer · 2008 · 6 claims · 4 setups

Full-text index only

Three protein spots were significantly altered in abundance between metastase-positive and metastase-negative breast cancer patient groups

excised formalin-fixed log-normalized two-dimensional liquid immunohistochemistry
Somatic mutations in RET exons 12 and 15 in sporadic medullary thyroid carcinomas: different spectrum of mutations in sporadic type from hereditary type.

PMID 10622534 · PMC5926019 · Japanese journal of cancer research : Gann · 1999 · 8 claims · 3 setups

Full-text index only

Novel somatic point mutations and an in-frame deletion were identified in RET exons 12 and 15 in sporadic MTC

formalin-fixed corresponding sporadic pcr clinical
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

Full-text index only

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
Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

PMID 16426447 · PMC1373649 · BMC medical genetics · 2006 · 7 claims · 4 setups

Full-text index only

MSI status can be determined in the absence of proband non-tumor tissue by comparing tumor alleles to alleles carried by the proband's progenitors

proband's peripheral hmsh2 microsatellite direct targeted
BRAF, KRAS and PIK3CA mutations in colorectal serrated polyps and cancer: primary or secondary genetic events in colorectal carcinogenesis?

PMID 18782444 · PMC2553419 · BMC cancer · 2008 · 8 claims · 7 setups

Full-text index only

KRAS, BRAF and PIK3CA mutations occur in the majority of colorectal polyps and are mutually exclusive

formalin-fixed colorectal sporadic polyps pcr bisulfite pentaplex
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 6 setups

Has reproduction · 53

spliceJAC quantifies multivariate mRNA splicing from unspliced/spliced count matrices to construct cell state-specific gene-gene (Jacobian) interaction matrices.

two-gene three-gene emt circuit simulation grn scrna-seq
SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PMID 18847484 · PMC2576268 · BMC bioinformatics · 2008 · 7 claims · 8 setups

Full-text index only

SPSmart is a novel tool for accessing and combining large-scale SNP genotype databases with population information

hapmap perlegen stanford michigan snp cross-database chromosome
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

Full-text index only

Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry
PCR-free method detects high frequency of genomic instability in prostate cancer.

PMID 19797393 · PMC2794161 · Nucleic acids research · 2009 · 7 claims · 6 setups

Full-text index only

A novel PCR-free random cloning/sequencing method can detect genomic variants that PCR-based approaches miss in heterogeneous tumor genomes.

blood normal prostate matched pcr-free degenerate-pcr blastn
Iterative class discovery and feature selection using Minimal Spanning Trees.

PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

Full-text index only

Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

simulated breast acute diffuse synthetic cdna microarray
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 80

BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr
Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

PMID 17634103 · PMC1947971 · BMC genomics · 2007 · 8 claims · 4 setups

Full-text index only

A closed-form approximation to the F-test non-centrality parameter (NCP) incorporating genetic model parameters (disease allele frequency, marker allele frequency, prevalence, genotype relative risk, sample size, genetic model, number of pools/replicates, machine variability) can be used to compute power for DNA pooling association studies

modeled analytic factorial power
Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

Full-text index only

LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

surgically tryptic set lysates lc-ms mascot immunohistochemistry
cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer.

PMID 19671129 · PMC2731783 · BMC cancer · 2009 · 8 claims · 6 setups

Full-text index only

cDNA sequencing detects P53 missense mutations in colorectal cancer more frequently and reliably than DNA sequencing

colorectal paired sequencing cdna real-time
A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma.

PMID 18715028 · PMC3769105 · Journal of proteome research · 2008 · 8 claims · 3 setups

Full-text index only

iTRAQ-based quantitative LC-MS/MS proteomics can identify and quantitate differentially expressed proteins between HCC tumor and adjacent noncancerous liver tissue

hcv-associated hcc formalin-fixed itraq western immunohistochemical
Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups

Has reproduction · 96

ID-seq combines antibody-based protein detection with DNA-sequencing of DNA-tagged antibodies to measure large numbers of (phospho-)proteins in many samples in parallel

epidermal fixed skin differentiating id-seq immuno-pcr in-cell-western
Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups

Has reproduction · 59

PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation

quiescent satellite regenerating situ atac-seq rna-seq motif
IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

PMID 11056671 · PMC17813 · Arthritis research · 2000 · 8 claims · 5 setups

Full-text index only

Somatically mutated IgVH genes with amino acid deletions and mixed IgV molecules were found in all three anatomical regions, suggesting a novel pathway for generating (auto)antibody specificities

synovial same cryosections formalin-fixed cdna seminested double

Experiments

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.

Most microsatellite unstable sporadic colorectal carcinomas carry MBD4 mutations.

Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

Somatic mutations in RET exons 12 and 15 in sporadic medullary thyroid carcinomas: different spectrum of mutations in sporadic type from hereditary type.

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

Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

BRAF, KRAS and PIK3CA mutations in colorectal serrated polyps and cancer: primary or secondary genetic events in colorectal carcinogenesis?

spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PCR-free method detects high frequency of genomic instability in prostate cancer.

Iterative class discovery and feature selection using Minimal Spanning Trees.

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer.

A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma.

Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.