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 14

System / cell line: independent ✕ Assay: copy-number ✕ Clear

Human and mouse oligonucleotide-based array CGH.

PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

bt474 normal gm01750 mda-mb-468 array fish
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

normalized individuals subset same affymetrix fluorescent snp
Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

Has reproduction · 84

MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

patient-derived tumor single paired single-nucleus infercnv aracne-ap
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

colon gbm cancer dbtrg array pcr colony
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.

PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 8 setups

Has reproduction · 35

ZBTB38 mRNA expression is significantly lower in prostate cancer than in normal/benign prostate tissue, and further reduced in metastatic versus localised tumours

localised tcga taylor metastatic microarray rna-sequencing clinico-pathological
Landscape of allele-specific transcription factor binding in the human genome.

PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups

Has reproduction · 82

A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.

gtrd k562 mcf7 types chip-seq variant bayesian
Challenges and standards in integrating surveys of structural variation.

PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

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There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

genomic hapmap reference independent comparative snp fosmid
Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.

PMID 18769486 · PMC2518524 · PloS one · 2008 · 8 claims · 4 setups

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Unsupervised clustering of expression profiles from 62 medulloblastomas identifies 5 molecular subtypes (A–E)

relapsed medulloblastoma independent expression array targeted
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

lms independent soft gene array immunohistochemistry
Increased DNA microarray hybridization specificity using sscDNA targets.

PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups

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A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA

cuhr k562 input sscdna microarray quantitative capillary
Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

PMID 19650893 · PMC2728732 · BMC evolutionary biology · 2009 · 8 claims · 7 setups

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Autochthonous Berber Y-chromosome lineages E-M81, E-M78 and J-M267 were detected in indigenous Canary Island remains, confirming a North West African origin for the aboriginal ancestors.

prehispanic indigenous ancient modern y-chromosome nested real-time
Paired-end mapping reveals extensive structural variation in the human genome.

PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

genomic na15510 stretched reference paired-end pcr array
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp

Experiments

Human and mouse oligonucleotide-based array CGH.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.

Landscape of allele-specific transcription factor binding in the human genome.

Challenges and standards in integrating surveys of structural variation.

Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

Increased DNA microarray hybridization specificity using sscDNA targets.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

Paired-end mapping reveals extensive structural variation in the human genome.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.