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 255

System / cell line: including ✕ Clear

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
Novel mutations in TARDBP (TDP-43) in patients with familial amyotrophic lateral sclerosis.

PMID 18802454 · PMC2527686 · PLoS genetics · 2008 · 8 claims · 6 setups

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Three heterozygous missense mutations (p.M337V, p.N345K, p.I383V) in exon 6 of TARDBP were identified in familial ALS patients

patients nd10588 lymphoblastoid neuroglioma sanger taqman copy-number
GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

PMID 18795106 · PMC2532782 · Experimental diabetes research · 2008 · 6 claims · 4 setups

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GeneSpeed Beta Cell is an online genomics data repository allowing simultaneous multiexperiment viewing and multidimensional (Boolean intersection/union) querying of pancreas- and islet-relevant datasets, integrated with GeneSpeed's domain-based gene categorization.

embryonic pancreatic panel pituitary affymetrix
Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups

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RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)

u937 saos-2 chip-chip chip-on-chip gene
Kinetoplastid genomics: the thin end of the wedge.

PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

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Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

brucei major cruzi kinetoplastid whole-genome gene shotgun
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

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High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

tuberculosis sanger spectra lc-ms sds-page signal
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

PMID 18500686 · PMC2516917 · The Prostate · 2008 · 8 claims · 5 setups

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Identified 32 genes (38 cDNAs) with an expression pattern of highest levels in seminal vesicle, lower in normal prostate, and lowest in prostate cancer

normal prostate microarray cdna cross-tissue gene
Clinical characterization and the mutation spectrum in Swedish adenomatous polyposis families.

PMID 18433509 · PMC2386495 · BMC medicine · 2008 · 8 claims · 8 setups

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A combination of mutation-screening techniques (PTT, SSCP/HD, D-HPLC, sequencing, MLPA, mosaicism analysis, expression analysis) achieved a 100% mutation detection frequency in classical FAP

peripheral genomic cdna truncation sscp d-hplc
OptiType: precision HLA typing from next-generation sequencing data.

PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

Has reproduction · 95

OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome
Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

PMID 19949810 · PMC2865568 · Journal of neurology · 2010 · 7 claims · 4 setups

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CNVs are a rare cause of non-CMT1A Charcot-Marie-Tooth disease

unrelated genomic mtmr2 array quantitative sanger
Visualization of shared genomic regions and meiotic recombination in high-density SNP data.

PMID 19696932 · PMC2725774 · PloS one · 2009 · 8 claims · 7 setups

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SNPduo is a command-line (SNPduo++) and web-accessible tool that analyzes and visualizes relatedness between two individuals using identity by state (IBS) from SNP genotypes.

trio family siblings synthetic snp synthetic mitochondrial
Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

paired list differentially oscc 2-de gene interaction
Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation
Segmented filamentous bacteria are worldwide human gut commensals.

PMID 41786702 · PMC13153320 · Nature communications · 2026 · 8 claims · 8 setups

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Identification and morphological/genomic characterization of a novel human SFB species, Anisomitus miae (Human-SFB-ML), from Malian/Gambian/Kenyan fecal samples, displaying SFB-specific morphology including the attachment tip structure

fecal sfb human-sfb-ml publicly pacbio maximum gram
Human-scATAC-Corpus: a comprehensive database of scATAC-seq data.

PMID 41296545 · PMC12807747 · Nucleic acids research · 2026 · 8 claims · 6 setups

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Human-scATAC-Corpus is a comprehensive database of human scATAC-seq data comprising 5,407,621 cells from 35 datasets across 37 tissues or cell lines

tissues scatac-seq five subset scatac-seq genome unified
The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus.

PMID 41495958 · PMC12917471 · The New phytologist · 2026 · 7 claims · 8 setups

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GpaV^vrn, derived from Solanum vernei, is the major resistance source shared by all tested resistant commercial potato varieties, indicating a narrow genetic basis of potato resistance to G. pallida

field pallida potato standard small serial
Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

Has reproduction · 75

A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

mcf7 promoter gene signals pol-ii clustering transcription
Radiogenomics predicts immune microenvironment heterogeneity and response to combination immunotherapy in hepatocellular carcinoma.

PMID 41555384 · PMC12895822 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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A parsimonious 2-gene immune-related signature (IRS = 0.425×KPNA2 + 0.302×SMG5) is significantly associated with immune heterogeneity and response to ICI plus anti-angiogenic combination therapy in HCC

hcc gse202642 paired hcc-derived bulk single-cell immunohistochemistry
FAP expression as a marker of malignant transformation enabling in vivo characterization in peripheral nerve sheath tumors: a multimodal and translational study.

PMID 41591566 · PMC12847211 · Acta neuropathologica · 2026 · 8 claims · 7 setups

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FAP is consistently upregulated in MPNSTs compared to neurofibromas at the transcript level across independent bulk datasets

archival tcga peripheral nf-1-associated bulk spatial single-cell

Experiments

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

Novel mutations in TARDBP (TDP-43) in patients with familial amyotrophic lateral sclerosis.

GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

Kinetoplastid genomics: the thin end of the wedge.

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

Clinical characterization and the mutation spectrum in Swedish adenomatous polyposis families.

OptiType: precision HLA typing from next-generation sequencing data.

Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

Visualization of shared genomic regions and meiotic recombination in high-density SNP data.

Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

Segmented filamentous bacteria are worldwide human gut commensals.

Human-scATAC-Corpus: a comprehensive database of scATAC-seq data.

The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus.

Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

Radiogenomics predicts immune microenvironment heterogeneity and response to combination immunotherapy in hepatocellular carcinoma.

FAP expression as a marker of malignant transformation enabling in vivo characterization in peripheral nerve sheath tumors: a multimodal and translational study.