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 171

System / cell line: sequencing ✕ Assay: copy ✕ Clear

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

PMID 18438408 · PMC2705838 · Nature genetics · 2008 · 8 claims · 8 setups

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Massively parallel paired-end sequencing can characterize somatic and germline structural rearrangements to base-pair resolution across a whole cancer genome

nci-h2171 nci-h1770 massively genomic rt-pcr
Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

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LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm
Personalized copy number and segmental duplication maps using next-generation sequencing.

PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.

genomes genomic interphase na18507 whole-genome array fluorescence
Mutation in mitochondrial complex I ND6 subunit is associated with defective response to hypoxia in human glioma cells.

PMID 15248896 · PMC481082 · Molecular cancer · 2004 · 8 claims · 8 setups

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An unreported T14634C mutation in the mtDNA-encoded ND6 subunit of Complex I is present in the hypoxia-sensitive glioma cell line M010b but not in hypoxia-tolerant lines.

gbm m010b m006x mtdna quantitative mitochondrial
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
Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.

PMID 34498918 · PMC8428246 · Microbiology resource announcements · 2021 · 7 claims · 7 setups

Has reproduction · 80

Complete chromosome-scale genome sequence of Leishmania (Mundinia) enriettii isolate CUR178, strain LV763 was assembled using combined short-read and long-read sequencing

leishmania whole-genome long-read genome
Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

PMID 17626639 · PMC1952070 · BMC cancer · 2007 · 7 claims · 4 setups

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EGFR mutations (exon 19 deletions, exon 21 L858R) did not correlate with gefitinib response in this cohort

microdissected formalin-fixed archival clinical pcr fluorescence laser
Probing the cancer genome.

PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

mcf-7 tumor lung oral sanger solexa gistic
Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects syndrome.

PMID 17033964 · PMC1698567 · American journal of human genetics · 2006 · 7 claims · 4 setups

Has reproduction · 75

Heterozygous de novo point mutations in HCCS (missense p.R217C and nonsense p.R197X) cause X-linked dominant MLS in females with normal karyotypes

patients family saccharomyces cho-k1 mutation deletion yeast
Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 5 setups

Has reproduction · 75

Stage-stratified molecular subclassification of Ta and T1 tumors provides greater biological understanding and more clinically meaningful information than subtypes derived from all NMIBCs combined.

stage tumors copy genome-wide whole-exome
Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

PMID 40936936 · PMC12420628 · Frontiers in immunology · 2025 · 7 claims · 8 setups

Has reproduction · 71

A highly stem-like C0 MAFF+ tumor cell subtype dominates invasive LUAD, producing chemokines and activating lipid metabolism

luad tumor a549 single-cell infercnv pseudotime
Alteration of the copy number and deletion of mitochondrial DNA in human hepatocellular carcinoma.

PMID 15150555 · PMC2409531 · British journal of cancer · 2004 · 8 claims · 5 setups

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mtDNA copy number and the content of mitochondrial respiratory proteins are reduced in HCC tumor tissue compared with corresponding non-tumorous liver.

hcc competitive quantitative immunoblot
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
Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

PMID 18772890 · PMC2671642 · Nature · 2008 · 8 claims · 5 setups

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NF1 is a genuine human glioblastoma suppressor gene, inactivated by mutation, deletion, or expression loss in at least 23% of GBM samples

glioblastoma gbm matched sequenced copy gene methylation
Sequencing the regulatory genome.

PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

interphase nine beta-globin drosophila nuclear digital chip
Epidermal growth factor receptor structural alterations in gastric cancer.

PMID 18199332 · PMC2244615 · BMC cancer · 2008 · 8 claims · 4 setups

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EGFR structural alterations are rare in gastric carcinoma

gastric genomic direct fluorescence pcr
A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

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A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

family k4425 embryonic scn9a-n641y linkage copy deletion
Understanding incidental findings in the context of genetics and genomics.

PMID 18547195 · PMC2581745 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 3 setups

Full-text index only

No consensus exists on researchers' responsibilities to disclose individual genetic/genomic research results to participants.

individual population whole-genome genome-wide
Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups

Has reproduction · 76

FOXM1 and RHNO1 are head-to-head bidirectional genes co-amplified and co-expressed in HGSC, regulated by a shared bidirectional promoter (F/R-BDP).

tcga ft282 fte hgsc copy expression rt-qpcr
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

Has reproduction · 85

Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

normal er+ epithelial malignant single-cell spatial copy

Experiments

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

Personalized copy number and segmental duplication maps using next-generation sequencing.

Mutation in mitochondrial complex I ND6 subunit is associated with defective response to hypoxia in human glioma cells.

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

Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.

Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

Probing the cancer genome.

Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects syndrome.

Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

Alteration of the copy number and deletion of mitochondrial DNA in human hepatocellular carcinoma.

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

Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Sequencing the regulatory genome.

Epidermal growth factor receptor structural alterations in gastric cancer.

A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

Understanding incidental findings in the context of genetics and genomics.

Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.