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 27

System / cell line: endogenous ✕ Assay: genome ✕ Clear

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr
Characterization of genome-wide p53-binding sites upon stress response.

PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

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Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

u2os saos-2 chip-on-chip chip-qpcr western
Identification of new ETV6 modulators through a high-throughput functional screening.

PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

Has reproduction · 68

A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

reh genome-wide qrt-pcr chip-seq
The Neandertal genome and ancient DNA authenticity.

PMID 19661919 · PMC2725275 · The EMBO journal · 2009 · 8 claims · 6 setups

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Only direct assays of DNA sequence positions where Neandertals differ from all contemporary humans can reliably estimate human contamination.

neandertal pcr high-throughput genome
Determination of complete chromosomal haplotypes by bulk DNA sequencing.

PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups

Has reproduction · 97

A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts

rpe-1 na12878 aneuploid linked-read hi-c bulk
Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

PMID 18157127 · PMC2397541 · Nature genetics · 2008 · 8 claims · 8 setups

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Homozygous truncating mutations in PCNT cause Seckel syndrome

consanguineous genomic lymphoblastoid lcls snp-microarray sanger immunofluorescence
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

hela hs578t nih3t3 genomic chap-chip conventional scanning
Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

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62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

genome insect yy1-related zinc blast sequence synonymous
Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.

PMID 19043545 · PMC2581785 · PLoS genetics · 2008 · 7 claims · 4 setups

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A GWA study using serum metabolomics identifies SNPs associated with metabolite concentrations, explaining up to 12% of variance for single metabolites

kora fasting genome-wide targeted metabolite
Atrial natriuretic peptide frameshift mutation in familial atrial fibrillation.

PMID 18614783 · PMC2518320 · The New England journal of medicine · 2008 · 7 claims · 5 setups

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A heterozygous frameshift mutation in NPPA (encoding atrial natriuretic peptide, ANP) causes familial atrial fibrillation

family plasma atria genome-wide fine exon
DNA methylation of cancer genome.

PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups

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Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.

embryonic germ heterozygous cancer gene hypomorphic methyltransferase
Recurring mutations found by sequencing an acute myeloid leukemia genome.

PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

aml-m1 tumor bone additional whole-genome snp gene-expression
The changing face of genomics.

PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

yeast drosophila zebrafish elegans chip-chip comparative insertional
CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups

Has reproduction

Genome-wide CRISPR/Cas9 screens in CD40L-stimulated Daudi B cells identify known CD40/NF-κB pathway components plus many novel positive and negative CD40 regulators.

daudi celf1 genome-wide flow immunoblot
Personalized genomic medicine with a patchwork, partially owned genome.

PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

phenotypically single genome chimpanzee molecular diploid encode
Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

Has reproduction · 55

RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

amir-sul col 14-day-old arabidopsis small rna-seq gel
Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups

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The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines

breast universal p53 subset qrt-pcr bioinformatic structure
Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

PMID 18820594 · PMC2905378 · Pharmacogenetics and genomics · 2008 · 7 claims · 8 setups

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The tRNA-Thr G15927A mutation has a potential modifier role that increases penetrance and expressivity of A1555G-associated deafness.

blood genomic lymphoblastoid same pcr-rflp mitochondrial northern
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

PMID 19860899 · PMC2774331 · BMC genomics · 2009 · 8 claims · 6 setups

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HaloCHIP is a functional antibody-free alternative to ChIP that uses covalent capture of HaloTag-fusion protein-DNA complexes on HaloLink resin

hela computational living halochip halochip-chip chip-chip
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr

Experiments

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

Characterization of genome-wide p53-binding sites upon stress response.

Identification of new ETV6 modulators through a high-throughput functional screening.

The Neandertal genome and ancient DNA authenticity.

Determination of complete chromosomal haplotypes by bulk DNA sequencing.

Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.

Atrial natriuretic peptide frameshift mutation in familial atrial fibrillation.

DNA methylation of cancer genome.

Recurring mutations found by sequencing an acute myeloid leukemia genome.

The changing face of genomics.

CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

Personalized genomic medicine with a patchwork, partially owned genome.

Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.