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 20

System / cell line: genome-wide ✕ Assay: luciferase ✕ Clear

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
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
VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING.

PMID 41820368 · PMC13121600 · Nature communications · 2026 · 8 claims · 8 setups

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CBFB (CBF-β) is a synthetic lethal interactor of VHL in ccRCC cell lines

786o ccrcc tcga genome-wide competitive immunoblot
Translating genome sequences into biological understanding.

PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups

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Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.

embryonic transfectable drosophila computational gene-trap pooled cross-species
Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

hela protein-free dual-luciferase reporter thermodynamic
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis
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
Viral and host determinants of RNA virus vector replication and expression.

PMID 15734041 · PMC7115378 · Vaccine · 2005 · 7 claims · 4 setups

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BMV RNA replication occurs in a virus-induced, membrane-bounded compartment rather than in the open cytoplasm.

bmv saccharomyces wild-type immunogold genome-wide northern
The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

PMID 30899024 · PMC6428865 · Nature communications · 2019 · 8 claims · 8 setups

Has reproduction · 85

Xrn1 promotes translation of a specific group of transcripts encoding membrane proteins

cerevisiae western renilla polysome
PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 8 claims · 8 setups

Has reproduction · 76

Drug repurposing screen of the LINCS transcriptional signature database identified PI3K/mTOR/Akt inhibitors as the most prominent pharmacological class capable of repressing REDD1/FKBP51 expression.

keratinocytes hacat skin ear computational rt-pcr western
An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

Has reproduction · 88

SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

kidney tubuloids immunodeficient tub rt-qpcr western histology
Cis-Regulation of the CFTR Gene in Pancreatic Cells.

PMID 40332394 · PMC12027686 · International journal of molecular sciences · 2025 · 7 claims · 8 setups

Has reproduction · 50

Multiple active CREs exist upstream and downstream of the CFTR gene in pancreatic (Capan-1) cells, identified via ATAC-seq, CUT&RUN-seq (H3K27ac), 4C-seq, and the ABC model

capan-1 caco-2 hepg2 atac-seq cut&run-seq 4c-seq
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

rt4d6 gst-sox10 microarray comparative real
Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

prostate subset lncap 22rv1 microrna quantitative western
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
Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

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DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

cd19+ leukemia raji jurkat quantitative cobra chromatin
Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

PMID 18443592 · PMC2742198 · Nature genetics · 2008 · 8 claims · 8 setups

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Osteoglycin (Ogn) is a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM

heart ogn cos-1 neonatal eqtl quantitative genome-wide
Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

sporadic wilms fetal 293t loh multiplex genome-wide
Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

PMID 42246540 · PMC13249099 · Investigative ophthalmology & visual science · 2026 · 8 claims · 7 setups

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ATF4 and BACH1 are identified as bZIP protein interactors of NRL

y2hgold hek293 p28 flow-sorted yeast co-immunoprecipitation immunofluorescence

Experiments

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

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

VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING.

Translating genome sequences into biological understanding.

Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

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

Viral and host determinants of RNA virus vector replication and expression.

The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

PI3K inhibitors protect against glucocorticoid-induced skin atrophy.

An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

Cis-Regulation of the CFTR Gene in Pancreatic Cells.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

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

Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.

Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.