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: nuclear ✕ Assay: region ✕ Clear

Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

PMID 16061936 · PMC1182164 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Oct-1, Oct-2, PU.1, Sp1 and Sp3 interact in vitro with the pol gene HS7 region

nuclear spodoptera hiv-infected nih3t3 electrophoretic supershift emsa
Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

PMID 14970870 · PMC3215949 · British journal of cancer · 2004 · 8 claims · 7 setups

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Nuclear β-catenin expression in GEJ adenocarcinoma cell lines correlates with enhanced TCF-mediated reporter gene transcription

gej paired showing tumours tcf pcr-sscp bidirectional
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
Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.

PMID 19844255 · PMC2824775 · European journal of human genetics : EJHG · 2010 · 7 claims · 7 setups

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A locus on chromosome 16q23-24 affects HDL-C levels in two independent French-Canadian family studies (QUE and SLSJ)

que slsj candidate skin genome-wide sanger tagging
Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

PMID 17446074 · PMC1885954 · Current biology : CB · 2007 · 8 claims · 8 setups

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Newly synthesized ribosomal proteins accumulate in nucleoli more quickly than other nucleolar proteins

hela post-mitotic pulsed fluorescence selective
A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

PMID 17222328 · PMC1784097 · BMC cancer · 2007 · 7 claims · 8 setups

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A workflow combining Alohomora, Mega2, MENDEL, SNPLINK and SimWalk2 enables linkage analysis with high-density SNP arrays in large pedigrees (>35-40 bits) that exceed the capacity of single existing programs

peripheral pedigree nuclear family snp two-point multipoint
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 the REST regulon reveals extensive transposable element-mediated binding site duplication.

PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

fibroblast hela hek293 set genome-wide electrophoretic rt-pcr
Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

PMID 33999949 · PMC8158866 · PLoS pathogens · 2021 · 8 claims · 8 setups

Has reproduction · 80

MCPyV generates two circular RNAs (circALTO1, circALTO2) spanning the early region/ALTO ORF, detectable in VP-MCC cell lines and patient tumors

mcpyv-infected vp-mcc waga mcc rna-seq inverse qrt-pcr
p53 mutations in cervical carcinogenesis--low frequency and lack of correlation with human papillomavirus status.

PMID 8142262 · PMC1968818 · British journal of cancer · 1994 · 7 claims · 6 setups

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Somatic mutation in the p53 gene hotspot regions occurs infrequently in cervical carcinomas

cervical tumour paired hpv-positive immunocytochemistry pcr sequencing
The gentle art of gene arrangement: the meaning of gene clusters.

PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

populations mhc interphase cartilaginous sequence codon comparative
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
Profiling human androgen receptor mutations reveals treatment effects in a mouse model of prostate cancer.

PMID 19010817 · PMC2748651 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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Somatic AR mutations in h/mAR-TRAMP tumors are non-random and their genomic location correlates with treatment type (castration/antiandrogen vs intact).

mar-tramp testis cv-1 ar-negative immunohistochemistry serum survival
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

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PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

PMID 36373634 · PMC9723646 · Nucleic acids research · 2022 · 8 claims · 8 setups

Has reproduction · 68

Specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells (OSCs)

drosophila ovarian osc melanogaster chip-seq sirna western
Mutations in APC, CTNNB1 and K-ras genes and expression of hMLH1 in sporadic colorectal carcinomas from the Netherlands Cohort Study.

PMID 16356174 · PMC1334229 · BMC cancer · 2005 · 8 claims · 5 setups

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CTNNB1 mutations at phosphorylation sites are rare and of minor importance in sporadic colorectal cancer

archival colorectal formalin-fixed tumour mutation immunohistochemistry microsatellite
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
The many uses of a genome sequence.

PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

recombinant mammalian chromosome chimpanzee x-ray quantitative tiling
Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

PMID 41253754 · PMC12627582 · Nature communications · 2025 · 7 claims · 8 setups

Has reproduction · 10

Fetal Gli1+ cells (including cells outside the cartilage) are the precursors of postnatal long-lived chondroprogenitors and give rise to most growth-plate chondrocytes juvenile/adult.

fetal left-cart-p21moe growth gli1creer single-nuclei bulk cre-based
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular

Experiments

Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

Sequencing the regulatory genome.

Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.

Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

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

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

p53 mutations in cervical carcinogenesis--low frequency and lack of correlation with human papillomavirus status.

The gentle art of gene arrangement: the meaning of gene clusters.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Profiling human androgen receptor mutations reveals treatment effects in a mouse model of prostate cancer.

Genetic variation in PARL influences mitochondrial content.

Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

Mutations in APC, CTNNB1 and K-ras genes and expression of hMLH1 in sporadic colorectal carcinomas from the Netherlands Cohort Study.

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

The many uses of a genome sequence.

Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.