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 23

System / cell line: nuclear ✕ Assay: tagged ✕ Clear

The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL.

PMID 17519046 · PMC1890283 · BMC cell biology · 2007 · 8 claims · 8 setups

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Deletion of the first 29 N-terminal amino acids (Bax 30-192) causes constitutive mitochondrial accumulation and high cytotoxicity that is poorly inhibited by Bcl-xL or Bcl-2.

jurkat drosophila hek apoptotic uas-gal4 western
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
Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

PMID 18987626 · PMC2656577 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 5 setups

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DNM1 SNP rs3003609 is significantly associated with Smoking Quantity (SQ) and Heaviness of Smoking Index (HSI) in the European-American (EA) sample, surviving correction for multiple testing.

nuclear same sh-sy5y snp haplotype-based quantitative
Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

PMID 19912651 · PMC2784748 · BMC cell biology · 2009 · 7 claims · 7 setups

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hnRNP L is a novel Sam68-interacting protein partner identified by proteomics and confirmed by co-immunoprecipitation

lncap hek293 nih3t3 co-immunoprecipitation sucrose indirect
Proteomic analysis of the mammalian nuclear pore complex.

PMID 12196509 · PMC2173148 · The Journal of cell biology · 2002 · 8 claims · 7 setups

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Mass spectrometry was used to identify all proteins present in a biochemically purified rat liver NPC fraction.

liver empigen transiently mass sds-page electron
Functional analysis of human mutations in homeodomain transcription factor PITX3.

PMID 17888164 · PMC2093940 · BMC molecular biology · 2007 · 7 claims · 5 setups

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Both S13N and G219fs mutants show partial loss-of-function in DNA-binding and/or transactivation activity, with G219fs more severely affected than S13N

lens western immunocytochemistry electrophoretic
The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

PMID 17438525 · PMC2669504 · Molecular vision · 2007 · 8 claims · 8 setups

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NR2E3 LBD fused to a heterologous Gal4 DBD mediates dose-dependent transcriptional repression on Gal4-responsive reporters.

cos-1 hela luciferase western electrophoretic
Mutational analysis of steroidogenic factor 1 (NR5a1) in 24 boys with bilateral anorchia: a French collaborative study.

PMID 17940071 · PMC2990861 · Human reproduction (Oxford, England) · 2007 · 8 claims · 7 setups

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A novel heterozygous V355M missense mutation in SF1 was identified in one boy with micropenis and testicular regression syndrome (bilateral anorchia)

peripheral tsa201 tm3 cho sanger transient mammalian
Mutational analysis of p80 coilin indicates a functional interaction between coiled bodies and the nucleolus.

PMID 7490287 · PMC2200013 · The Journal of cell biology · 1995 · 8 claims · 7 setups

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p80 coilin plays an important role in subnuclear organization and there is a functional interaction between coiled bodies and nucleoli

multi-tissue rabbit hela northern transcription western
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

PMID 16209721 · PMC1262696 · BMC biology · 2005 · 8 claims · 9 setups

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hLsg1 is the human orthologue of yeast Lsg1p and defines a family of circularly permuted GTPases named YRG (YlqF Related GTPases)

multi-species recombinant immunoprecipitated hela phylogenetic gtp gtpase
Phosphoproteomics: new insights into cellular signaling.

PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

yeast hela beta2-adrenergic erk phosphopeptide targeted silac
NovelFam3000--uncharacterized human protein domains conserved across model organisms.

PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining
Evolution of organelle-associated protein profiling.

PMID 19110081 · PMC2680700 · Journal of proteomics · 2009 · 8 claims · 8 setups

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Traditional biochemical organelle isolation followed by MS cataloguing suffers high false-positive rates because organelles cannot be purified to homogeneity and are structurally heterogeneous

golgi nuclear lipid clathrin-coated density qualitative silac
A haplotype variation affecting the mitochondrial transportation of hMYH protein could be a risk factor for colorectal cancer in Chinese.

PMID 18811933 · PMC2565682 · BMC cancer · 2008 · 7 claims · 2 setups

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The hMYH haplotype T/A variant allele is present at significantly higher frequency in CRC patients than in healthy controls

peripheral cos-7 dhplc immunofluorescence
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
Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.

PMID 34795257 · PMC8602323 · Nature communications · 2021 · 8 claims · 12 setups

Has reproduction · 67

PYK2 was identified as a putative IRF5 kinase via a kinase inhibitor library screen in macrophages

raw264.7 hektlr4 hoxb8-derived colon kinase co-immunoprecipitation co-ip
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 74

ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

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PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

subset drosophila ensembl lc-ms icat peptide-to-genome
Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

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IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin
Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.

PMID 18302774 · PMC2266716 · BMC medical genetics · 2008 · 8 claims · 4 setups

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The SNF2L gene spans 77 kb and is encoded by 25 exons that undergo alternative splicing to generate multiple distinct transcripts.

lines genomic 293hek rt-pcr genomic indirect

Experiments

The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL.

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

Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

Proteomic analysis of the mammalian nuclear pore complex.

Functional analysis of human mutations in homeodomain transcription factor PITX3.

The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

Mutational analysis of steroidogenic factor 1 (NR5a1) in 24 boys with bilateral anorchia: a French collaborative study.

Mutational analysis of p80 coilin indicates a functional interaction between coiled bodies and the nucleolus.

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

Phosphoproteomics: new insights into cellular signaling.

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

Evolution of organelle-associated protein profiling.

A haplotype variation affecting the mitochondrial transportation of hMYH protein could be a risk factor for colorectal cancer in Chinese.

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

Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.