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 32

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

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
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

PMID 34875090 · PMC8887463 · Nucleic acids research · 2022 · 6 claims · 8 setups

Has reproduction · 56

Halo-seq pairs a light-activatable Halo-DBF ligand with Click chemistry to label and purify spatially defined RNA populations in living cells with high spatial specificity (~100 nm radius)

hela apex-seq proximity dot comparative
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
The nuclear pore complex.

PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

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NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a
Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

PMID 15287975 · PMC507878 · Genome biology · 2004 · 8 claims · 6 setups

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3,848 Arabidopsis proteins were identified as likely plant-specific based on phylogenetic profiling and EST confirmation in multiple plant species

arabidopsis phylogenetic tblastn subcellular
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
A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.

hct116 silac silac-based immunofluorescence
Genetic changes of Wnt pathway genes are common events in metaplastic carcinomas of the breast.

PMID 18593979 · PMC3060761 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 6 setups

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Aberrant β-catenin protein expression (nuclear/cytoplasmic accumulation or reduced membrane staining) is present in nearly all metaplastic breast carcinomas, indicating Wnt pathway deregulation.

metaplastic immunohistochemistry pcr
7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress.

PMID 39952919 · PMC11828898 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 93

Heat shock induces de novo transcription and nuclear accumulation of 7SL RNA together with SRP proteins, which then bind chromatin at promoters

embryonic nih3t3 pro-seq fractionation fluorescence
Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

PMID 18160415 · PMC2275099 · Nucleic acids research · 2008 · 8 claims · 8 setups

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HMGB1 is a novel HNF1α-interacting protein identified via a co-IP-MS screening strategy

hepg2 recombinant co-immunoprecipitation immunofluorescence gst
Human protein reference database--2006 update.

PMID 16381900 · PMC1347503 · Nucleic acids research · 2006 · 7 claims · 6 setups

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HPRD is a comprehensive, continually expanded resource cataloging human protein domains, PTMs, protein-protein interactions, and other annotations.

proteins hela nucleolus signaling literature mass subcellular
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
H-DBAS: human-transcriptome database for alternative splicing: update 2010.

PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

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RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

dld-1 rna-seq western real-time
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
Transcriptional and proteomic profiling in a cellular model of DYT1 dystonia.

PMID 19665049 · PMC2774817 · Neuroscience · 2009 · 8 claims · 7 setups

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Accumulation of mutant torsinA(ΔE) in the nuclear envelope is not sufficient to cause transcriptional dysregulation

pc6-3 hek293 microarray 2-dige mass
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

Has reproduction · 57

Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

cast inbred gfp mescs single-cell smfish flow
Direct in-gel fluorescence detection and cellular imaging of O-GlcNAc-modified proteins.

PMID 18683930 · PMC2649877 · Journal of the American Chemical Society · 2008 · 7 claims · 5 setups

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Y289L GalT-mediated transfer of UDP-GalNAz followed by Cu(I)-catalyzed azide-alkyne cycloaddition enables selective, highly sensitive fluorescent/biotin labeling of O-GlcNAc-modified proteins

α-crystallin forebrain hela chemoenzymatic in-gel nanolc-ms
Genomics research and malaria control: great expectations.

PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups

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Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.

plasmodium anopheles malaria whole-genome computational microarray
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

Functional analysis of human mutations in homeodomain transcription factor PITX3.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

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.

The nuclear pore complex.

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

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

A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

Genetic changes of Wnt pathway genes are common events in metaplastic carcinomas of the breast.

7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress.

Proteomic screen defines the hepatocyte nuclear factor 1alpha-binding partners and identifies HMGB1 as a new cofactor of HNF1alpha.

Human protein reference database--2006 update.

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

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Phosphoproteomics: new insights into cellular signaling.

Transcriptional and proteomic profiling in a cellular model of DYT1 dystonia.

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

Direct in-gel fluorescence detection and cellular imaging of O-GlcNAc-modified proteins.

Genomics research and malaria control: great expectations.

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