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 15

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

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.

one nci60 cerevisiae cancer multidimensional cellular two-color
Alexander Meissner: learning the reprogramming code.

PMID 19704017 · PMC2733751 · The Journal of cell biology · 2009 · 8 claims · 6 setups

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A defined set of factors present in oocytes and embryonic stem (ES) cells can reprogram a somatic cell to pluripotency, as shown by nuclear transfer and ES cell/somatic cell fusion experiments

blastocysts somatic fused genomic nuclear inducible fusion
Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.

PMID 15907206 · PMC1156890 · BMC genomics · 2005 · 8 claims · 5 setups

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Regulation of mRNA stability accounts for as much as 50% of all measured changes in polyA mRNA levels, inferred from absence of corresponding nuclear transcription changes.

jurkat nuclear polya single
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
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
Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

brasiliensis gp43 ratio codon-based mutational
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow
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
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

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A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

upstream co-expression pre-b microarray-based motif gene
Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

genomic postmortem nimhgi esr1 targeted case-control family-based
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
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
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
Dark matter in a deep-sea vent and in human mouth.

PMID 17803764 · PMC2040194 · Environmental microbiology · 2007 · 7 claims · 8 setups

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The first genome sequence from the uncultured TM7 phylum was obtained by capturing and sequencing DNA from a single cell using a microfluidic device, yielding a 2.86 Mb assembly with 3245 predicted genes.

uncultured mycoplasma cyanidioschyzon kineococcus single-cell genome whole-genome
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

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

Alexander Meissner: learning the reprogramming code.

Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.

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

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

Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

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

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

Genetic variation in PARL influences mitochondrial content.

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

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

Dark matter in a deep-sea vent and in human mouth.

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