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 16

System / cell line: embryonic ✕ Assay: transcription ✕ Clear

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
Gata-3 and mammary cell fate.

PMID 17381824 · PMC1868924 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Gata-3 is required for formation of mammary placodes during embryonic development

mammary gata-3 k14-cre mmtv-cre microarray lacz cre
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

Has reproduction · 59

Short-term stress and long-term adaptations share common metabolic pathways

great embryonic gef mapk1 bulk gene transcription
Cohesin regulates alternative splicing.

PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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Cohesin regulates alternative splicing independently of its effects on transcription.

hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

normal dld1 beas2b ramos tss comparative
Toward stem cell systems biology: from molecules to networks and landscapes.

PMID 19329576 · PMC2738746 · Cold Spring Harbor symposia on quantitative biology · 2008 · 7 claims · 6 setups

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Stem-cell-fate specification is an extremely complex process regulated by multiple mutually interacting molecular mechanisms with numerous regulatory feedback loops.

stem embryonic promyelocytic genome-wide serial chip-chip
A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

PMID 37277355 · PMC10241789 · Nature communications · 2023 · 8 claims · 8 setups

Has reproduction · 94

2232 genome-wide putative super-enhancers (SEs) were identified in mouse cranial neural crest cell (CNCC) subpopulations

e10.5 embryonic pa2 h3k27ac promoter hi-c
Human microglial cells synthesize albumin in brain.

PMID 18665237 · PMC2483733 · PloS one · 2008 · 8 claims · 8 setups

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Human microglial cells synthesize albumin de novo in the brain.

hmo6 microglial fetal alzheimer's immunocytochemistry immunohistochemistry tandem
Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

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A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

genomic hek293 m17 south sscp dual-luciferase pcr-rflp
Novel insights into adipogenesis from omics data.

PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based
miRGen 2.0: a database of microRNA genomic information and regulation.

PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

lung organ malme embryonic polii small nucleosome
Translation affects mRNA stability in a codon-dependent manner in human cells.

PMID 31012849 · PMC6529216 · eLife · 2019 · 8 claims · 6 setups

Has reproduction · 87

Translation affects mRNA stability in a codon-dependent manner in human cells

293t time-course orfome slam-seq
Epigenetics and phenotypic variation in mammals.

PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

mammalian mhc chromosomes embryonic methylation high-throughput chip
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based
With the finished human genome in hand, what next?

PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

domestic saccharomyces systemic schistosoma comparative functional genetic
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

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

Gata-3 and mammary cell fate.

Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

Cohesin regulates alternative splicing.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

Toward stem cell systems biology: from molecules to networks and landscapes.

A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

Human microglial cells synthesize albumin in brain.

Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

Novel insights into adipogenesis from omics data.

miRGen 2.0: a database of microRNA genomic information and regulation.

Translation affects mRNA stability in a codon-dependent manner in human cells.

Epigenetics and phenotypic variation in mammals.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

With the finished human genome in hand, what next?

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