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 14

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

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
RNA structure maps across mammalian cellular compartments.

PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

Has reproduction · 45

icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.

v6.5 mes icshape rt-qpcr western
Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

PMID 17127212 · PMC5054077 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 6 setups

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GMFG is a cytokine-responsive protein in EPO-induced (erythroid) and G-CSF-induced (myeloid) hematopoietic lineage development

ac133+ excised e14 tissues 2-de lc-ms rt-pcr
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
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
Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 8 setups

Has reproduction · 19

Shared differentially expressed genes link glioblastoma with ischemic stroke and with moyamoya disease, revealing molecular associations among the diseases.

glioblastoma ischemic moyamoya shared bulk microarray gene
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
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

Has reproduction · 91

175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

one sinensis small-molecular-weight leaves small genome mirna
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
Genetic architecture of natural variation of cardiac performance from flies to humans.

PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

Has reproduction · 74

Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

drosophila dgrp gene induced high-speed genome-wide epistasis
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
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
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

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

RNA structure maps across mammalian cellular compartments.

Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

Cohesin regulates alternative splicing.

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

Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

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

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

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

Genetic architecture of natural variation of cardiac performance from flies to humans.

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

Novel insights into adipogenesis from omics data.

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.