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).

• GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

  PMID 18795106 · PMC2532782 · Experimental diabetes research · 2008 · 6 claims · 4 setups

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  GeneSpeed Beta Cell is an online genomics data repository allowing simultaneous multiexperiment viewing and multidimensional (Boolean intersection/union) querying of pancreas- and islet-relevant datasets, integrated with GeneSpeed's domain-based gene categorization.

  embryonic pancreatic panel pituitary affymetrix

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups

  Has reproduction · 67

  A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.

  mammary five singlecellexperiment individual droplet-based quality doublet

• The use of multiple displacement amplification to amplify complex DNA libraries.

  PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

  hes3 hes3-derived coli plasmids isolation flcdna gis-pet

• Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

  PMID 17486137 · PMC2673710 · Molecular systems biology · 2007 · 8 claims · 7 setups

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  Global MudPIT-based proteomic profiling across six mouse lung developmental time points (E13.5–P56) identifies thousands of proteins and captures developmental/cell-biological expression patterns.

  lung analysis embryonic homologues shotgun microarray k-nearest

• 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

• 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

• 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

• 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

• Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

  PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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  Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

  orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection

• Contributions of proteomics to understanding phagosome maturation.

  PMID 18331591 · PMC2613258 · Cellular microbiology · 2008 · 8 claims · 8 setups

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  Proteomic studies across many species have identified hundreds of proteins associated with phagosomes, revealing conserved functional classes (vATPase subunits, GTPases, hydrolases, SNAREs, Rabs, cytoskeletal proteins).

  macrophage dictyostelium drosophila entamoeba quantitative 2dge prefractionation

• Unraveling the histone's potential: a proteomics perspective.

  PMID 18849650 · PMC2662511 · Epigenetics · 2008 · 8 claims · 8 setups

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  Mass spectrometry can determine the full repertoire of histone PTMs, their residue-specific location, and combinatorial patterns without requiring prior knowledge of the modification, unlike antibody-based methods

  histone overexpressed lysate top-down middle-down quantitative

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence

• 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