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).

• Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics.

  PMID 17331236 · PMC1868942 · Genome biology · 2007 · 8 claims · 8 setups

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  moDCs and KG-1 cells show significant proteomic differences from primary mDCs, particularly in proteins involved in cell growth/maintenance and cell-cell interaction/integrity.

  mdcs mdc freshly peripheral two-dimensional maldi-tof capture

• Proteomic identification of secreted proteins as surrogate markers for signal transduction inhibitor activity.

  PMID 17211472 · PMC2360009 · British journal of cancer · 2007 · 5 claims · 5 setups

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  Inhibiting EGFR signalling with Gefitinib alters the pattern of proteins secreted by cancer cells, and these changes can serve as an indirect quantitative assay for drug action

  a431 a549 excised gel maldi-tof western

• The current state of proteomics in GI oncology.

  PMID 19104933 · PMC3045515 · Digestive diseases and sciences · 2009 · 8 claims · 8 setups

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  More than 130 exploratory proteomic studies have defined candidate biomarkers in serum, GI fluids, or cancer tissue for GI oncology

  serum laser-capture-microdissected seldi-ms 2-de antibody

• Proteomic surveillance of retinal autoantigens in endogenous uveitis: implication of esterase D and brain-type creatine kinase as novel autoantigens.

  PMID 18552983 · PMC2426731 · Molecular vision · 2008 · 7 claims · 6 setups

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  Six novel candidate retinal autoantigens (β-actin, esterase D, tubulin β-2, brain-type creatine kinase, VDAC, aspartate aminotransferase) were identified by 2D-WB and mass spectrometry in EAU mice

  c57bl retinal recombinant eau two-dimensional maldi-tof one-dimensional

• Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

  PMID 18544707 · PMC2518503 · Diabetes · 2008 · 8 claims · 4 setups

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  None of the selected GWAS-identified SNPs individually were associated with increased diabetes incidence in the DPP cohort

  dpp snp cox oral

• Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

  PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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  Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

  bxpc-3 2-d maldi-tof-ms western

• Comparative analysis of the tear protein profile in mycotic keratitis patients.

  PMID 18385783 · PMC2268856 · Molecular vision · 2008 · 8 claims · 5 setups

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  A glutaredoxin-related protein is expressed only in the tears of fungal keratitis patients and is absent in control tears.

  pooled in-gel peptide 2de two-dimensional maldi-tof post

• Proteomic profiling in ovarian cancer.

  PMID 19955909 · PMC7319026 · International journal of gynecological cancer : official journal of the International Gynecological Cancer Society · 2009 · 8 claims · 6 setups

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  No validated or cost-efficient screening program exists for ovarian cancer; physical exam, CA125, and transvaginal ultrasound lack sufficient sensitivity/specificity for early-stage detection.

  serum tumor rolling mass microarray

• Characterization of detergent-insoluble proteins in ALS indicates a causal link between nitrative stress and aggregation in pathogenesis.

  PMID 19956584 · PMC2780298 · PloS one · 2009 · 8 claims · 8 setups

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  The Triton X-100-insoluble fraction (TIF) from spinal cord of G93A SOD1 mice is enriched in specific proteins (cytoskeletal, chaperone, mitochondrial, metabolic, signaling) compared to WT mice, already at a preclinical stage.

  spinal tif lumbar ventral gel maldi-tof western

• 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

• DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

  PMID 15550986 · PMC529316 · PLoS biology · 2004 · 8 claims · 3 setups

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  The human MHC methylation profile is strongly bimodal, with the vast majority of analysed regions being either hypo- (≤30%) or hypermethylated (≥70%)

  mhc subset heterogeneously bisulphite maldi-ms sub-cloning

• Target SNP selection in complex disease association studies.

  PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

  genes pooled primer computational maldi-tof blast

• A pilot study of proteomic profiles of human hepatocellular carcinoma in the United States.

  PMID 19535095 · PMC2859432 · The Journal of surgical research · 2009 · 8 claims · 3 setups

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  19 protein spots showed significant (>2-fold, P<0.01) abundance differences between HCC tumor and nonmalignant liver tissue

  liver tryptic solubilized gel maldi-tof quantification

• On consensus biomarker selection.

  PMID 17570864 · PMC1892093 · BMC bioinformatics · 2007 · 7 claims · 2 setups

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  Four popular feature ranking criteria (t-statistic, mutual information, peak probability contrasts, random forest variable importance) produce different rankings of the same features on the same dataset.

  serum seldi-tof maldi-tof

• An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

  PMID 15005801 · PMC341449 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  An XML schema called Annotated Gel Markup Language (AGML) is proposed to manage, analyze, and disseminate annotated 2D gel electrophoresis and MS results.

  biological 2de agml gel mass visualization

• Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible Mammaliicoccus sciuri from Diseased Animals.

  PMID 36125295 · PMC9583799 · Microbiology resource announcements · 2022 · 7 claims · 7 setups

  Has reproduction · 92

  Draft genomes of a methicillin-resistant Mammaliicoccus sciuri strain (2254A, from an armadillo) and a methicillin-susceptible strain (6942A, from a cow) are reported.

  sciuri bacterial assembled 2254a long-read maldi-tof genome

• Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

  PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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  Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

  lung scanned excised peptide 2-d 2-de maldi-tof-ms

• Proteomics: characterizing the cogs in the machinery of life.

  PMID 14630521 · PMC1241753 · Environmental health perspectives · 2003 · 8 claims · 5 setups

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  Protein expression patterns in blood serum, detected via SELDI-TOF mass spectrometry and analyzed with a genetic algorithm, can distinguish ovarian cancer patients from healthy individuals with very high sensitivity and specificity.

  blood lung hemoglobin proteins seldi-tof proteome tandem

• Identification of proteins differentially expressed in the conventional renal cell carcinoma by proteomic analysis.

  PMID 15953868 · PMC2782202 · Journal of Korean medical science · 2005 · 6 claims · 4 setups

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  Eight proteins from 11 differentially expressed spots were identified in conventional RCC versus normal kidney tissue by 2D-PAGE and MALDI-TOF-MS

  conventional trypsin-digested lysates 2d-page maldi-tof bradford

• Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human.

  PMID 17127214 · PMC5054074 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 7 setups

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  15 differential protein spots were detected in 11 of 12 (91.7%) breast cancer tissue samples compared with adjacent normal tissue

  breast spots 2d-page stained sds-page 2d-page maldi-tof