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 6

System / cell line: lysate ✕ Assay: profile ✕ Clear

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

PMID 19828875 · PMC2816009 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 6 setups

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A stacked-ring ion guide (S-lens) increases ion transmission from the source into the instrument roughly 10-fold in MS/MS mode and 3-5-fold in full scan mode

intact bsa hela model top-down nanoflow ion
Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

PMID 17949499 · PMC2148065 · BMC genomics · 2007 · 8 claims · 8 setups

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ECM-stimulated hMSC and OS-media-stimulated hMSC represent two distinct intermediate/transitional phenotypes en route to becoming osteoblasts

naive hmsc osteoblasts proteomic lc-ms gene computational
Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

PMID 37223250 · PMC10117727 · microLife · 2021 · 8 claims · 9 setups

Has reproduction · 50

Grad-seq resolves in-gradient sedimentation profiles for ~87-88% of annotated C. difficile transcripts and ~50% of annotated proteins, providing a comprehensive RNA-protein complexome resource

difficile grad-seq rna-seq lc-ms
Expression patterns of cardiac myofilament proteins: genomic and protein analysis of surgical myectomy tissue from patients with obstructive hypertrophic cardiomyopathy.

PMID 19808356 · PMC2765062 · Circulation. Heart failure · 2009 · 8 claims · 4 setups

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Myofilament protein levels (MYBPC3 and MYH7) are increased, not decreased, in HCM patients carrying a mutation in either gene compared to healthy heart tissue

genomic lysate formalin-fixed myectomy mutational western immunohistochemistry
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).

PMID 33793824 · PMC8136920 · The Plant cell · 2021 · 8 claims · 6 setups

Has reproduction · 100

Grad-seq resolves complexes with overlapping subunits, such as CpcG1-type versus CpcL-type phycobilisomes or PsaK1 versus PsaK2 photosystem I (pre)complexes, validating the approach.

synechocystis gradient proteins grad-seq grad-seq denaturing sds-polyacrylamide
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

Experiments

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

Expression patterns of cardiac myofilament proteins: genomic and protein analysis of surgical myectomy tissue from patients with obstructive hypertrophic cardiomyopathy.

Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.