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: proteins ✕ Assay: whole-cell ✕ Clear

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

gingivalis whole-cell comparative gene
A large-scale proteomic analysis of human embryonic stem cells.

PMID 18162134 · PMC2211323 · BMC genomics · 2007 · 8 claims · 5 setups

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Two large-scale western blot systems (PowerBlot, Kinexus) identify over 600 proteins expressed in undifferentiated hESCs across 18 functional classes

bg01 bg03 hescs powerblot kinexus immunofluorescence
Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

PMID 18654835 · PMC4973579 · Biogerontology · 2009 · 8 claims · 7 setups

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Treatment of HCA3 human diploid fibroblasts with a mild dose of H2O2 (600 μM) induces premature senescence without killing the cells.

hca3 differentially mudpit cdna semi-quantitative
Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

PMID 18560578 · PMC2409963 · PloS one · 2008 · 8 claims · 6 setups

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Ovarian cancer cells exhibit extensive shedding of extra-cellular domains from cell surface proteins into the extracellular milieu.

ovcar3 analysis lc-ms cell-surface silac
Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

PMID 17446074 · PMC1885954 · Current biology : CB · 2007 · 8 claims · 8 setups

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Newly synthesized ribosomal proteins accumulate in nucleoli more quickly than other nucleolar proteins

hela post-mitotic pulsed fluorescence selective
Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.

PMID 41427637 · PMC12794154 · The journal of physical chemistry. B · 2026 · 8 claims · 6 setups

Has reproduction · 67

Assembly pathways for 21 unique macromolecular complexes (RNAP, ribosome, degradosome, ATP synthase, ABC transporters, etc.) were incorporated into the existing Syn3A whole-cell model

jcvi-syn3a coli syn3a simulated hybrid ribosome atp
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

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The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

aureus 2-d 1-d gelc-ms
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
Shotgun proteomics and biomarker discovery.

PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups

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Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.

urine yeast cysteine-containing hemoglobin 2d-ge lc-ms imac
Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

PMID 18922787 · PMC3523710 · Science signaling · 2008 · 8 claims · 8 setups

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VILIP1 was identified via a proteomic (GST pull-down) approach as a protein interacting with the P2X2 receptor C-terminal tail

brain hek gst co-immunoprecipitation immunocytochemistry
Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

PMID 19912651 · PMC2784748 · BMC cell biology · 2009 · 7 claims · 7 setups

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hnRNP L is a novel Sam68-interacting protein partner identified by proteomics and confirmed by co-immunoprecipitation

lncap hek293 nih3t3 co-immunoprecipitation sucrose indirect
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
Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.

PMID 19122847 · PMC2585750 · Circulation. Arrhythmia and electrophysiology · 2008 · 7 claims · 5 setups

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A missense R99H mutation in KCNE3 was identified in a Brugada Syndrome proband and cosegregates with the phenotype in the family (4/4 phenotype-positive, 0/3 phenotype-negative members carried it)

genomic cho-k1 left ventricular sscp whole-cell co-immunoprecipitation
Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

e2348 hep-2 blast colony transformation
A catalog of human cDNA expression clones and its application to structural genomics.

PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

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A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

hex1 ensembl coli recombinant small-scale tag-sequencing blastp
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide

Experiments

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

A large-scale proteomic analysis of human embryonic stem cells.

Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.

A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

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

Shotgun proteomics and biomarker discovery.

Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

Cohesin regulates alternative splicing.

Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.

Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

A catalog of human cDNA expression clones and its application to structural genomics.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.