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 10

System / cell line: whole-cell ✕ Assay: mass ✕ 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
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
Identification of two late acyltransferase genes responsible for lipid A biosynthesis in Moraxella catarrhalis.

PMID 18795947 · PMC2585779 · The FEBS journal · 2008 · 8 claims · 8 setups

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Two late acyltransferase genes, lpxX and lpxL, were identified in M. catarrhalis O35E by informatics analysis of the partial genome sequence

lipid proteinase catarrhalis suspensions maldi-tof fatty sds-page
Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

PMID 19789534 · PMC2768081 · British journal of cancer · 2009 · 8 claims · 7 setups

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Cathepsin D, identified via comparative 2D PAGE of conditioned media from RCC cell lines vs normal renal cultures, is a candidate secreted biomarker of RCC

htb49 excised conditioned urine page maldi western
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
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
Characterisation and protein expression profiling of annexins in colorectal cancer.

PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

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Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

dukes colorectal immunised whole-cell gel immunohistochemistry elisa
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
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 74

ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot
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.

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

Identification of two late acyltransferase genes responsible for lipid A biosynthesis in Moraxella catarrhalis.

Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

Shotgun proteomics and biomarker discovery.

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

Characterisation and protein expression profiling of annexins in colorectal cancer.

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.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

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