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ProteomicsMHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection
We sought to build a catalog of epitopes presented by breast cancers using a renewable resource of well-characterized breast cancer cell lines. Starting from 70 breast cancer cell lines, we measured MHC class I abundance and used pre-existing RNAseq data to identify either HLA-A*02 or MHC class I-po...
ORGANISM(S): Homo sapiens (Human) 
2018-01-16 | PXD006406 | Pride
Immune system Mass spectrometry Human Mhc class 1 ligands Hla typing Peptide sequencing Breast cancer Cell lines Immunoprecipitation Rna-seq 
MetabolomicsAntiviral metabolite 3'-Deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19

BACKGROUND: There is a critical need for rapid viral infection diagnostics to enable prompt case identification in pandemic settings and support targeted antimicrobial prescribing.

METHODS: Using untargeted high-resolution liquid chromatography coupled with...

2022-02-10 | MTBLS718 | MetaboLights
UnknownReduced fish diversity despite increased fish biomass in a Gulf of California Marine Protected Area.
Not available
S-EPMC7151750 | biostudies-literature
TranscriptomicsEXPRESSION QTL MAPPING ACROSS SOIL MOISTURE ENVIRONMENTS REVEALS CONTRASTING ASSOCIATIONS WITH GENOMIC FEATURES IN ARABIDOPSIS THALIANA
Understanding the patterns and processes driving natural genetic variation in gene expression is of fundamental importance to biology. In this study, we examined genetic variation in gene transcription through expression QTL (eQTL) analysis in the Tsu-1 x Kas-1 recombinant inbred line (RIL) mapping ...
ORGANISM(S): Arabidopsis thaliana 
2013-03-02 | E-GEOD-42408 | biostudies-arrayexpress
UnknownBest practices for multi-ancestry, meta-analytic transcriptome-wide association studies: Lessons from the Global Biobank Meta-analysis Initiative.
Not available
S-EPMC9631681 | biostudies-literature
ProteomicsRegulation of dendritic cells and macrophages by an anti-apoptotic cell natural Ab that inhibits inflammatory arthritis
Although natural antibodies (NAbs) are present from birth, little is known about what drives their selection, and whether they have housekeeping functions. We now show that the prototypic T15-NAb, first identified because of its protective role in infection, is representative of a previously unknown...
ORGANISM(S): unidentified 
2010-05-06 | E-GEOD-14969 | biostudies-arrayexpress
ProteomicsBiomechanical rigidity and quantitative proteomics analyses of segmental regions of the ocular trabecular meshwork at physiologic and elevated pressures
The extracellular matrix (ECM) of the ocular trabecular meshwork (TM) builds resistance to aqueous humor outflow, thereby regulating intraocular pressure (IOP). Glaucoma, a leading cause of blindness worldwide, is associated with changes in the ECM of the TM. The elastic modulus indicates glaucomato...
ORGANISM(S): Homo sapiens (Human) 
2018-01-22 | PXD006424 | Pride
Glaucoma Biomechanical rigidity High resolution mass spectrometry Multi-notch isolation Extended multiplexing Trabecular mesh Quantitative proteomics Human Tandem mass tags 
TranscriptomicsTranscription profiling of transgenic mice overexpressing human alpha-synuclein under the PDGF beta promoter to wildtype littermates at 3 months and 9 months of age.
Microarray comparison of transgenic mice overexpressing human alpha-synuclein under the PDGF beta promoter to wildtype littermates at 3 months and 9 months of age. RNA was extracted from substantia nigral cells that were isolated by laser capture microdissection.
ORGANISM(S): Mus musculus 
2007-12-20 | E-MEXP-1383 | biostudies-arrayexpress
TranscriptomicsChemokine Transcripts as Targets of the RNA-Binding Protein HuR in Human Airway Epithelium
HuR is a regulator of mRNA turnover or translation of inflammatory genes through binding to adenylate-uridylate-rich elements (ARE) and related motifs present in the 3’untranslated region (UTR) of mRNAs. We aimed to identify HuR targets in the human airway epithelial cell line BEAS-2B challenged wit...
ORGANISM(S): Homo sapiens 
2010-11-10 | E-GEOD-25264 | biostudies-arrayexpress
UnknownIntrinsically microporous polymer (PIM-1) enhanced degradation of heptadecafluoro-1-nonanol at graphitic carbon nitride (g-C<sub>3</sub>N<sub>4</sub>).
Not available
S-EPMC12757717 | biostudies-literature
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