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ProteomicsUsing Adaptive Focused Acoustics (AFA) to Digest the Protein Corona around Nanoparticles in Preparation for LC-MS Analysis
The study evaluates the use of Adaptive Focused Acoustics (AFA) for rapid reduction and enzymatic digestion of nanoparticle-associated protein coronas prior to bottom-up proteomic analysis by LC-MS/MS.
ORGANISM(S): Homo sapiens (Human) 
2026-09-05 | PXD080079 | Pride
Protein corona Sample preparation Adaptive focus acoustics 
ProteomicsMethod optimization for FFPE proteomics of hepatocellular carcinoma
Archival formalin-fixed, paraffin-embedded (FFPE) tissues are invaluable resources for translational research, as clinical outcomes and treatment histories are often available. FFPE blocks provide a standardized and cost-effective alternative to frozen specimens, with formalin-induced protein crossl...
ORGANISM(S): Homo Sapiens (human) 
2026-10-06 | PXD070191 | JPOST Repository
ProteomicsOld FFPE proteomics of hepatocellular carcinoma
Archival formalin-fixed, paraffin-embedded (FFPE) tissues are invaluable resources for translational research, as clinical outcomes and treatment histories are often available. FFPE blocks provide a standardized and cost-effective alternative to frozen specimens, with formalin-induced protein crossl...
ORGANISM(S): Homo Sapiens (human) 
2026-10-06 | PXD070497 | JPOST Repository
ProteomicsFFPE proteomics for hepatocellular carcinoma
Formalin-fixed paraffin-embedded (FFPE) tissues are crucial clinical archives linked with long-term follow-up data, yet the suitability of deep proteomic analysis on samples stored over 30 years remains largely unexplored. This study aimed to verify the feasibility of deep proteomic analysis on extr...
ORGANISM(S): Homo Sapiens (human) 
2026-04-01 | PXD062456 | JPOST Repository
OtherIntegration sites sequencing of HIV infection on ZNF417 ZNF587 dKO 293T cells
We infected ZNF417 ZNF587 dKO 293T or control 293T with NL4.3 virus for 48 hours. Then genomic DNA was purified from cell lysis with by phenol chloroform. DNA was sheared into 300 bp-500 bp random fragments using Covaris Adaptive Focused Acoustics (Covaris, Woburn, MA). Sheared DNA was ligated with ...
ORGANISM(S): Homo sapiens 
2021-12-31 | GSE174239 | GEO
TranscriptomicsExamination of tumor samples obtained after laparoscopic supracervical hysterectomy and a derivative leiomyosarcoma
Unexpected malignant tumors are a rare finding after surgery for symptomatic leiomyomas but there is little doubt that morcellation of these lesions is associated with a higher risk of iatrogenic peritoneal spread compared to women having surgery without morcellation. Thus, the FDA has issued a warn...
ORGANISM(S): Homo sapiens 
2018-04-30 | E-MTAB-6039 | biostudies-arrayexpress
MetabolomicsActivated ATF6α is a hepatic tumor driver restricting immunosurveillance

Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF...

2025-11-17 | MTBLS13241 | MetaboLights
GenomicsmiRNAs trigger widespread epigenetically-activated siRNAs from transposons inM-BM- Arabidopsis (bisulfite-seq)
Utilizing whole-genome BIS-seq to analyze transposon methylation in DNA methylation mutants, and RNAi mutants, compared to wildtype. DNA extracted from plant inflorescence tissue, bisulphite-treated and libraries sequenced Illumina HiSEq, mapped by BiSMark.
ORGANISM(S): Arabidopsis thaliana 
2014-03-18 | E-GEOD-52346 | biostudies-arrayexpress
MetabolomicsTissue metabolites in diffuse glioma and their modulations by IDH1 mutation, histology, and treatment
The discovery of the oncometabolite 2-hydroxyglutarate in isocitrate dehydrogenase 1-mutated (IDH1-mutated) tumor entities affirmed the role of metabolism in cancer. However, large databases with tissue metabolites that are modulated by IDH1 mutation remain an area of development. Here, we present a...
2022-09-07 | MTBLS3873 | MetaboLights
ProteomicsHigh-Throughput Acoustic FFPE Proteomics Reveals ATP5IF1-Associated Mitochondrial Remodeling in Acral Melanoma
Formalin-fixed, paraffin-embedded (FFPE) archives underpin dermatopathology and translational oncology, enabling clinically annotated melanoma cohorts, but cohort-scale proteomics remains limited by labor and variability in upstream processing. We established a plate-scale, acoustic FFPE proteomics ...
ORGANISM(S): Homo sapiens (Human) 
2026-09-09 | PXD074156 | Pride
Ai-digital pathology  atp synthase inhibitor if1  adaptive focused acoustics  acral melanoma Oxidative phosphorylation  plate-scale ffpe proteomics 
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