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MetabolomicsCharacterization of Whole Blood EVs Using PRotein Organic Solvent PRecipitation

Blood plays a vital role in diagnostic medicine by providing essential information for assessing health and diagnosing various conditions. Routine blood tests can reveal important biomarkers that support early diagnosis and timely intervention. Recently, extracellular vesicles (EVs) have emerged ...

2026-08-24 | MTBLS12801 | MetaboLights
ProteomicsPEPPI-SP3: Robust and Simple Sample Prefractionation Workflow for Top-Down Proteomics
In this study, we developed a complete, robust, and simple sample preparation workflow named PEPPI-SP3 for top-down proteomics by combining PEPPI-MS with the magnetic bead-based protein purification approach used in SP3 (single-pot, solid-phase-enhanced sample preparation), now one of the standard s...
ORGANISM(S): Homo Sapiens (human) 
2025-01-23 | PXD056413 | JPOST Repository
TranscriptomicsTranscription profiling of E. coli during lag phase of cells previously starved in stationary phase for 1 day (young cells) or 16 days (old cells)
transcriptional response during lag phase (several time points) of bacterial cells starved previously in stationary phase for 1 day (young cells) and 16 days (old cells)
ORGANISM(S): Escherichia coli 
2009-10-22 | E-MEXP-2379 | biostudies-arrayexpress
TranscriptomicsThe Extracellular RNA Quality Control (exRNAQC) study: Small RNA sequencing of RNA purification kit study (exRNAQC011)
To evaluate the impact of the RNA purification method on extracellular RNA (exRNA) sequencing, 8 different RNA purification kits were compared by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma. Minimum and maximum plasma input volumes recommended by the manufacture...
ORGANISM(S): Homo sapiens 
2021-06-10 | E-MTAB-10505 | biostudies-arrayexpress
ProteomicsGlobal mapping of RNA-binding proteins in multi-drug resistant Staphylococcus aureus using PTex
Phenol Toluol extraction (PTex) carried out two steps organic-phase separation: first pH neutral phenol–Toluol extraction separated RNA and protein from DNA: RNA and proteins to the top aqueous phase but DNA and membranes in the interface. Aqueous phase then went through two rounds acid-phenol extra...
ORGANISM(S): Staphylococcus aureus 
2022-05-31 | PXD023414 | Pride
Uv cross-linking Rbdome Protein-rna interactions Organic phase purification Rna-binding proteins Rbpome Staphylococcus aureus 
GenomicsHigh-resolution mapping of transcription factor binding sites on native chromatin
Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) and sequencing is widely used for genome-wide profiling of pro...
ORGANISM(S): Drosophila melanogaster 
2013-12-14 | E-GEOD-45672 | biostudies-arrayexpress
ProteomicsUV-crosslinking mapping of LARP6 interaction sites with RNA
To map the regions of LARP6 that interacts directly with RNA, we developed a mass spectrometry-based approach termed IP-OOPS (Immunoprecipitation coupled with Orthogonal Organic Phase Separation. This approach combines the isolation of UV-C crosslinked RNA–protein adducts via Orthogonal Organic Phas...
ORGANISM(S): Homo sapiens (Human) 
2026-01-22 | PXD064029 | Pride
Lc-ms/ms  rna-protein interactions  organic phase separation  rna crosslinking 
ProteomicsIdentification of whole-cell dsRNA-binding proteins by phase separation
Interactions between double-stranded RNA (dsRNA) and proteins play an important role in cellular homeostasis by regulating the editing, stability, and splicing of intracellular RNA. The identification of dsRNA-binding proteins (dsRBPs) is key; however, it has long been challenging to purify dsRBPs f...
ORGANISM(S): Sus scrofa domesticus (domestic pig) 
2024-10-17 | PXD048971 | Pride
Dsrna-binding domain Dsrna-binding protein capture Armadillo/beta-catenin-like repeats Dsrna-binding proteome Dsrna-binding proteins 
UnknownEn route to single-step, two-phase purification of carbon nanotubes facilitated by high-throughput spectroscopy.
Not available
S-EPMC8134628 | biostudies-literature
TranscriptomicsThe Extracellular RNA Quality Control (exRNAQC) study: RNA Exome sequencing of RNA purification kit study (exRNAQC004)
To evaluate the impact of the RNA purification method on extracellular RNA (exRNA) sequencing, 8 different RNA purification kits were compared by applying RNA Exome sequencing (Illumina) to exRNA from human healthy donor plasma. Minimum and maximum plasma input volumes recommended by the manufacture...
ORGANISM(S): Homo sapiens 
2021-05-10 | E-MTAB-10504 | biostudies-arrayexpress
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