Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optimizing high molecular weight extractions

ABSTRACT: Optimizing high molecular weight extractions

PROVIDER: PRJNA1114081 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Visual automated fluorescence electrophoresis provides simultaneous quality, quantity, and molecular weight spectra for genomic DNA from archived neonatal blood spots

2013-07-01 | GSE44249 | GEO

The distribution of individual miRNA species between high-molecular weight and low-molecular weight RISC complexes by small RNA sequencing in thyroid cancer cell lines

Project description:Thyroid cancer is the most prevalent malignancy of the endocrine system. We and others have shown that several microRNAs, which are ~21-24nt post-transcriptional gene regulators, are aberrantly expressed in anaplastic thyroid cancer (ATC) and papillary thyroid cancer (PTC) tissues and cell lines. In the cell, miRNAs are bound to Argonaute (AGO) proteins as low molecular weight RNA Induced Silencing Complexes (LMW-RISCs) that can then assemble into high molecular weight RISCs (HMW-RISCs) that also include additional proteins and mRNA. In this study, we sought to analyze the association of miRNAs across RISC complexity in ATC and PTC. For both ATC and PTC lines, miRNAs were enriched in HMW-RISC and LMW-RISC fractions compared with intermediate fractions or very low molecular weight (AGO-poor) fractions. Furthermore, 60% of all miRNAs were more abundant in LMW-RISC versus HMW- RISC fractions by ~2-4 fold. Surprisingly, miR-21-5p, one of the most abundant miRNAs in both ATC and PTC lines, was consistently one the least abundant miRNAs in HMW-RISC and the most enriched miRNA in LMW-RISC fractions. These findings suggest that miR-21 may be uniquely distributed in RISCs relative to other miRNAs. Furthermore, the methodology described here is a useful way to assess the relative magnitude of miR-21association with HMW and LMW-RISCs and may help to reveal the true roles of this miRNA in thyroid cancer development, progression, and treatment.

2020-02-28 | GSE146015 | GEO

The distribution of individual miRNA species between high-molecular weight and low-molecular weight RISC complexes by small RNA sequencing in thyroid cancer cell lines

Project description:The distribution of individual miRNA species between high-molecular weight and low-molecular weight RISC complexes by small RNA sequencing in thyroid cancer cell lines

| PRJNA609056 | ENA

Effects of high molecular weight phthalates on LPS-stimulated THP-1 macrophages - phosphoproteome

Project description:In this study, the effects of three high molecular weight phthalates (DINP, DIDP, DPHP) and their metabolites (MHINP, MCINP, OHMPHP) were investigated in THP-1 macrophages. For this purpose, the phosphoproteome was evaluated.

2023-09-13 | PXD042912 | Pride

Effects of high molecular weight phthalates on LPS-stimulated THP-1 macrophages - proteome

2023-09-13 | PXD043025 | Pride

Effects of high molecular weight phthalates on LPS-stimulated THP-1 macrophages - redoxome

2023-09-13 | PXD043139 | Pride

Visual automated fluorescence electrophoresis provides simultaneous quality, quantity, and molecular weight spectra for genomic DNA from archived neonatal blood spots

Project description:The Guthrie 903 card archived dried blood spots (DBS) are a unique but terminal resource amenable for individual and population wide genomic profiling. The limited amounts of DBS-derived genomic DNA (gDNA) can be whole-genome amplified (WGA) producing sufficient gDNA for genomic applications, albeit with variable success, and optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential. Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology affording precise quality, quantity and molecular weight of double-stranded DNA from a single microliter of sample. The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array. The Swedish Repository of DBS samples collected on Guthrie 903 cards for neonatal screening of inborn diseases provided deidentified 3mm blood spot punches. There were total of eight (8) samples representing two (2) decades; 1970s: 1975, 1976, 1977, 1978; 1980s: 1980, 1982, 1984, 1986. gDNA was extracted and whole genome amplified prior to aCGH experiments using control female reference genomic DNA. The objective was to show that large rearrangements (e.g. loss of chrX in male samples) can be detected in WGA gDNA from blood spots >30 years old.

2013-07-01 | E-GEOD-44249 | biostudies-arrayexpress

A sub-optimal protein precipitation method to improve identification of low molecular weight less abundant proteins

Project description:Mass spectrometry-based proteomics studies have enabled identification and quantification of thousands of proteins from biological samples. High molecular weight abundant proteins are readily sampled in global proteomics studies compared to low molecular weight less abundant proteins. Although extensive fractionation can facilitate identification of low molecular weight less abundant proteins, it requires additional infrastructure, mass spectrometry time and labour. There is a need for a simple method that can deplete high molecular weight proteins and enrich for low molecular weight proteins to improve their coverage in proteomics studies. We developed a simple method that depletes high molecular weight proteins from various biological samples including cell lines, tissues, and serum. Using this strategy, we demonstrate identification of proteins that are often underrepresented in proteomics datasets. This approach also enabled identification of low abundant serum proteins that are often not detected using immunodepletion strategy. We also identified several novel proteins encoded by annotated non-coding regions in the human genome including lncRNAs and UTRs. Our approach can complement existing proteomics workflows to increase detection and coverage of low molecular weight less abundant proteins.

2021-08-19 | PXD023648 | Pride

Optimizing Cell Therapy by Sorting Cells with High Extracellular Vesicle Secretion

Project description:Optimizing Cell Therapy by Sorting Cells with High Extracellular Vesicle Secretion

| PRJNA1005988 | ENA

Draft genome sequence of Paracoccus aminovorans HPD-2, a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterium

Project description:Draft genome sequence of Paracoccus aminovorans HPD-2, a high molecular weight polycyclic aromatic hydrocarbon-degrading bacterium

| PRJEB11544 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data