Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA isolation and informatics for microbiome studies

ABSTRACT: Toward standards in clinical microbiome studies: comparison of DNA extraction methods and bioinformatic pipelines

PROVIDER: PRJEB34118 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Long-read Nanopore sequencing of synthetic "sequin" controls

Project description:Purpose: To generate a reference long-read transcriptomic data set for use in developing new analysis pipelines and comparing their performance with existing methods. Synthetic “sequin” RNA standards (Hardwick et al. 2016) were sequenced using the Oxford Nanopore Technologies (ONT) GridION platform.

2020-06-18 | GSE151984 | GEO

soil microbiome

Project description:A comparative study of several methods for extraction of soil microbiome

| PRJEB20469 | ENA

soil microbiome

Project description:A comparative study of several methods for extraction of soil microbiome

| PRJEB20470 | ENA

Equus caballus

Project description:aDNA extraction methods

| PRJNA289200 | ENA

Project description:Microvolume DNA Extraction Methods for Microscale Amplicon and Metagenomic Studies

| PRJNA766133 | ENA

extraction of soil microbiome

Project description:A comparative study of several methods for extraction of soil microbiome

| PRJEB20467 | ENA

extraction of soil microbiome

Project description:A comparative study of several methods for extraction of soil microbiome

| PRJEB20466 | ENA

ASAP – Automated Sonication free Acid assisted Proteomes from cells & FFPE tissues

Project description:Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for retrospective studies but protein extraction and subsequent sample processing steps have shown to be challenging for mass spectrometry (MS) analysis. Streamlined high-throughput sample preparation workflows are essential for efficient peptide extraction from complex clinical specimens such as fresh frozen tissues or FFPE. Overall, proteome analysis has gained significant improvements in the instrumentation, acquisition methods, sample preparation workflows and analysis pipelines yet even the most recent FFPE workflows remain complex and are not readily scalable. Here, we present an optimized workflow for Automated Sonication-free Acid-assisted Proteome (ASAP) extraction from FFPE sections. ASAP enables efficient protein extraction from FFPE specimens achieving similar proteome coverage as established methods using time in equipment-heavy sonication-based methods at reduced sample processing time. The broad applicability of ASAP on archived pediatric tumor FFPE specimens resulted in high-quality data with increased proteome coverage and quantitative reproducibility. Our study demonstrates the practicality and superiority of the ASAP workflow as a streamlined, time and cost-effective pipeline for high-throughput FFPE proteomics of clinical specimens.

2024-05-21 | PXD036910 | Pride

Project description:A real Listeria monocytogenes groundtruth dataset for validating bioinformatic pipelines

| PRJNA355549 | ENA

Bacterial DNA normalisation in microbiome studies

Project description:Exploring the impact of bacterial DNA variation in fish microbiome studies

| PRJEB33241 | ENA