Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Microbial DNA extraction of high-host content and low biomass samples: optimized protocol for nasopharynx metagenomic studies

PROVIDER: PRJNA876384 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21423009_1.fastq.gz	Fastqsanger.gz
	SRR21423009_2.fastq.gz	Fastqsanger.gz
	SRR21423010_1.fastq.gz	Fastqsanger.gz
	SRR21423010_2.fastq.gz	Fastqsanger.gz
	SRR21423011_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 34

Similar Datasets

Project description:EMG produced TPA metagenomics assembly of PRJNA876384 data set (Microbial DNA extraction of high-host content and low biomass samples: optimized protocol for nasopharynx metagenomic studies).

| PRJEB75188 | ENA

LC-MS/MS Analysis Explored the Gluten Map in beers Combined with Optimized Extraction Protocol

Project description:We optimized the extraction protocol of gluten in beer, investigated the deamidated gluten peptides and gluten fragments in beer, and explored the gluten map of eight commercial beers using optimized gluten extraction protocol followed by LC-MS/MS analysis.

2021-01-04 | PXD023387 |

Project description:16S rRNA gene sequencing of low-microbial biomass samples using new nucleic acid extraction protocol

| PRJNA1080104 | ENA

Optimization of Proteomics Sample Preparation for Forensic Analysis of Skin Samples

Project description:We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples.

2021-11-02 | PXD022720 | Pride

Evaluation of extraction solvents for untargeted metabolomics analysis of enrichment reactor cultures performing enhanced biological phosphorus removal (EBPR)

Project description:INTRODUCTION: The extraction solvent mixtures were optimized for untargeted metabolomics analysis of microbial communities from two laboratory scale activated sludge reactors performing enhanced biological phosphorus removal (EBPR).OBJECTIVE: To develop a robust and simple analytical protocol to analyse microbial metabolomics from EBPR bioreactors.METHODS: Extra- and intra-cellular metabolites were extracted using five methods and analysed by ultraperformance liquid chromatography mass spectrometry (UPLC-MS).RESULTS: The optimal extraction method was biomass specific and methanol:water (1:1 v/v) and methanol:chloroform:water (2:2:1 v/v) were chosen, respectively, for each of the two different bioreactors.CONCLUSION: Our approach provides direct surveys of the metabolic state of PAO-enriched EBPR communities, showing that extraction methods should be carefully tailored to the microbial community under study

2019-08-16 | MTBLS884 | MetaboLights

The Neonatal Microbiome and NEC

Project description:The Neonatal Microbiome and Necrotizing enterocolitis (NEC) study is a multi-centered case control study testing the hypothesis that NEC is a direct or indirect consequence of the enteric biomass, its products, or both. Very low birth weight infants (VLBW; birth weight ≤ 1500 grams) admitted to the neonatal intensive care unit are prospectively followed over the first 5 week or until they reach 36 weeks gestation, whichever occurs later. VLBW infants with a lethal clinical condition are excluded. Over the course of the study period, prospective samples are obtained on all infants, and include all stools, and weekly blood samples, palm and oral swabs. Clinical data is collected over the course of the entire hospitalization. Cases are identified based on Bell's staging for NEC, requiring Bell's stage II (abdominal clinical signs and radiographic evidence of pneumatosis, portal venous gas or pneumoperitoneum). Controls are identified from the pool of prospectively enrolled subjects, matching for gestational age, birth weight, post-natal age and birth date. The microbial components of stool and its products before and at the onset of NEC, are then compared between cases and controls. The Aims of this proposal are to (1) conduct a case cohort study in which we compare clinical data and biological specimens from cases and well-matched controls; (2) determine if the kind and density of intestinal biomass, its gene content, and transcriptional activity are associated with, and potential determinants of, NEC; and (3) determine if host risk alleles for intestinal inflammation play a role in the development of NEC.

| phs000247 | dbGaP

A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples.

Project description:Here we have designed a full processing pipeline of P. falciparum RNA that innclues RNA preservation, extraction, cDNA synthesis and amplification, globin depletion and final transcriptome readout. To validate the protocol we have analyzed transcriptomes of P. falciaprum samples derived from filed studies as well as 3D7 lab strains. This dataset have been used to establish the best conditions for whole transcriptome amplification protocol. Additionally it inclues the validation of bead extraction protocol. It also contains field samples used for validation of the entire protocol.

2020-10-20 | GSE151754 | GEO

A novel integrated extraction protocol for multi-omic studies in heavily degraded samples

Project description:A novel integrated extraction protocol for multi-omic studies in heavily degraded samples

| PRJEB61253 | ENA

Laser-capture proteomics of human FFPE substantia nigra

Project description:Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. In this study, we have developed an optimized protocol to facilitate efficient LCM analysis of FFPE tissue specimens. First, we optimized protein extraction from FFPE tissue by comparing different extraction buffers and investigating the influence of immunohistochemical and haematoxylin & eosin staining on proteins. SDS present in the protein extracts was removed with the SP3 digest method, which was modified to improve protein and peptide recoveries. Using a label-free approach protein expression of microdissected samples was compared to intact tissue sections from substantia nigra to evaluate the efficiency of LCM for the purification of small cell populations. The optimized protocol was used to analyse samples containing as few as ~3,000 cells isolated from the substantia nigra, using FFPE tissue. Replicate samples of 15 healthy donors were analysed in five separate TMT10plex batches, resulting in the quantification of >5,600 protein groups.

2020-03-05 | PXD016563 | Pride

Project description:Optimisation of a DNA extraction protocol

| PRJNA1040473 | ENA