Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High throughput sequencing of fungal soil samples from volcanic and non volcanic areas

ABSTRACT: High throughput sequencing of fungal soil samples from volcanic and non volcanic areas

PROVIDER: PRJNA1024925 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26315168_1.fastq.gz	Fastqsanger.gz
	SRR26315168_2.fastq.gz	Fastqsanger.gz
	SRR26315169_1.fastq.gz	Fastqsanger.gz
	SRR26315169_2.fastq.gz	Fastqsanger.gz
	SRR26315170_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

High throughput sequencing of bacterial soil samples from volcanic and non volcanic areas

Project description:High throughput sequencing of bacterial soil samples from volcanic and non volcanic areas Raw sequence reads

| PRJNA1024930 | ENA

Microbial life in geothermal and volcanic areas

Project description:Microbial life in geothermal and volcanic areas

| PRJEB9039 | ENA

Soil microorganisms at different depths in volcanic areas

Project description:Soil microorganisms at different depths in volcanic areas Raw sequence reads

| PRJNA1223562 | ENA

Soil microorganisms at different depths in volcanic areas

Project description:Soil microorganisms at different depths in volcanic areas Raw sequence reads

| PRJNA1223695 | ENA

volcanic fungal community

Project description:volcanic fungal community Raw sequence reads

| PRJNA911411 | ENA

volcanic bacterial community

Project description:volcanic bacterial community Raw sequence reads

| PRJNA911355 | ENA

Northeast Fungal Diversity In Agricultural areas

Project description:Northeast Thailand Fungal Diversity In Agricultural areas Raw sequence reads

| PRJNA1118038 | ENA

High-throughput Bifidobacterium isolation

Project description:High-throughput Bifidobacterium isolation

| PRJEB98585 | ENA

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils.

Project description:Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in PCR, and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.

| S-EPMC4431839 | biostudies-literature

High-throughput sequencing of in vitro fecal fermentation samples

Project description:We report the use of high-throughput sequencing technology to detect the microbial composition and abundance of human feces after in vitro co-fermentation with citrus peel flavonoid extracts. The genomic DNA was obtained by the QIAamp PowerFecal DNA Kit. Then, the DNA samples were sent to Biomarker Bio-Tech (Beijing, China) for V3-V4 region of the 16S rDNA gene high-throughput sequencing with an Illumina MiSeq platform. DNA samples were sequenced using primers 338F (forward primer sequence ACTCCTACGGGAGGCAGCAG)-806R (reverse primer sequence GGACTACHVGGGTWTCTAAT). A total of 8,816,250 pairs of Reads were obtained from the 112 samples sequenced, and 8,721,112 Clean Reads were generated from the double-ended Reads after quality control and splicing. The sequencing analyses were carried out using the SILVA database as a reference for the assignation of operational taxonomic units (OTUs) with 97% of identity.

2022-04-02 | GSE199749 | GEO

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