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ABSTRACT: Meta-transcriptomic discovery of divergent RNA viruses in geckos

PROVIDER: PRJNA1207091 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR31912492_1.fastq.gz	Fastqsanger.gz
	SRR31912492_2.fastq.gz	Fastqsanger.gz
	SRR31912493_1.fastq.gz	Fastqsanger.gz
	SRR31912493_2.fastq.gz	Fastqsanger.gz

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Project description:Meta-transcriptomic survey of groundnut viruses

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Validation data for Lawrence Livermore Microbial Detection Array version 2

Project description:We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR. Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.

2010-10-15 | E-GEOD-24626 | biostudies-arrayexpress

Validation data for Lawrence Livermore Microbial Detection Array version 1

2010-10-15 | E-GEOD-24699 | biostudies-arrayexpress

Validation data for Lawrence Livermore Microbial Detection Array version 1

2010-10-15 | GSE24699 | GEO

Validation data for Lawrence Livermore Microbial Detection Array version 2

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Project description:spatial meta-transcriptomic analysis

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A microarray meta-dataset of non-small cell lung cancer

Project description:This data is part of a pre-publication release. Here, we present a meta-dataset exclusively comprising of 1,118 samples including primary non-small cell lung cancer (NSCLC) tumors and normal lung tissues from ten independent GEO datasets. The meta-dataset has been merged, normalized, batch effect corrected and filtered for genes with low variance using our developed bioinformatics pipeline utilising multiple open source R packages. This meta-dataset serves as an accurate and powerful 'discovery cohort' for clinical model development.

2018-03-23 | E-MTAB-6043 | biostudies-arrayexpress

Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition from transcriptomic and proteomic profiles in Dingyuan pigs

Project description:we collected tissues of subcutaneous fat and longissimus dorsi (LD) muscle from individuals that have divergent of backfat thickness and intramuscular fat content, and have similar age and body weight. The transcriptomic and proteomic data were gained using RNA-Seq and TMT to identify the key genes and pathways that specifically regulate the subcutaneous fat and intramuscular fat deposition in Dingyuan pig.

2022-04-04 | PXD027061 | Pride

Adamo et al. 2017

Project description:RNA extraction from decaying wood for (meta)transcriptomic analyses

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Discovery of a Novel Human Polyomavirus in Acute Diarrheal Samples from Children

Project description:By unbiased deep sequencing, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. From Mexico, 12 samples (out of 96) were positive for MxPyV by MXPyV-specific PCR. We used the ViroChip microarray and PCR to screen these 12 samples for co-infection with common diarrheal viruses. Six of 12 MxPyV-positive diarrheal samples tested negative by the ViroChip and PCR, and the other 6 samples were positive for at least one known diarrheal virus. The ViroChip microarray (version 5.0, Viro5AG-60K platform, GPL15905) was used to screen RNA extracts from MX polyomavirus (MXPyV)-positive pediatric diarrheal samples from Mexico for common diarrheal viruses.

2012-10-01 | E-GEOD-40008 | biostudies-arrayexpress

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