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DaCymMura

ABSTRACT: Cymbalaria muralis (Kenilworth ivy), genomic and transcriptomic data

PROVIDER: PRJEB81008 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR13800542.fastq.gz	Fastqsanger.gz
	ERR13802674_1.fastq.gz	Fastqsanger.gz
	ERR13802674_2.fastq.gz	Fastqsanger.gz
	ERR13802675_1.fastq.gz	Fastqsanger.gz
	ERR13802675_2.fastq.gz	Fastqsanger.gz

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daCymMura

Project description:Cymbalaria muralis (Kenilworth ivy)

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Ivy Glioblastoma Atlas Project (SNP)

Project description:The Ivy Glioblastoma Atlas Project (Ivy GAP) is a detailed anatomically based transcriptomic atlas of human glioblastoma tumors. As collaborators, the Ivy Foundation funded the Allen Institute and the Swedish Neuroscience Institute to design and create the atlas. The Paul G. Allen Family Foundation also supported the project. This resource consists of a viewer interface that resolves the manually- and machine-annotated histologic images (H&E and RNA in situ hybridization) at 0.5 µm/pixel, a transcriptome browser to view and mine the anatomically-based RNA-Seq samples, an application programming interface, help documentation that describes the methods and how to use the resource, as well as SNP array data and the supporting longitudinal clinical information and MRI time course data. The resource is made available to the public without charge as part of the Ivy GAP (http://glioblastoma.alleninstitute.org/) via the Allen Institute data portal (http://www.brain-map.org), the Ivy GAP Clinical and Genomic Database (http://ivygap.org/) via the Swedish Neuroscience Institute (http://www.swedish.org/services/neuroscience-institute), and The Cancer Imaging Archive (https://wiki.cancerimagingarchive.net/display/Public/Ivy+GAP). The Ivy GAP processed data at GEO includes normalized RNA-Seq FPKM files used for analysis in "An anatomic transcriptional atlas of glioblastoma,” which is under review. Other processed data files as well as sample and donor meta-data and QC metrics are available at http://glioblastoma.alleninstitute.org/static/download.html. The raw RNA-Seq and SNP array data will be submitted to dbGaP.

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Project description:Podarcis muralis (common wall lizard), genomic and transcriptomic data

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Distinct immune responses and pruritic mechanisms in oxazolone- and urushiol- induced ACD (Allergic contact dermatitis) models.

Project description:The mechanisms underlying pruritus and skin inflammation of poison ivy ACD remain poorly understood,due to limited clinical data and animal studies. Most of the mechanistic understanding of ACD is based upon animal models using experimental allergens not present in the environment, such as oxazolone,DNFB or SADBE . Recently, it has become evident that different allergens elicit widely divergent immune responses in both human and animals, suggesting these models may not be representative of environmental forms of ACD . Given the high incidence and public health impact of poison ivy-induced ACD, it is necessary to establish and characterize a clinically relevant animal model using the actual allergen urushiol. In this study we applied transcriptome microarray to evaluate the cutaneous immune response in urushiol ACD model.

2019-05-31 | GSE131963 | GEO

Project description:Ivy gourd transcriptome

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Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

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Project description:Potentilla anserina, genomic and transcriptomic data

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