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The PRIDE database and related tools and resources in 2019: improving support for quantification data
TLDR
Key statistics on the current data contents and volume of downloads are outlined, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas are outlined.
Transcriptome and genome sequencing uncovers functional variation in humans
TLDR
Se sequencing and deep analysis of messenger RNA and microRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project—the first uniformly processed high-throughput RNA-sequencing data from multiple human populations with high-quality genome sequences discover extremely widespread genetic variation affecting the regulation of most genes.
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data
TLDR
The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Global transcriptional responses of fission yeast to environmental stress.
TLDR
Transcriptional responses of the fission yeast Schizosaccharomyces pombe to various environmental stresses were explored and promoter motifs associated with some of the groups of coregulated genes were identified.
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
TLDR
The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
TLDR
An analysis of single-cell transcriptomics datasets from different tissues shows that ACE2 and TMPRSS2 are co-expressed in respiratory, corneal and intestinal epithelial cell populations, and that respiratory expression of ACE2 is associated with genes involved in innate immunity.
ArrayExpress—a public repository for microarray gene expression data at the EBI
ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As
Periodic gene expression program of the fission yeast cell cycle
Cell-cycle control of transcription seems to be universal, but little is known about its global conservation and biological significance. We report on the genome-wide transcriptional program of the
An integrated encyclopedia of DNA elements in the human genome
TLDR
The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
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