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Dataset Information

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149 Citations

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Omics score: 33

RNA-Seq of human individual tissues and mixture of 16 tissues (Illumina Body Map)

ABSTRACT: Transcription profiling by high throughput sequencing of individual and mixture of 16 human tissues RNA.

REANALYSIS of: E-MTAB-513

ORGANISM(S): Homo sapiens

PROVIDER: E-MTAB-513 | ExpressionAtlas | 2015-08-06

REPOSITORIES: ExpressionAtlas

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Publications

Dissecting the expression landscape of RNA-binding proteins in human cancers.

Kechavarzi Bobak B Janga Sarath Chandra SC

Genome biology 20140110 1

RNA-binding proteins (RBPs) play important roles in cellular homeostasis by controlling gene expression at the post-transcriptional level.We explore the expression of more than 800 RBPs in sixteen healthy human tissues and their patterns of dysregulation in cancer genomes from The Cancer Genome Atlas project. We show that genes encoding RBPs are consistently and significantly highly expressed compared with other classes of genes, including those encoding regulatory components such as transcripti ...[more]

PMID: 24410894

Publication: 1/6

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RNA-Seq of human individual tissues and mixture of 16 tissues (Illumina Body Map)

Project description:Transcription profiling by high throughput sequencing of individual and mixture of 16 human tissues RNA.

2011-05-05 | E-MTAB-513 | ArrayExpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

RNA-Seq of 14 tissues from a female adult olive baboon (Papio anubis) from the non-human primate reference transcriptome resource (NHPRTR) project

Project description:This data set consists of tissue-specific RNA-seq reads from 14 different tissues from a single female adult olive baboon (Papio anubis): bone marrow, brain cerebellum, brain frontal cortex, brain pituitary, brain temporal lobe, colon, heart, kidney, liver, lymph node, spleen, lung, skeletal muscle and thymus. The data set was generated by the non-human primate reference transcriptome resource (NHPRTR) project (http://nhprtr.org/), and was first made public on 14 Jan 2014.

2013-12-09 | E-MTAB-2848 | ArrayExpress

Transcription profiling by high throughput sequencing of different Arabidopsis genotypes that compromise the dicing of siRNA precursors

Project description:24 nucleotide siRNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes DNA methylation at transposable elements to ensure genome stability. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is thought to transcribe RdDM loci to produce primary transcripts that serve as precursors to siRNAs. Yet, no such transcripts have ever been reported. Here, through RNA sequencing and double-stranded RNA sequencing in genotypes that compromise the dicing of siRNA precursors, we were able to identify Pol IV-dependent transcripts from tens of thousands of loci. We show that Pol IV-dependent transcripts correspond to both DNA strands, while the Pol II-dependent transcripts produced upon de-repression of the loci are derived from primarily one strand. We show that Pol IV-dependent transcripts have a 5’ monophosphate, lack a polyA tail at the 3’ end, and contain no introns; these features distinguish them from Pol II-dependent transcripts. Moreover, RDR2 is shown to play similar roles with Pol IV in both the abundance of siRNA precursors and siRNAs as well as the CHH DNA methylation. The decreased CHH methylation at dcl234 can inhibit the transcription of Pol IV at DRM2-target sites. Finally, the regulations of siRNA biogenesis were explored. To detect siRNA precursors transcribed by RNA polymerase IV, the genome wide profiling of RNA were carried out at dcl234 and dcl234 nrpd1. Different types of RNA (including Total RNA, polyA+ RNA, polyA- RNA, double stranded RNA) libraries were built to detect different transcripts. RDR2 is a RNA-dependent RNA polymerase in Pol IV complex, so the RNA-seq libraries with the mutation of RDR2 were also built. In addition, smRNA libraries with mutations blocking siRNA biogenesis were also built

2014-11-11 | E-GEOD-57215 | ArrayExpress

RNA-Seq of 14 tissues from a female adult olive baboon (Papio anubis) from the non-human primate reference transcriptome resource (NHPRTR) project

2015-11-23 | E-MTAB-2848 | ExpressionAtlas

Promoter capture and whole genome in situ Hi-C of human iPSC and iPSC-derived cardiomyocytes from an Yoruban individual (NA19101)

Project description:We generated Hi-C interaction maps of iPSC and iPSC-derived cardiomyocytes as a resource to help identifying regulatory elements and their target genes in these tissues.

2018-07-11 | E-MTAB-6014 | ArrayExpress

Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency (Chip-Seq)

Project description:We recently showed that some human induced pluripotent stem cell (iPSC) clones were defective in neural differentiation and were marked with the activation of long term repeats (LTRs) of human endogenous retroviruses (HERVs). We herein demonstrated that these LTRs were transiently overexpressed during the generation of iPSCs and contributed to reprogramming. When the generation of iPSCs was completed, LTRs were re-suppressed to levels similar to those in human ES cells. However, differentiation-defective iPSC clones maintained high LTR expression levels, which indicated that these clones failed to complete reprogramming. lincRNA-RoR, a long intergenic non-coding RNA (lincRNA) that was previously shown to support the induction and maintenance of pluripotency, was detected among the LTR-driven transcripts. Short hairpin RNAs against the conserved sequence in LTRs or lincRNA-RoR markedly reduced the efficiency of iPSC generation. Reprogramming factors including OCT3/4, SOX2, and KLF4 bound to most LTRs. The expression of KLF4 was low in normal iPSC clones, but remained high in differentiation-defective clones. The forced expression of KLF4 in human embryonic stem cells led to the activation of LTRs and defects in neural differentiation. These results demonstrated that the transient overexpression of KLF4/LTR/lincRNA-RoR played crucial roles in reprogramming toward pluripotency in humans, whereas a failure in its re-silence resulted in differentiation defects. OCT3/4, SOX2 and KLF4 bindings in human dermal fibroblast and iPSC

2014-08-04 | E-GEOD-56567 | ArrayExpress

5-hydroxymethylcytosine (5hmC) methylation profiling of adult mouse brain and liver tissues (hMeDIP-seq)

Project description:5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. It is a key intermediate in cytosine demethylation, and have potential regulatory functions with emerging importance in mammalian biology. In this work, we used a chemical capture-based technique that coupled with next-generation sequencing to investigate the global 5hmC methylation in five brain subregions (cerebellum, cortex, hippocampus, hypothalamus and thalamus) and liver tissues from female and male adult mice. We also performed total RNA sequencing to study the association between 5hmC and gene expression. The enriched 5-hmC library was sequenced on a HiSeq2500 by paired-end sequencing with 100 bp read length.

2017-01-31 | E-MTAB-5167 | ArrayExpress

MicroRNAome of pig adipose and muscle tissues

Project description:Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context. Eleven small RNA libraries from eight adipose tissues, two skeletal muscle tissues and cardiac muscle of pig were sequenced.

2012-05-16 | E-GEOD-30334 | ArrayExpress

Next Generation Sequencing Analysis of Saccharopolyspora erytharea transcriptomes

Project description:We report the high-throughput profiling of saccharopolyspora erythraea life cycle in bioreactors. RNA was harvested at seven time-points from bioreactors, three points immediately before, one during and three following the metabolic switch (as evidenced by biomass cell dry weight). We prepared unstranded RNA libraries and sequenced 363 million reads for a total of 32.7Gb and a mean ~4,000 fold coverage of the genome. Our comprehensive sequencing showed the S.erythraea genome to be prevalently transcribed, with at least 85.8% of genome sequence from either strand being transcribed. We sequenced a bioreactor fermentation at seven time points.

2013-06-18 | E-GEOD-39722 | ArrayExpress

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