E-PROT-29
Ontology highlight
ABSTRACT:
PROVIDER: E-PROT-29 | ExpressionAtlas | 2021-05-25
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:We generated a systematic, quantitative and deep proteome and transcriptome abundance atlas from 29 paired healthy human to serve as a molecular baseline to study human biology.
2019-03-02 | MSV000083508 | MassIVE
Project description:We generated a systematic, quantitative and deep proteome and transcriptome abundance atlas from 29 paired healthy human to serve as a molecular baseline to study human biology.
2019-07-10 | PXD010154 | Pride
Project description:We re-analyzed the deep proteome atlas of 29 paired healthy human from the published paper (Wang, Dongxue, et al. Molecular systems biology 15.2 (2019)) to identify missing proteins.
2020-11-17 | PXD021391 | Pride
Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.
2015-03-10 | E-PROT-1 | biostudies-arrayexpress
Project description:Background: A comprehensive transcriptome survey, or "gene atlas", provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and 3 cattle cell lines. Results: The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the bovine genome accounting for 85% of the total raw tag abundance. Filtering these tags yielded 87,764 unique tag sequences that unambiguously mapped to 16,517 annotated protein-coding loci in the genome accounting for 45% of the total raw tag abundance. Clustering of tissues based on tag abundance profiles generally confirmed ontology classification based on anatomy. There were 5,429 constitutively expressed loci and 3,445 constitutively expressed unique tag sequences mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. Physical measures such as inferred transcript length or antisense tag abundance identified tissues with atypical transcriptional tag profiles. We report for the first time the tissue specific variation in the proportion of mitochondrial transcriptional tag abundance. The Bovine Gene Atlas can be examined at http://www.agbase.msstate.edu/bovineatlas . Conclusions: The Bovine Gene Atlas is the deepest and broadest transcriptome survey of any livestock genome to date. Commonalities and variation in sense and antisense transcript tag profiles identified in different tissues facilitate the examination of the relationship between gene expression, tissue, and gene function. An atlas of mRNA abundance for 92 adult, juvenile and fetal cattle tissues and 3 cattle cell lines.
2010-09-28 | E-GEOD-21544 | biostudies-arrayexpress
Project description:Deep muscle proteome - Deep skeletal muscle proteome. Triceps muscle from C57BL6 mouse and C2C12 myotubes were measure by LC-MS.
2022-01-14 | E-PROT-10 | ExpressionAtlas
Project description:Deep proteome of HeLa, A549, HCT116, MCF7, and SHSY5Y cell lines
2021-05-25 | E-PROT-19 | ExpressionAtlas
Project description:To investigate the presence and abundance of piRNAs in Colorectal Cancer (CRC), we performed deep-sequencing of the small RNA transcriptome of eight human CRC cell lines (HT-115, Caco-2, SW-1417, SW 403, COLO 205, HT-29, HCT 116 and RKO).
2020-08-06 | E-MTAB-8117 | biostudies-arrayexpress
Project description:Background: A comprehensive transcriptome survey, or "gene atlas", provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and 3 cattle cell lines. Results: The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the bovine genome accounting for 85% of the total raw tag abundance. Filtering these tags yielded 87,764 unique tag sequences that unambiguously mapped to 16,517 annotated protein-coding loci in the genome accounting for 45% of the total raw tag abundance. Clustering of tissues based on tag abundance profiles generally confirmed ontology classification based on anatomy. There were 5,429 constitutively expressed loci and 3,445 constitutively expressed unique tag sequences mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. Physical measures such as inferred transcript length or antisense tag abundance identified tissues with atypical transcriptional tag profiles. We report for the first time the tissue specific variation in the proportion of mitochondrial transcriptional tag abundance. The Bovine Gene Atlas can be examined at http://www.agbase.msstate.edu/bovineatlas . Conclusions: The Bovine Gene Atlas is the deepest and broadest transcriptome survey of any livestock genome to date. Commonalities and variation in sense and antisense transcript tag profiles identified in different tissues facilitate the examination of the relationship between gene expression, tissue, and gene function.
2010-09-29 | GSE21544 | GEO