Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Individual variability of protein expression in human tissues

ABSTRACT: A retrospective analysis of proteomics data from nine different human tissues, to understand the inter-individual and inter-tissue variability in protein expression. We used the data to build robust classifiers to predict the tissue of origin.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Ovary, Temporal Lobe, Blood Plasma, Monocyte, Substantia Nigra, Cerebrospinal Fluid, Liver, Blood Serum, Pancreas

SUBMITTER: Matthew Monroe

LAB HEAD: Samuel Payne

PROVIDER: PXD010271 | Pride | 2018-10-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	61928_PT_S1_6029_A_13Jan14_Frodo_13-12-03.mgf	Mgf
	61928_PT_S1_6029_A_13Jan14_Frodo_13-12-03.pride.mgf.gz	Mgf
	61928_PT_S1_6029_A_13Jan14_Frodo_13-12-03.raw	Raw
	61928_PT_S1_6029_A_13Jan14_Frodo_13-12-03_msgfplus.mzid.gz	Mzid
	61928_PT_S1_6051_A_13Jan14_Frodo_13-12-03.mgf	Mgf

Items per page:

1 - 5 of 1008

Publications

Individual Variability of Protein Expression in Human Tissues.

Kushner Irena K IK Clair Geremy G Purvine Samuel Owen SO Lee Joon-Yong JY Adkins Joshua N JN Payne Samuel H SH

Journal of proteome research 20181018 11

Human tissues are known to exhibit interindividual variability, but a deeper understanding of the different factors affecting protein expression is necessary to further apply this knowledge. Our goal was to explore the proteomic variability between individuals as well as between healthy and diseased samples, and to test the efficacy of machine learning classifiers. In order to investigate whether disparate proteomics data sets may be combined, we performed a retrospective analysis of proteomics ...[more]

PMID: 30300549

Similar Datasets

Measurement of inter-individual variability in gene expression in mouse neutrophils

Project description:We extracted RNA from C57BL/6 mouse neutrophils to measure inter-individual variability in gene expression. 5 of the 10 blood samples were analyzed separately, the other 5 were pooled then split into 5 technical replicates to measure technical variability. We could then measure inter-individual variability in gene expression and compare it to the amplitude of miRNA-guided repression by miR-223.

2016-09-21 | GSE59549 | GEO

Evaluation of preservation quality and viability of FFPE ovarian cancer tissue samples

Project description:Analysis of 60 FFPE (formalin-fixed, paraffin-embedded) ovarian cancer tissue samples to evaluate preservation quality and viability of global and phosphoproteomic analysis

2018-10-19 | PXD008832 | Pride

Liquid Chromatography Ion Mobility Mass Spectrometry analysis of CPTAC Comparator Reference sample CompRef P6

Project description:Proteomic discovery and targeted monitoring of proteins in a breast cancer xenograft tissue sample using LC Ion Mobility Mass Spectrometry.

2016-08-10 | PXD004569 | Pride

High-resolution spatially-resolved proteome mapping using automated, sacrificial liquid-mediated sample transfer from laser microdissection to nanodroplet sample preparation

Project description:Method development for high-resolution spatially-resolved proteome mapping of tissue heterogeneity. Laser microdissection was coupled with nanodroplet sample preparation and ultrasensitive LC-MS.

2018-07-03 | PXD008844 | Pride

Widespread inter-individual gene expression variability in Arabidopsis thaliana

Project description:Widespread inter-individual gene expression variability in Arabidopsis thaliana

| PRJNA475542 | ENA

Individual Variability in Human Cell Type Transcriptomes and Epigenomes

Project description:Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function. We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

2023-12-15 | GSE247988 | GEO

Probing Xist RNA structure in cells using Targeted Structure-Seq

Project description:The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. Examination of dimethylsufate reactivity of Xist lncRNA and 18S rRNA in cells using targeted reverse transcription to determine reactivity, and comparisons with untreated control samples.

2016-02-09 | E-GEOD-67667 | biostudies-arrayexpress

Widespread inter-individual gene expression variability in Arabidopsis thaliana

Project description:A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability over a 24 hours time-course between individual Arabidopsis thaliana plants growing in stable conditions. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene size, the number of transcription factors regulating a gene and the chromatin environment. These results will bring a new light into the impact of transcriptional variability in gene expression regulation in plants.

2018-12-06 | GSE115583 | GEO

Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF2B]

2023-12-14 | GSE201933 | GEO

Individual Variability in Human Cell Type Transcriptomes and Epigenomes [OF1B]

2023-12-14 | GSE193296 | GEO