Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HS_iPOP_PBMC2011_SecondBatch_81719202114_r02

ABSTRACT: HS_iPOP_PBMC2011_SecondBatch_81719202114_r02

OTHER RELATED OMICS DATASETS IN: PRJNA154369PRJNA154385PRJNA148005

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Others

SUBMITTER: Chen R et al.

PROVIDER: PAe003777 | PeptideAtlas | 2012-12-31

REPOSITORIES: PeptideAtlas

ACCESS DATA

Json Xml

Publications

Personal omics profiling reveals dynamic molecular and medical phenotypes.

Chen Rui R Mias George I GI Li-Pook-Than Jennifer J Jiang Lihua L Lam Hugo Y K HY Chen Rong R Miriami Elana E Karczewski Konrad J KJ Karczewski Konrad J KJ Hariharan Manoj M Dewey Frederick E FE Cheng Yong Y Clark Michael J MJ Im Hogune H Habegger Lukas L Balasubramanian Suganthi S O'Huallachain Maeve M Dudley Joel T JT Hillenmeyer Sara S Haraksingh Rajini R Sharon Donald D Euskirchen Ghia G Lacroute Phil P Bettinger Keith K Boyle Alan P AP Kasowski Maya M Grubert Fabian F Seki Scott S Garcia Marco M Whirl-Carrillo Michelle M Gallardo Mercedes M Blasco Maria A MA Greenberg Peter L PL Snyder Phyllis P Klein Teri E TE Altman Russ B RB Butte Atul J AJ Ashley Euan A EA Gerstein Mark M Nadeau Kari C KC Tang Hua H Snyder Michael M

Cell 20120301 6

Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes ...[more]

PMID: 22424236

Similar Datasets

Reanalysis of Pandey lab's draft of the human proteome

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

Antibody array profiling for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions (100 FCS)

Project description:Antibody Arrays with 100X FCS used in Figure 6 of Haab, Dunham, and Brown, Genome Biology 2001 2(2): research0004.1-0004.13

2005-06-30 | E-SMDB-109 | biostudies-arrayexpress

Tandem mass tag (TMT) quantification data from knee chondrocytes for 12 osteoarthritis patients, comparing disease tissue against control tissue in each individual

Project description:This data set is made up of 4 experiments (batches) analysing chondrocytes from healthy and diseased knees in 12 patients with osteoarthritis. There are 6 samples (from 3 patients) for each batch, where diseased and control samples were extracted from each patient and compared within patient. The batches were necessary due to the maximum sample capacity (6) of the mass spectrometer. The raw data files were deposited at EBI PRIDE database under accession number PXD002014 ( http://www.ebi.ac.uk/pride/archive/projects/PXD002014 ). This ArrayExpress record contains sample meta-data and processed data in the form of ratios and the log2 fold changes. The ratios were calculated for each patient as diseased vs control (the reference). Please note that one patient (number 52) was excluded from the fold change analysis as no proteins showed any significant change which suggests the samples were not correct or something went wrong with them. There is also the median and standard deviation across the patients.

2017-10-01 | E-PROT-4 | biostudies-arrayexpress

Human immunochemistry data on 83 different normal cell types from 44 tissue types from the Human Protein Atlas project

Project description:This experiment consists of expression profiles for proteins in human tissues based on immunohistochemistry tissue microarrays. The tissue and cell samples came from 144 normal individuals. Normal tissues are represented by samples from three individuals each (except for endometrium, skin, soft tissue and stomach which are represented by samples from six individuals each), one core per individual. <br> The data presented here is based on The Human Protein Atlas version 13 and Ensembl version 75.37. This entry represents a top level summary of the metadata only. For more information about the immunochemistry assays and how the tissue microarrays work for the assays, please visit the Human Protein Atlas website: http://www.proteinatlas.org/about/assays+annotation#ih

2015-07-15 | E-PROT-3 | biostudies-arrayexpress

Proteomics profiling of sera from normoglycaemic twins for which the body mass index is known

Project description:Bead-based proteomics MolPAGE study using sera from normoglycaemic twins

2008-11-02 | E-TABM-370 | biostudies-arrayexpress

MRSA and MSSA

Project description:A strategy for the high-throughput screening of a peptide nucleic acid (PNA) encoded peptide library to allow the identification of MRSA and MSSA selective peptides including AMPs. This novel screening approach allows simultaneous screening of cell selective peptides with different uptake mechanisms including lytic peptides and non-lytic CPPs. MRSA and MSSA were incubated with Library-18 (50 uM; corresponding to 39 nM of each library member) under short incubation times (30 min) to ensure collection of both live and apoptotic cells, which allowed selection of lytic peptides as well as non-lytic CPPs. Incubation was followed by washing and lysis and the intracellular and membrane associated library members were extracted and purified by filter centrifugation (between 3,000 and 10,000 Da). The extracted PNA tags were hybridized onto custom designed microarrays. Each microarray consisted of 4 sub-arrays of 44,000 features each with 33 replicates of each oligonucleotide complementary to each member of the library as well as 1232 non-coding negative controls. Microarray scanning and data analysis (BlueFuse, BlueGenome) was used to extract the intensity of the FAM label, thereby giving the relative amount of PNA hybridized to each spot and the identity of the peptide.

2012-12-01 | E-MEXP-3327 | biostudies-arrayexpress

HipSci project pilot submission for 18 IPS cell lines

Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Raw data files for this study can be accessed from the PRIDE database at EMBL-EBI under accession number PXD003903: http://www.ebi.ac.uk/pride/archive/projects/PXD003903.

2016-06-22 | E-PROT-5 | biostudies-arrayexpress

Antigen array profiling for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions

Project description:Antigen Arrays from Figures 2, 4, and 6 of Haab, Dunham, and Brown, Genome Biology 2001 2(2): research0004.1-0004.13

2005-06-30 | E-SMDB-103 | biostudies-arrayexpress

Antibody array profiling for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions

Project description:Antibody Arrays from Figure 1 of Haab, Dunham, and Brown, Genome Biology 2001 2(2): research0004.1-0004.13

2005-06-30 | E-SMDB-101 | biostudies-arrayexpress

Proteomic profiling of NCI60 cell lines from Cancer Cell Line Encyclopedia

Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.

2017-01-27 | E-PROT-2 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data