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idr0043-study.txt
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# STUDY DESCRIPTION SECTION
# Section with generic information about the study including title, description, publication details (if applicable) and contact details
Comment[IDR Study Accession] idr0043
Study Title Tissue-based map of the human proteome
Study Type protein localization
Study Type Term Source REF EFO
Study Type Term Accession GO:0008104
Study Description Sequencing the human genome gave new insights into human biology and disease. However, the ultimate goal is to understand the dynamic expression of each of the approximately 20,000 protein-coding genes and the function of each protein. Uhlen et al. now present a map of protein expression across 32 human tissues. They not only measured expression at an RNA level, but also used antibody profiling to precisely localize the corresponding proteins.
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606
Study Experiments Number 1
Study External URL https://www.proteinatlas.org
Study Public Release Date 2018-11-01
# Study Publication
Study PubMed ID 25613900
Study Publication Title Proteomics. Tissue-based map of the human proteome.
Study Author List Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F
Study PMC ID
Study DOI https://doi.org/10.1126/science.1260419
# Study Contacts
Study Person Last Name HPAIT
Study Person First Name HPAIT
Study Person Email [email protected]
Study Person Address Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm
Study Person Roles submitter
# Study License and Data DOI
Study License CC BY-SA 3.0
Study License URL https://v18.proteinatlas.org/about/licence
Study Copyright Uhlen et al
Study Data Publisher University of Dundee
Study Data DOI
Term Source Name NCBITaxon EFO CMPO FBbi
Term Source URI http://purl.obolibrary.org/obo/ http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/cmpo/ http://purl.obolibrary.org/obo/
# EXPERIMENT SECTION
# Experiment Section containing all information relative to each experiment in the study including materials used, protocols names and description, phenotype names and description. For multiple experiments this section should be repeated. Copy and paste the whole section below and fill out for the next experiment
Experiment Number 1
Comment[IDR Experiment Name] idr0043-uhlen-humanproteinatlas/experimentA
Experiment Sample Type tissue
Experiment Description Mapping of protein expression across all major tissues and organs in the human body
Experiment Size 5D Images: Average Image Dimension (XYZCT): Total Tb: # fill in any values you know
Experiment Example Images https://idr.openmicroscopy.org/webclient/?show=image-3977054
Experiment Imaging Method bright-field microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession Fbbi_00000243 http://www.ebi.ac.uk/ols/ontologies/fbbi
Experiment Comments
# assay files
Experiment Assay File # put in the name of the assay file
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions # if there were any experimental conditions some cells were grown under as part of the study enter the information here e.g. different environmental stress conditions, or mutant background compared to wild type.
Assay Experimental Conditions Term Source REF # leave blank
Assay Experimental Conditions Term Accession # leave blank
Quality Control Description # a brief description of the kind of quality control measures that were taken (if applicable)
# Protocols
Protocol Name growth protocol treatment protocol image aquistion and feature extraction protocol data analysis protocol
Protocol Type growth protocol treatment protocol image aquistion and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0003969
Protocol Description # text about how the cells were grown here # text about any specific treatment to the cells here # text about labeling, the imaging hardware and software, feature extraction methods. # text about the analysis of the images and features if applicable
# Phenotypes
Phenotype Name # if any specific phenotypes were identified in the experiment enter the information here. Each phenotype should be in a separate column.
Phenotype Description # give a brief description of each phenotype, or how it was determined e.g. if score X is greater than Y then this phenotype assigned.
Phenotype Score Type # choose from: manual, automatic
Phenotype Term Source REF CMPO
Phenotype Term Name # if your phenotype matches a term in the Cellular Microscopy Phenotype Ontology enter it here http://www.ebi.ac.uk/CMPO
Phenotype Term Accession # if your phenotype matches a term in the Cellular Microscopy Phenotype Ontology enter the accession for the term here http://www.ebi.ac.uk/CMPO
# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name # list any feature level table files here
Feature Level Data File Format # a description of the table
Feature Level Data File Description # tab-delimited text or other format
Feature Level Data Column Name # list all the columns in the table, each column in the table should be in a separate column here
Feature Level Data Column Description # describe the values in each column
# Processed Data Files
Processed Data File Name # the name of the processed data file
Processed Data File Format tab-delimited text
Processed Data File Description # a brief description of the what is in the file
Processed Data Column Name # list each of the columns in the processed data file here, each column in the table should be ain a separate column here
Processed Data Column Type # state the type of value in each column. Choose from: location, reagent identifier, gene identifier, gene symbol, gene description, data, phenotype, experimental condition
Processed Data Column Annotation Level # for data and phenotype columns enter the level of the annotation so that it is clear if the value is derived from data from a image, is averaged over many images. E.g. gene, experimental condition
"experimental condition and gene, phenotype, image, protein"""
Processed Data Column Description # for each data and phenotype column, enter a brief description of what the value represents
Processed Data Column Link To Assay File # enter which column can be used to link the information in the processed data file to the assay file e.g. targeted protein, or gene identifier