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idr0070-study.txt
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# FILL IN AS MUCH INFORMATION AS YOU CAN. HINTS HAVE BEEN PUT IN SOME FIELDS AFTER THE HASH # SYMBOL. REPLACE THE HINT WITH TEXT WHERE APPROPRIATE.
# STUDY DESCRIPTION SECTION
# Section with generic information about the study including title, description, publication details (if applicable) and contact details
Comment[IDR Study Accession] idr0070
Study Title HDBR Atlas: Gene Expression in Early Human Development
Study Type protein localization in-situ hybridization assay
Study Type Term Source REF EFO EFO
Study Type Term Accession GO_0008104 OBI_0001686
Study Description Gene expression studies in early human development from 3 to 17 post conceptional weeks (PCW).
Study Key Words Human Embryo Fetus Gene Expression Development Immunohistochemistry In Situ Hybridization
Study Organism Homo sapiens
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606
Study Experiments Number 1
Study External URL http://hdbratlas.org
Study BioImage Archive Accession
Study Public Release Date 2020-06-30
# Study Publication
Study PubMed ID 20979583
Study Publication Title The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain.
Study Author List Kerwin J, Yang Y, Merchan P, Sarma S, Thompson J, Wang X, Sandoval J, Puelles L, Baldock R, Lindsay S
Study PMC ID
Study DOI https://doi.org/10.1111/j.1469-7580.2010.01290.x
# Study Contacts
Study Person Last Name Kerwin Cheng Lisgo Copp Henderson
Study Person First Name Janet YuZhu Steven Andrew Deborah
Study Person Email [email protected] [email protected] [email protected] [email protected] [email protected]
Study Person Address HDBR, Newcastle University, international Centre for Life, Newcastle, NE1 4EP HDBR, Newcastle University, international Centre for Life, Newcastle, NE1 4EP HDBR, Newcastle University, international Centre for Life, Newcastle, NE1 4EP HDBR, UCL Institute of Child Health, 30 Guilford Street, London WC1N 1EH HDBR, Newcastle University, international Centre for Life, Newcastle, NE1 4EP
Study Person ORCID
Study Person Roles submitter
# Study License and Data DOI
Study License CC BY 4.0
Study License URL https://creativecommons.org/licenses/by/4.0/
Study Copyright Kerwin et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000137
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] idr0070-kerwin-hdbr/experimentA
Experiment Sample Type tissue
Experiment Description Immunohistochemistry and in situ hybridization analysis in early human development from 3 to 17 weeks post conception.
Experiment Size 5D Images: Average Image Dimension (XYZCT): Total Tb:
Experiment Example Images
Experiment Imaging Method bright-field microscopy dark-field microscopy
Experiment Imaging Method Term Source REF Fbbi Fbbi
Experiment Imaging Method Term Accession Fbbi_00000243 FBbi_00000244
Experiment Comments
# assay files
Experiment Assay File
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description
# Protocols
Protocol Name growth protocol treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type growth protocol treatment protocol image acquisition and feature extraction protocol data analysis protocol
Protocol Type Term Source REF EFO EFO
Protocol Type Term Accession EFO_0003789 EFO_0003969
Protocol Description
# Phenotypes
Phenotype Name
Phenotype Description
Phenotype Score Type
Phenotype Term Source REF CMPO
Phenotype Term Name
Phenotype Term Accession
# Feature Level Data Files (give individual file details unless there is one file per well)
Feature Level Data File Name
Feature Level Data File Format
Feature Level Data File Description
Feature Level Data Column Name
Feature Level Data Column Description
# Processed Data Files
Processed Data File Name
Processed Data File Format tab-delimited text
Processed Data File Description
Processed Data Column Name
Processed Data Column Type
Processed Data Column Annotation Level
Processed Data Column Description
Processed Data Column Link To Assay File