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idr0154-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] idr0154
Study Title Novel genes in human embryonic arterial valves
Study Type histology RNAscope
Study Type Term Source REF EFO
Study Type Term Accession EFO_0010965
Study Description Validation of novel genes identified by Spatial Transcriptomics in human embryonic arterial valves at CS16 and CS19.
Study Key Words Human embryo heart valves spatial transcriptomics
Study Organism Homo sapiens Mus musculus
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 9606 10090
Study Experiments Number 1
Study External URL https://hdbratlas.org/heart-st.html
Study BioImage Archive Accession
Study Public Release Date 2024-03-05
# Study Publication
Study PubMed ID 38011284
Study Publication Title Spatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves
Study Author List Queen R, Crosier M, Eley L, Kerwin J, Turner JE, Yu J, Alqahtani A, Dhanaseelan T, Overman L, Soetjoadi H, Baldock R, Coxhead J, Boczonadi V, Laude A, Cockell SJ, Kane MA, Lisgo S, Henderson DJ
Study PMC ID PMC10703419
Study DOI https://doi.org/10.1371/journal.pgen.1010777
# Study Contacts
Study Person Last Name Kerwin
Study Person First Name Janet
Study Person Email [email protected]
Study Person Address 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 Queen et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000196
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] idr0154-queen-hdbr/experimentA
Experiment Sample Type tissue
Experiment Description RNAscope and immunofluorescence data for novel genes identified by spatial transcriptomic analysis of human embryonic arterial valves at CS16 and CS19. H&E sections from mouse wild-type and RBP1 knockout.
Experiment Size 5D Images: Average Image Dimension (XYZCT): Total Tb:
Experiment Example Images RBP1 RNAScope CS20_13737_Overview4.jpg
Experiment Imaging Method bright-field microscopy fluorescence microscopy
Experiment Imaging Method Term Source REF Fbbi Fbbi
Experiment Imaging Method Term Accession Fbbi_00000243 FBbi_00000246
Experiment Organism
Experiment Organism Term Source REF NCBITaxon
Experiment Organism Term Accession
Experiment Comments Spatial transcriptomics, Immunofluorescence, RNAscope
# assay files
Experiment Assay File idr0154-experimentA-annotation.csv
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