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idr0138-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] idr0138
Study Title Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
Study Type seqFISH
Study Type Term Source REF EFO
Study Type Term Accession EFO_0008991
Study Description Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8–12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain–hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal–ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.
Study Key Words seqFISH mouse organogenesis development multiplexed RNA barcoded gene expression
Study Organism Mus musculus
Study Organism Term Source REF NCBITaxon
Study Organism Term Accession 10090
Study Experiments Number 1
Study External URL https://marionilab.cruk.cam.ac.uk/SpatialMouseAtlas
Study BioImage Archive Accession
Study Public Release Date 2024-09-10
# Study Publication
Study PubMed ID 34489600
Study Publication Title Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
Study Author List Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CHL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC
Study PMC ID PMC8763645
Study DOI https://doi.org/10.1038/s41587-021-01006-2
# Study Contacts
Study Person Last Name Ghazanfar
Study Person First Name Shila
Study Person Email [email protected]
Study Person Address The University of Sydney, Camperdown, New South Wales, 2006, AUSTRALIA
Study Person ORCID 0000-0001-7861-6997
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 Lohoff et al
Study Data Publisher University of Dundee
Study Data DOI https://doi.org/10.17867/10000198
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] idr0138-lohoff-seqfish/experimentA
Experiment Sample Type tissue
Experiment Description seqFISH study of sagittal sections of mouse embryos at 8-10 somite stage. An additional round of hybridisation to capture cell membrane is performed to accurately segment cell boundaries.
Experiment Size 5D Images: Average Image Dimension (XYZCT): Total Tb: 0.5
Experiment Example Images
Experiment Imaging Method spinning disk confocal microscopy
Experiment Imaging Method Term Source REF Fbbi
Experiment Imaging Method Term Accession FBbi_00000253
Experiment Organism
Experiment Organism Term Source REF NCBITaxon
Experiment Organism Term Accession
Experiment Comments seqFISH imaging. Additional files include field of view (fov) information for the entire sample, low-resolution brightfield image of entire sample, and barcoding information for each hybridisation and channel.
# assay files
Experiment Assay File idr0138-experimentA-annotation
Experiment Assay File Format tab-delimited text
Assay Experimental Conditions WT
Assay Experimental Conditions Term Source REF
Assay Experimental Conditions Term Accession
Quality Control Description Additional imaging rounds before and after hybridisation, including a repeat of HybCycle_0 to assess maintaining of data quality.
# 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 HybCycle_readouts.xlsx
Feature Level Data File Format Excel
Feature Level Data File Description Description of each Hybridisation Cycle and corresponding Readout image round.
Feature Level Data Column Name HybCycle Description Readout
Feature Level Data Column Description Hybridisation Cycle, Description of the type of imaging performed in the hybridisation cycle, readout ID for quantitative images.
Feature Level Data File Name Supplementary_Table_2_barcoding_decoding_SG.xlsx
Feature Level Data File Format Excel (multisheet)
Feature Level Data File Description Barcoding schema for seqFISH imaging. Matching table between HybCycle and Channel to Readout probe ID, specification of readout probe sequence, barcoded pseudocolour assignment of each gene to the four barcoding rounds, and readout probe assignment for each gene and hybridisation.
Feature Level Data Column Name ID HybCycle Channel Channel Number Readout_sequence Barcoded_Hyb Pseudocolors; ID Hyb1_pseudocolour Hyb2_pseudocolour Hyb3_pseudocolour Hyb4_pseudocolour; ID Hyb1_readout_sequence Hyb2_readout_sequence Hyb3_readout_sequence Hyb4_readout_sequence
Feature Level Data Column Description Readout ID, Hybridisation Cycle number, Channel colour value, Channel Number in image, Readout_sequence, Barcoded hybridisation number out of 4, Pseudocolor value out of 12; Gene ID, Hyb1_pseudocolour out of 12, Hyb2_pseudocolour out of 12, Hyb3_pseudocolour out of 12, Hyb4_pseudocolour out of 12; Gene ID, Hyb1 readout sequence, Hyb2 readout sequence, Hyb3 readout sequence, Hyb4 readout sequence
Feature Level Data File Name Sequential_readout-ID_v3_TL_ID_SG.csv
Feature Level Data File Format csv
Feature Level Data File Description Schema for single molecule FISH rounds following seqFISH.
Feature Level Data Column Name <NAME> Readout Readout_sequence 15nt_color HybCycle Channel
Feature Level Data Column Description Gene name, Readout ID, Readout sequence, Channel color value, Hybridisation Cycle, Channel number for Hybridisation cycle.
Feature Level Data File Name TimEmbryos-102219/fovinfo.csv
Feature Level Data File Format csv
Feature Level Data File Description Table of relative positions of fields of view in physical space.
Feature Level Data Column Name fov x y bound_x_1 bound_x_2 bound_x_3 bound_x_4 bound_y_1 bound_y_2 bound_y_3 bound_y_4
Feature Level Data Column Description field of view ID (fov1 = Pos0), x centroid, y centroid, four corners of bounding box x-coordinate, four corners of bounding box y-coordinate.
Feature Level Data File Name TimEmbryos-120919/fovinfo.csv
Feature Level Data File Format csv
Feature Level Data File Description Table of relative positions of fields of view in physical space.
Feature Level Data Column Name fov x y bound_x_1 bound_x_2 bound_x_3 bound_x_4 bound_y_1 bound_y_2 bound_y_3 bound_y_4
Feature Level Data Column Description field of view ID (fov1 = Pos0), x centroid, y centroid, four corners of bounding box x-coordinate, four corners of bounding box y-coordinate.
Feature Level Data File Name TimEmbryos-120919/Slide Explorer.tif
Feature Level Data File Format tif
Feature Level Data File Description Low resolution brightfield image of entire slide.
Feature Level Data Column Name
Feature Level Data Column Description
Feature Level Data File Name TimEmbryos-102219/Slide Explorer.tif
Feature Level Data File Format tif
Feature Level Data File Description Low resolution brightfield image of entire slide.
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