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Series GSE166692 Query DataSets for GSE166692
Status Public on Jul 01, 2021
Title Sci-Space E14 Mouse Embryo Data
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Spatial patterns of gene expression span many scales, and are shaped by both local (e.g. cell-cell interactions) and global (e.g. tissue, organ) context. However, most in situ methods for profiling gene expression either average local contexts or are restricted to limited fields of view. Here we introduce sci-Space, a scale-flexible method that retains single cell resolution while resolving spatial heterogeneity in gene expression at larger scales. As a proof-of-concept, we apply sci-Space to the developing mouse embryo (E14), capturing the approximate spatial coordinates of profiled cells from whole embryo serial sections.
 
Overall design Combinatorially indexed single cell TNA sequencing libraries. Each read contains a combination of PCR indices and a 3-prime barcode that uniquely identify the reads from a single cell. Sequenced molecules consist of both barcoded cDNA and barcoded synthetic hash-oligo molecules used to mark the spatial position from which a cell is derrived.
 
Contributor(s) Srivatsan SR, Regier M
Citation https://science.sciencemag.org/content/373/6550/111
Submission date Feb 12, 2021
Last update date Apr 20, 2022
Contact name Sanjay R Srivatsan
E-mail(s) sanjays@uw.edu, sanjayrsrivatsan@gmail.com
Organization name University of Washington
Department Genome Sciences
Lab Trapnell Lab
Street address 3720 15TH Ave NE Genome Sciences S Foefe Bldg
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (960)
GSM5077869 Developing mouse embryo sections A01G01_S193
GSM5077870 Developing mouse embryo sections A01G02_S289
GSM5077871 Developing mouse embryo sections A01G05_S1
Relations
BioProject PRJNA701618
SRA SRP306203

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE166692_sciSpace_cell_metadata.tsv.gz 11.7 Mb (ftp)(http) TSV
GSE166692_sciSpace_count_matrix.mtx.gz 441.7 Mb (ftp)(http) MTX
GSE166692_sciSpace_gene_metadata.tsv.gz 500.0 Kb (ftp)(http) TSV
GSE166692_sciSpace_hashTable.tsv.gz 359.8 Mb (ftp)(http) TSV
GSE166692_sciSpace_imaging.RDS.gz 78.6 Mb (ftp)(http) RDS
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Raw data are available in SRA
Processed data are available on Series record
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