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Series GSE157299 Query DataSets for GSE157299
Status Public on Oct 11, 2020
Title Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Single-cell RNA-sequencing (scRNA-seq) is a powerful technique for describing cell states. Unfortunately, identifying the spatial arrangement of these states in tissues remains challenging. Here, we describe SEgmentation by Exogenous Perfusion (SEEP), a rapid and integrated method to link positional location to transcriptional identity within three-dimensional (3D) disease models. The method utilizes the steady-state diffusion kinetics of a fluorescent dye to establish a gradient along the radial axis of 3D disease models. Classification of sample layers based on dye accessibility permits dissociated and sorted cells to be retrospectively characterized by transcriptomic and regional identity. Using SEEP, we analyze spheroid, organoid, and in vivo tumor models of high grade serous ovarian cancer (HGSOC). The results validate long-standing beliefs regarding the relationship between cell state and position while also revealing new concepts on how the spatially unique microenvironment of individual cells within tumors influences cell identity.
 
Overall design Spatially segmented single-cell RNA sequencing was performed using the SEEP method and the inDrop protocol as detailed in the manuscript related to this work
 
Contributor(s) Morse D
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Submission date Sep 01, 2020
Last update date Nov 02, 2020
Contact name David Morse
Organization name National Institutes of Health
Department National Center for Advancing Translational Sciences
Street address 9800 Medical Center Drive
City Rockville
State/province Maryland
ZIP/Postal code 20850
Country USA
 
Platforms (2)
GPL21626 NextSeq 550 (Mus musculus)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (34)
GSM4761102 tumor spheroid - center layer - rep1
GSM4761103 tumor spheroid - center layer - rep2
GSM4761104 tumor spheroid - center layer - rep3
Relations
BioProject PRJNA660781
SRA SRP279726

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
GSE157299_RAW.tar 109.7 Mb (http)(custom) TAR (of TSV)
GSE157299_biopsy_all_filtered_barcodes.tsv.gz 11.1 Kb (ftp)(http) TSV
GSE157299_biopsy_all_filtered_genes.tsv.gz 285.5 Kb (ftp)(http) TSV
GSE157299_biopsy_all_filtered_matrix.mtx.gz 14.1 Mb (ftp)(http) MTX
GSE157299_organoid_center_barcodes.tsv.gz 84.6 Kb (ftp)(http) TSV
GSE157299_organoid_center_genes.tsv.gz 197.4 Kb (ftp)(http) TSV
GSE157299_organoid_center_matrix.mtx.gz 28.3 Mb (ftp)(http) MTX
GSE157299_organoid_middle_barcodes.tsv.gz 50.2 Kb (ftp)(http) TSV
GSE157299_organoid_middle_genes.tsv.gz 197.4 Kb (ftp)(http) TSV
GSE157299_organoid_middle_matrix.mtx.gz 24.0 Mb (ftp)(http) MTX
GSE157299_organoid_surface_barcodes.tsv.gz 75.5 Kb (ftp)(http) TSV
GSE157299_organoid_surface_genes.tsv.gz 197.4 Kb (ftp)(http) TSV
GSE157299_organoid_surface_matrix.mtx.gz 27.2 Mb (ftp)(http) MTX
GSE157299_spheroid_all_barcodes.tsv.gz 45.9 Kb (ftp)(http) TSV
GSE157299_spheroid_all_genes.tsv.gz 122.4 Kb (ftp)(http) TSV
GSE157299_spheroid_all_matrix.mtx.gz 33.2 Mb (ftp)(http) MTX
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Raw data are available in SRA
Processed data provided as supplementary file
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