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Series GSE186714 Query DataSets for GSE186714
Status Public on Mar 01, 2022
Title Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human cell pellet array]
Organism Homo sapiens
Experiment type Other
Summary Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). We validated the human and mouse WTA assays using cell lines to demonstrate concordance with orthogonal gene expression profiling methods in profiled region sizes ranging from ∼10-500 cells. By benchmarking against bulk RNAseq and single-molecule fluorescence in situ hybridization, we demonstrate robust transcript detection possible down to ∼100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. We show that spatial profiling with WTA can detect expected spatial gene expression differences between tumor and tumor microenvironment, identify spatial disease-specific heterogeneity in gene expression in histological structures of the human kidney, and comprehensively map transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.
 
Overall design This dataset contains RNA expression from 11 human cell lines from an FFPE cell pellet array using the human Whole Transcriptome Atlas for Digital Spatial Profiling
 
Contributor(s) Zimmerman S
Citation(s) 36100434
Submission date Oct 27, 2021
Last update date Jan 06, 2023
Contact name Stephanie Zimmerman
E-mail(s) stzimmerman@nanostring.com
Organization name NanoString Technologies
Street address 530 Fairview Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (36)
GSM5659278 DSP-1001250003218-C-A01
GSM5659279 DSP-1001250003218-C-A02
GSM5659280 DSP-1001250003218-C-A03
This SubSeries is part of SuperSeries:
GSE190089 Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
Relations
BioProject PRJNA775634
SRA SRP343477

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
GSE186714_Human_11CPA_CollapsedTargetCounts.xlsx 6.6 Mb (ftp)(http) XLSX
GSE186714_Human_11CPA_RawCounts.xlsx 5.2 Mb (ftp)(http) XLSX
GSE186714_Human_11CPA_SampleAnnotations.xlsx 16.3 Kb (ftp)(http) XLSX
GSE186714_RAW.tar 2.0 Mb (http)(custom) TAR (of DCC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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