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Series GSE207843 Query DataSets for GSE207843
Status Public on Feb 09, 2023
Title Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue
Organism Mus musculus
Experiment type Other
Summary In this study, we present a multiplexed version of Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with spots of 50 µm×50 µm. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared with previous reports. Furthermore, the introduction of alignment markers allows seamless registration of images and spatial transcriptomic spot coordinates. Together with technological advances, we provide an open-source computational pipeline to transform raw sequencing data from xDBiT experiments into the AnnData format. The functionality of xDBiT was demonstrated by the acquisition of 16 spatially resolved transcriptomic datasets from five different murine organs, including cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of xDBiT spatial transcriptomes allowed for in-depth characterization of the murine kidney.
Overall design Spatial transcriptomics samples of cerebellum, heart, liver, spleen and kidney from 3-month old mice.
Contributor(s) Wirth J, Huber N, Yin K, Brood S, Chang S, Martinez-Jimenez CP, Meier M
Citation(s) 36934108
Submission date Jul 10, 2022
Last update date Apr 13, 2023
Contact name Johannes Wirth
Organization name Helmholtz Zentrum Munich
Street address Ingolstädter Landstraße 1
City Neuherberg
ZIP/Postal code 85764
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (26)
GSM6320933 Spleen, mouse 1, replicate 1
GSM6320934 Spleen, mouse 1, replicate 2
GSM6320935 Heart, mouse 1, replicate 1
BioProject PRJNA857431

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Supplementary file Size Download File type/resource
GSE207843_RAW.tar 12.8 Gb (http)(custom) TAR (of H5AD, TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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