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Status |
Public on Feb 09, 2023 |
Title |
Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue |
Organism |
Mus musculus |
Experiment type |
Other
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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.
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Overall design |
Spatial transcriptomics samples of cerebellum, heart, liver, spleen and kidney from 3-month old mice.
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Contributor(s) |
Wirth J, Huber N, Yin K, Brood S, Chang S, Martinez-Jimenez CP, Meier M |
Citation(s) |
36934108 |
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Submission date |
Jul 10, 2022 |
Last update date |
Apr 13, 2023 |
Contact name |
Johannes Wirth |
E-mail(s) |
johannes.wirth@helmholtz-muenchen.de
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Organization name |
Helmholtz Zentrum Munich
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Street address |
Ingolstädter Landstraße 1
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City |
Neuherberg |
ZIP/Postal code |
85764 |
Country |
Germany |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (26)
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GSM6320936 |
Heart, mouse 1, replicate 2 |
GSM6320937 |
Liver, mouse 1, replicate 1 |
GSM6320938 |
Kidney, mouse 1, replicate 1 |
GSM6320939 |
Kidney, mouse 1, replicate 2 |
GSM6320940 |
Spleen, mouse 2, replicate 1 |
GSM6320941 |
Spleen, mouse 2, replicate 2 |
GSM6320942 |
Heart, mouse 2, replicate 1 |
GSM6320943 |
Heart, mouse 2, replicate 2 |
GSM6320944 |
Liver, mouse 2, replicate 1 |
GSM6320945 |
Kidney, mouse 2, replicate 1 |
GSM6320946 |
Kidney, mouse 2, replicate 2 |
GSM6320947 |
Cerebellum, mouse 3, replicate 1 |
GSM6320948 |
Cerebellum, mouse 3, replicate 2 |
GSM6934366 |
Cross-contamination experiment: Liver, mouse 3, replicate 1 |
GSM6934367 |
Cross-contamination experiment: Liver, mouse 3, replicate 2 |
GSM6934368 |
Cross-contamination experiment: Liver, mouse 3, replicate 3 |
GSM6934369 |
Cross-contamination experiment: Liver, mouse 3, replicate 4 |
GSM6934370 |
Cross-contamination experiment: Liver, mouse 4, replicate 1 |
GSM6934371 |
Cross-contamination experiment: Liver, mouse 4, replicate 2 |
GSM6934372 |
Cross-contamination experiment: Liver, mouse 4, replicate 3 |
GSM6934373 |
Cross-contamination experiment: Liver, mouse 4, replicate 4 |
GSM6934374 |
Pancreas, mouse 1, replicate 1 |
GSM6934375 |
Pancreas, mouse 1, replicate 2 |
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Relations |
BioProject |
PRJNA857431 |
Supplementary file |
Size |
Download |
File type/resource |
GSE207843_RAW.tar |
12.8 Gb |
(http)(custom) |
TAR (of H5AD, TAR) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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