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Series GSE228891 Query DataSets for GSE228891
Status Public on Jun 07, 2023
Title Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary In comparison to bulk sequencing or single cell sequencing, spatial transcriptomics preserves the spatial information in tissue slices and can even be mapped to immunofluorescent stainings. This enables to unravel complex interactions of neighboring cells or to link cell morphology to transcriptome data. The 10x genomics visium spatial assay offers to combine spatial transcriptomics with immunofluorescent staining of cryo-sectioned tissue slices. We applied this technique to 10 µm fresh frozen mouse brain slices and developed a protocol that still protects RNA integrity while improving buffers for immunofluorescent staining. We investigated the influence of various parameters on RNA integrity and on antibody binding of blocking, staining as well as wash buffers. Finally, we propose a protocol that does not alter RNA integrity in comparison the 10x genomics demonstrated protocol but allows the usage of several antibodies that have not been compatible with the protocol before. In addition, we discuss the influence of the tested parameters which offers further development of application specific staining protocols.
Overall design Transcriptome data of a newly established immunostaining protocol improving spatial transcriptomic applications
Treatment PCI stands for Peritoneal contamination and infection.
Contributor(s) Hahn N, Bens M, Reißig C, Kempfer M, Schmidl L, Geis C
Citation(s) 37274189
Submission date Apr 03, 2023
Last update date Jun 08, 2023
Contact name Marco Groth
Organization name Leibniz Institute on Aging - FLI
Department Core Facility - Next Generation Sequencing
Street address Beutenbergstraße 11
City Jena
ZIP/Postal code 07747
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM7142286 mouse brain coronal tissue section 1, SHAM
GSM7142287 mouse brain coronal tissue section 2, PCI
GSM7142288 mouse brain coronal tissue section 3, PCI
BioProject PRJNA951864

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Supplementary file Size Download File type/resource
GSE228891_RAW.tar 1.8 Gb (http)(custom) TAR (of CSV, TIFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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