Dataset

DZNE-2024-00225

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Dataset: Spatial Transcriptomics Mouse Hippocampal Slices for MEA-seqX Platform

Amin, H.DZNE* ; Emery, B.DZNE* ; Khanzada, S.DZNE* ; Hu, X.DZNE* ; Klütsch, D. (Project Member)DZNE* ; Larsson, L. (Project Member) ; Dumitru, I. (Project Member) ; Frisén, J. (Project Member) ; Lundeberg, J. (Project Member) ; Kempermann, G. (Project Member)DZNE*

2024
Zenodo

This record in other databases:

Please use a persistent id in citations: doi:10.5281/ZENODO.10626258

Abstract: Sequencing data (fastq.gz) was processed using the 10X Genomics Space Ranger Count pipeline. L75027 = Mouse_Hippocampus_SD L75031 = Mouse_Hippocampus_ENR Outputs include a spatial folder containing outputs that capture the spatiality of the data and a filtered_feature_bc matrix folder containing the tissue-associated barcodes in MEX format. spatial/ aligned_fiducials.jpg: Aligned fiducials QC image detected_tissue_image.jpg: Detected tissue QC image scalefactors_json.json: Scale conversion factors for spot diameter and coordinates at various image resolutions tissue_hires_image.png: Downsampled full resolution image tissue_lowres_image.png: Full resolution image downsampled to 600 pixels on the longest dimension tissue_positions_list.csv: CSV containing spot barcode filtered_feature_bc_matrix.h5: Contains only tissue-associated barcodes in in HDF5 format filtered_feature_bc_matrix/ barcodes.tsv.gz: List of barcodes features.tsv.gz: List of features matrix.mtx.gz: Count matrix

Keyword(s): Spatial transcriptomics ; Large-scale HD-MEA recordings ; Connectome ; Experience-dependent plasticity ; Neuroinformatics ; AI/ML ; Spatiotemporal dynamics ; Predictive modeling

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Contributing Institute(s):

1. Biohybrid Neuroelectronics (BIONICS) (AG Amin)
2. Adult Neurogenesis (AG Kempermann)

Research Program(s):

1. 351 - Brain Function (POF4-351) (POF4-351)
2. 352 - Disease Mechanisms (POF4-352) (POF4-352)

Appears in the scientific report 2024

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