DATASET of Spatial Transcriptomics Mouse Hippocampal Slices for MEA-seqX Platform

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