Published February 6, 2024
| Version v1
Dataset
Open
DATASET of Spatial Transcriptomics Mouse Hippocampal Slices for MEA-seqX Platform
Contributors
-
1.
German Center for Neurodegenerative Diseases
-
2.
KTH Royal Institute of Technology
-
3.
Karolinska Institutet
Description
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
Files
L75027_aligned_fiducials.jpg
Files
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Additional details
Dates
- Created
-
2024-02-06Available dataset
Software
- Repository URL
- https://github.com/HayderAminLab/MEA-seqX
- Programming language
- Python