Subject	Neuroscience: General
Specific subject area	Secondary brain injury after intracranial hemorrhage, mouse model, spatial transcriptome analysis
Type of data	Table Image Figure
How the data were acquired	A mouse model with striatal injection of heme, hemopexin or vehicle control (saline) was used. Histological images were acquired on an AxioObserver (Zeiss) at a 10x magnification. mRNA extraction and library construction from cryosections using a Visium Spatial Slide (10X Genomics, Pleasanton, CA, USA) according to the manufacturer's instructions (User Guide CG000239, Rev A). Sequencing was performed on an Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA) using a 28 bp + 120 bp paired-end sequencing mode. The mapping and counting of the reads to the reference genome GRCm38.p6 (mm10), as well as the alignment of the barcodes in each read with the 55-µm features in the spatial dimension was performed using Space Ranger 1.1.0. (10X Genomics, Pleasanton, CA, USA). Visualization, data processing and downstream analysis was performed using the Scanpy python package (version 1.4.4).
Data format	Raw Analyzed Filtered
Description of data collection	The spatial transcriptomes of coronal brain sections from mice 24h after striatal injection of 10 µL heme, heme-hemopexin or vehicle control (saline) solution were sequenced using the Visium workflow from 10X Genomics (Pleasanton, CA, USA).
Data source location	•Institution: Division of Internal Medicine, Universitätsspital and University of Zurich •City/Town/Region: Zurich •Country: Switzerland
Data accessibility	Repository name: Gene expression omnibus Permanent identification number: GSE182127 Direct link to the dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182127). Repository name: Zenodo Permanent identification number: 10.5281/zenodo.5638720 Direct link to the dataset: https://doi.org/10.5281/zenodo.5638720.
Related research article	Buzzi, R. M., Akeret, K., Schwendinger, N., Klohs, J., Vallelian, F., Hugelshofer, M., & Schaer, D. J. (2021). Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain. Free Radical Biology and Medicine. https://doi.org/10.1016/j.freeradbiomed.2021.11.011