Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization

Program
bican
Collection Type
Dynamic
Keywords
Stereo-seq Spatial transcriptomics Human Basal Ganglia single-cell atlas transcript topography cross-species comparison Basal Ganglia

This project generates large scale spatial transcriptomics of the human basal ganglia using recently emerging spatial genomic technologies (Stereo-seq and MERFISH+). This submission includes the raw and processed Stereo-seq dataset from three postmortem human brain tissues. The raw data has three major components: (1) fastq files that contains the sequencing reads, (2) the CID mask file that contains the spatial coordiante of the sequenced RNA reads within the tissue section, and (3) the mosaic image of the ssDNA staining (staining for nuclei). The data was processed using the standard Stereo-seq Analysis Workflow (SAW) pipeline. The output file contains: (1) BAM file, binary format file for saving sequence alignment and gene annotation data, (2) feature expression matrix, (3) image files after registration, and (4) visualization file for presentation and manual processing in StereoMap (visualization software).

Data citation
No data citation listed
Funding agency
NIMH
Grant numbers
UM1MH130994
Access
open
License
No license listed

Download URLs

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Anatomical Regions

  • basal ganglia

Taxa

human

Projects this collection belongs to

Assays, Modalities & Techniques

Assays
spatial transcriptome
Modalities
multimodal
Techniques
Stereo-seq

Child collections

No child collections listed for Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization collection.

Parent collections

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URL Protocols

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Contributors

Show 17 more contributors
  • Ren Li No affiliation listed
  • Benjamin Esser No affiliation listed
  • Qiao Ye No affiliation listed
  • Mahsa Nafisi No affiliation listed
  • Samuel S Park No affiliation listed
  • Pedro Adolfo Sequeira Mendieta No affiliation listed
  • Jillian Berry No affiliation listed
  • Firoza Mamdani No affiliation listed
  • Quan Zhu No affiliation listed
  • Todd C Holmes No affiliation listed
  • Daofeng Li No affiliation listed
  • Ting Wang Washington University School of Medicine 0000-0002-6800-242X
  • Maria Margarita Behrens No affiliation listed 0000-0002-7168-8186
  • Bing Ren University of California, San Diego 0000-0002-5435-1127
  • Joseph R Ecker Salk Institute for Biological Studies 0000-0001-5799-5895
  • Xiangmin Xu University of California, Irvine 0000-0002-5828-1533
  • Bogdan Bintu No affiliation listed

Cross-archive links

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Documentation & resources