Resource
| Id | summary/johansen2025Crossspecies/10x_multiomics_cell_meta_data | ||||||||||||||||||||||||||||||||||||||||||||||||
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| Type | data_frame | ||||||||||||||||||||||||||||||||||||||||||||||||
| Version | 0 | ||||||||||||||||||||||||||||||||||||||||||||||||
| Summary | Cell barcodes and cell-type annotations for Johansen 2025 | ||||||||||||||||||||||||||||||||||||||||||||||||
| Description |
Annotated cells were obtained from the Human, Macaque, and Marmoset comprehensive RNA-expression matrix resources. These resources contain the cell barcode, sample identity, and cell-type annotations directly in AnnData.obs, including Neighborhood, Class, Subclass, Group, and Cluster. The AnnData index was retained as cell_label. The resulting table contains 1,896,133 annotated cells. An ATAC-specific cell identifier, atac_cell_id, is also provided. For Human and Marmoset, this identifier corresponds to the full cell_label. For Macaque, ATAC fragment files use the cell barcode with a trailing “-1”. For harmonization across the barcode resources, sample_id, barcode, and class were added as common namespace columns; sample_id is equivalent to the original sample field, barcode is equivalent to atac_cell_id, and class is equivalent to Subclass. Representative examples are shown below.
ATAC-resource availability was determined using the corresponding cell metadata. All Human and Macaque annotated cells were associated with available ATAC fragment resources. Of the 313,033 Marmoset cells, 294,480 were associated with an available ATAC resource, while 18,553 belonged to samples without an ATAC fragment resource. For those 18,553 cells, atac_cell_id is left blank. Representative ATAC fragment resources from each species were checked directly to confirm the species-specific identifier conventions. Prepared on 2026-09-28. Processing details: The table can be regenerated by running barcodes_johansen25.py. This produces johansen2025_annotated_barcode_namespace.csv. The extended validation can be rerun by setting RUN_EXTENDED_VALIDATION = True in the script. |
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| Labels |
| Columns | count | unique | top | freq |
|---|---|---|---|---|
| species | 1896133 | 3 | Human | 1034819 |
| sample_id | 1896133 | 417 | 936_A03 | 15121 |
| barcode | 1877580 | 1716797 | TACTTGTTCCATAAGC-1 | 7 |
| class | 1896133 | 36 | STR D2 MSN | 386255 |
| cell_label | 1896133 | 1896133 | AAACAGCCAAATGCCC-2362_A05 | 1 |
| cell_barcode | 1896133 | 680274 | AGCCAGTGTGACATAT | 14 |
| atac_cell_id | 1877580 | 1716797 | TACTTGTTCCATAAGC-1 | 7 |
| Neighborhood | 1896133 | 4 | Subpallium GABA | 1045252 |
| Class | 1896133 | 12 | CN LGE GABA | 854597 |
| Subclass | 1896133 | 36 | STR D2 MSN | 386255 |
| Group | 1896133 | 61 | Oligo OPALIN | 254120 |
| Cluster | 1896133 | 1435 | Human-1 | 141852 |
Files
| Filename | Size | md5 |
|---|---|---|
| barcodes_johansen25.py | 15.45 KB | c8587dc1465d59ccf3d783f4f4652dc1 |
| genomic_resource.yaml | 2.74 KB | eacf61a30c4d7fce9e1a32a51f131028 |
| johansen2025_annotated_barcode_namespace.csv.gz | 27.47 MB | b5391315e8921391a3d3f8deafe8a5ad |
| statistics/ |