Resource
| Id | summary/zemke2023Conserved/10x_multiomics_cell_meta_data | ||||||||||||||||||||||||||||||||||||||||
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| Type | data_frame | ||||||||||||||||||||||||||||||||||||||||
| Version | 0 | ||||||||||||||||||||||||||||||||||||||||
| Summary | Cell barcodes and cell-type annotations for Zemke 2023 | ||||||||||||||||||||||||||||||||||||||||
| Description |
Annotated cells and subclass assignments were obtained from the Human, Macaque, Marmoset, and Mouse GRR RNA-expression matrices. RNA sample names were compared with the canonical namespace in the sample-description table sample_description_Ivan260918_zemke23.txt. Eight Mouse RNA resource names required canonicalization; these mappings are explicitly checked during processing. The sample-description table was also used to associate each canonical sample with the corresponding RNA+ATAC matrix and ATAC-fragment resource names. These modality-specific names are retained because resource names are not always identical across modalities. For harmonization across the barcode resources, sample_id and class were added as common namespace columns: sample_id is equivalent to canonical_sample, and class is equivalent to subclass.
Extended validation confirmed that all 157,424 annotated barcodes were present in their corresponding RNA+ATAC matrix resources. For samples with an ATAC-fragment resource, all 155,872 expected annotated barcodes were also found in the corresponding fragment resources, with no missing barcodes. The remaining 1,552 annotated cells belong to M1_donor3_rep2, for which no ATAC-fragment resource is listed. Prepared on 2026-09-24. Processing details: The table can be regenerated by running barcodes_zemke23.py. This produces zemke2023_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 | 157424 | 4 | mouse | 47404 |
| sample_id | 157424 | 23 | Mop_5D_rep1 | 11838 |
| canonical_sample | 157424 | 23 | Mop_5D_rep1 | 11838 |
| rna_expression_matrix | 157424 | 23 | mop5d1 | 11838 |
| rna_expression_atac_matrix | 157424 | 23 | Mop_5D_rep1 | 11838 |
| atac_fragments | 155872 | 22 | 5D_rep1_deep | 11838 |
| cell | 157424 | 157424 | M1_donor1_AAACAGCCAACAACAA-1 | 1 |
| barcode | 157424 | 141759 | CCATAAGGTGATTTGG-1 | 4 |
| class | 157424 | 20 | ODC | 41448 |
| subclass | 157424 | 20 | ODC | 41448 |
Files
| Filename | Size | md5 |
|---|---|---|
| barcodes_zemke23.py | 13.67 KB | 44bb68e71fcfeeb109c5576106793ff2 |
| genomic_resource.yaml | 2.5 KB | 96657b74ced6ea6ab6a4a846bb4abef8 |
| sample_description_Ivan260918_zemke23.txt | 1.83 KB | 6f82f4c92bdf707157a799ab409ed6a1 |
| zemke2023_annotated_barcode_namespace.csv.gz | 1.36 MB | e9b476b6add67edfbe1602a7b9071cab |
| statistics/ |