file: liu2026Multiomics-supplentary-tables.xlsx
format: excel
meta:
  description: '| column_name                 | column_description                                                                                                                                            |

    | --------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------
    |

    | `sample`                    | unique sample name                                                                                                                                            |

    | `exp_batch`                 | SHARE-seq experiment batch that the sample was
    processed in                                                                                                   |

    | `exp_barcode_row`           | Rows in SHARE-seq round 1 split-and-pool barcoding
    plate that the sample was distributed to; important for demultiplexing sequencing
    reads in preprocessing   |

    | `tissue_storage_code`       | unique sample ID                                                                                                                                              |

    | `organ`                     | sample organ name                                                                                                                                             |

    | `organ_code`                | abbreviated sample organ name                                                                                                                                 |

    | `tissue_PCW`                | sample age in post conception weeks                                                                                                                           |

    | `tissue_bioID`              | unique individual ID                                                                                                                                          |

    | `tissue_sex`                | sample sex based on expression of sex marker genes                                                                                                            |

    | `exp_run_date`              | SHARE-seq experiment date                                                                                                                                     |

    | `cutoff_rna_nUMIs`          | cutoff used in preprocessing for RNA number of
    UMIs per cell                                                                                                  |

    | `cutoff_rna_nGenes`         | cutoff used in preprocessing for RNA number of
    genes per cell                                                                                                 |

    | `cutoff_rna_pctMT`          | cutoff used in preprocessing for RNA percentage
    of mitochondrial reads per cell                                                                               |

    | `cutoff_atac_TSS`           | cutoff used in preprocessing for ATAC TSS enrichment
    ratio per cell                                                                                           |

    | `cutoff_atac_nFrags`        | cutoff used in preprocessing for ATAC number of
    fragments per cell                                                                                            |

    | `cutoff_nFrags_nUMIs_ratio` | cutoff used in preprocessing for the ratio between
    ATAC number of fragments and RNA number of UMIs per cell                                                   |

    | `nCells`                    | total number of final whitelisted cells from sample                                                                                                           |

    | `median_rna_nGenes`         | median RNA number of genes per cell for final
    whitelisted cells                                                                                               |

    | `median_rna_nUMIs`          | median RNA number of UMIs per cell for final whitelisted
    cells                                                                                                |

    | `median_rna_pctMT`          | median RNA percentage of mitochondrial reads per
    cell for final whitelisted cells                                                                             |

    | `median_atac_TSS`           | median ATAC TSS enrichment ratio per cell for
    final whitelisted cells                                                                                         |

    | `median_atac_nFrags`        | median ATAC number of fragments per cell for final
    whitelisted cells                                                                                          |

    | `median_atac_frip`          | median ATAC fraction of reads in peaks per cell
    for final whitelisted cells                                                                                   |'
  summary: Sample meta data + QC thresholds per sample, related to Fig. 1
  labels:
    assay: SHARE-seq
    vendor: unknown
    sequencing_platform: Illumina
    dataset: liu2026Multiomics
    reference_genome: reference/Human/genome/ucsc-hg38
    species: human
parameters:
  sheet_name: S1
type: data_frame