Multi-omics datasets of human fetal blood and hematopoietic organs

It includes processed single-cell RNA sequencing data, T-cell and B-cell receptor annotations, flow cytometry data, Olink normalized protein expression (NPX) measurements, single-cell pseudobulk expression data, bulk transcriptomic data from PHA-stimulated peripheral blood mononuclear cells (PBMCs), and sample metadata.

Analysis code and supporting documentation are available in the linked GitHub repository.</p><p dir="ltr"><b>Data files</b></p><ul><li><b>Fetal_Immune_Atlas.h5ad</b> — Integrated single-cell atlas containing 235,494 cells from blood, liver, thymus and spleen, with gene expression data and cell metadata.</li><li><b>Fetal_Immune_Atlas_TCR.h5ad</b> — TCR-associated single-cell data and annotations.</li><li><b>Fetal_Immune_Atlas_BCR.h5ad</b> — BCR-associated single-cell data and annotations.</li><li><b>Fetal_Immune_Atlas_Sample_Metadata.csv</b> — Sample metadata and assay availability for 37 samples from 25 donors.</li><li><b>Fetal_Immune_Atlas_Olink_NPX.xlsx</b> — Olink NPX measurements.</li><li><b>Fetal_Immune_Atlas_scRNA_Pseudobulk_TPM.csv</b> — Gene-level expression aggregated from single-cell RNA sequencing for 21 PBMC samples, with 20,719 genes and expression values reported as TPM.</li><li><b>Fetal_Immune_Atlas_PHA_Bulk_TPM.csv</b> — Bulk RNA sequencing expression values in TPM for 16 PHA-stimulated PBMC samples, with 39,453 gene entries.</li><li><b>Fetal_Immune_Atlas_Flow_Blood_FCS_01.zip</b> and <b>Fetal_Immune_Atlas_Flow_Blood_FCS_02.zip</b> — Blood flow cytometry FCS files, distributed across two archives.</li><li><b>Fetal_Immune_Atlas_Flow_Organs_FCS_01.zip</b>, <b>Fetal_Immune_Atlas_Flow_Organs_FCS_02.zip</b>, and <b>Fetal_Immune_Atlas_Flow_Organs_FCS_03.zip</b> — Organ flow cytometry FCS files, distributed across three archives.</li><li><b>Fetal_Immune_Atlas_Flow_Blood_23Color.wsp</b> — FlowJo workspace for the 23-color blood flow cytometry analysis.</li><li><b>Fetal_Immune_Atlas_Flow_Organs_24Color.wsp</b> — FlowJo workspace for the 24-color organ flow cytometry analysis.</li><li><b>Fetal_Immune_Atlas_Flow_Sample_Metadata.xlsx</b> — Sample information for the spectral flow cytometry experiments.</li><li><b>Fetal_Immune_Atlas_Flow_Proportions.xlsx</b> — Cell proportions measured by flow cytometry.</li></ul><p dir="ltr"><b>Using the data</b></p><p dir="ltr">The H5AD files can be opened with AnnData or Scanpy.