2026-10-08T14:02:25Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34003890 2026-09-26T19:49:00Z category_24616 item_type_3 month_year_09_2026

Multi-omics datasets of human fetal blood and hematopoietic organs Xiufang Wang (301064) Lipeng Mao (25114968) Ruiling Yan (13240035) Ka Cheuk Yip (13942559) Andong He (12236852) Daiqiang Lu (8824670) Hanhui Nie (18598211) Xiaman Huang (18598205) Yun Wang (32846) Wei Cao (50866) Qiao Zhang (138583) Guobing Chen (5005724) Oscar Junhong Luo (11957882) Ruiman Li (9620029) Feng Gao (3548) Cellular immunology single-cell RNA sequencing fetal immune development T-cell receptor B-cell receptor spectral flow cytometry Olink proteomics PHA stimulation This dataset accompanies the study “Atlas of the immune cell development in the human fetal blood”. 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.Data files<ul><li>Fetal_Immune_Atlas.h5ad — Integrated single-cell atlas containing 235,494 cells from blood, liver, thymus and spleen, with gene expression data and cell metadata.</li><li>Fetal_Immune_Atlas_TCR.h5ad — TCR-associated single-cell data and annotations.</li><li>Fetal_Immune_Atlas_BCR.h5ad — BCR-associated single-cell data and annotations.</li><li>Fetal_Immune_Atlas_Sample_Metadata.csv — Sample metadata and assay availability for 37 samples from 25 donors.</li><li>Fetal_Immune_Atlas_Olink_NPX.xlsx — Olink NPX measurements.</li><li>Fetal_Immune_Atlas_scRNA_Pseudobulk_TPM.csv — 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>Fetal_Immune_Atlas_PHA_Bulk_TPM.csv — Bulk RNA sequencing expression values in TPM for 16 PHA-stimulated PBMC samples, with 39,453 gene entries.</li><li>Fetal_Immune_Atlas_Flow_Blood_FCS_01.zip and Fetal_Immune_Atlas_Flow_Blood_FCS_02.zip — Blood flow cytometry FCS files, distributed across two archives.</li><li>Fetal_Immune_Atlas_Flow_Organs_FCS_01.zip, Fetal_Immune_Atlas_Flow_Organs_FCS_02.zip, and Fetal_Immune_Atlas_Flow_Organs_FCS_03.zip — Organ flow cytometry FCS files, distributed across three archives.</li><li>Fetal_Immune_Atlas_Flow_Blood_23Color.wsp — FlowJo workspace for the 23-color blood flow cytometry analysis.</li><li>Fetal_Immune_Atlas_Flow_Organs_24Color.wsp — FlowJo workspace for the 24-color organ flow cytometry analysis.</li><li>Fetal_Immune_Atlas_Flow_Sample_Metadata.xlsx — Sample information for the spectral flow cytometry experiments.</li><li>Fetal_Immune_Atlas_Flow_Proportions.xlsx — Cell proportions measured by flow cytometry.</li></ul>Using the dataThe H5AD files can be opened with AnnData or Scanpy. Tabular data are provided in CSV or Excel format. Each flow cytometry ZIP archive can be extracted independently; extract all five archives into the same directory to preserve the FCS folder structure. The WSP files contain the corresponding FlowJo workspaces. When opening a workspace, locate the extracted FCS files if prompted. Sample identifiers and assay availability are documented in the sample metadata tables.Analysis codeAnalysis scripts, preprocessing workflows, figure-specific documentation and data placement instructions are available at <a href="https://github.com/thekingofall/scFetallife_Blood" target="_blank">https://github.com/thekingofall/scFetallife_Blood</a>.Author contributionsXiufang Wang, Lipeng Mao and Ruiling Yan contributed equally to the associated study. 2026-09-26T19:49:00Z Dataset Dataset 10.6084/m9.figshare.34003890.v1 https://figshare.com/articles/dataset/Multi-omics_datasets_of_human_fetal_blood_and_hematopoietic_organs/34003890 CC BY 4.0 Open Access after 2030-01-01