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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Robust temporal map of human in vitro myelopoiesis using single-cell genomics (RNAseq data)

ABSTRACT: We performed a detailed analysis of the in vitro differentiation of induced pluripotent stem cells to macrophages and dendritic cells.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Clara Alsinet

PROVIDER: E-MTAB-11623 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Robust temporal map of human in vitro myelopoiesis using single-cell genomics (ATAC data)

Project description:We performed a detailed analysis of the in vitro differentiation of induced pluripotent stem cells to macrophages and dendritic (chromatin accessibility data).

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Robust temporal map of human in vitro myelopoiesis using single-cell genomics.

Project description:Myeloid cells are central to homeostasis and immunity. Characterising in vitro myelopoiesis protocols is imperative for their use in research, immunotherapies, and understanding human myelopoiesis. Here, we generate a >470K cells molecular map of human induced pluripotent stem cells (iPSC) differentiation into macrophages. Integration with in vivo single-cell atlases shows in vitro differentiation recapitulates features of yolk sac hematopoiesis, before definitive hematopoietic stem cells (HSC) emerge. The diversity of myeloid cells generated, including mast cells and monocytes, suggests that HSC-independent hematopoiesis can produce multiple myeloid lineages. We uncover poorly described myeloid progenitors and conservation between in vivo and in vitro regulatory programs. Additionally, we develop a protocol to produce iPSC-derived dendritic cells (DC) resembling cDC2. Using CRISPR/Cas9 knock-outs, we validate the effects of key transcription factors in macrophage and DC ontogeny. This roadmap of myeloid differentiation is an important resource for investigating human fetal hematopoiesis and new therapeutic opportunities.

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scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

Robust temporal map of human in vitro myelopoiesis using single-cell genomics (RNAseq data)

Project description:Robust temporal map of human in vitro myelopoiesis using single-cell genomics (RNAseq data)

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Robust temporal map of human in vitro myelopoiesis using single-cell genomics (ATAC data)

Project description:Robust temporal map of human in vitro myelopoiesis using single-cell genomics (ATAC data)

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Multiome experiment of the neuroepithelial stage of brain organoid developement

Project description:To investigate the heterogeneity during the neuroepithelial stage of organoid development, we performed a multiome experiment on day 15-18 old brain organoids

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A robust experimental and computational framework analysis at multiple resolutions, modalities and coverages

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Single-cell 5' Gene Expression and V(D)J Amplification (10X Genomics) of splenic CD4+ T cells from Plasmodium chabaudi infected mice

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2020-11-13 | E-MTAB-9691 | biostudies-arrayexpress

scRNA-seq data from GLI3 KO in brain organoids

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