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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of single CD41 cell transcriptomes from Zebrafish

ABSTRACT: Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes, and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Danio rerio

SUBMITTER: Valentine Svensson

PROVIDER: E-MTAB-3947 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

Macaulay Iain C IC Svensson Valentine V Labalette Charlotte C Ferreira Lauren L Hamey Fiona F Voet Thierry T Teichmann Sarah A SA Cvejic Ana A

Cell reports 20160121 4

The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from s ...[more]

PMID: 26804912

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Single-cell RNA-Seq data of zebrafish blood cells

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Gene expression analyses of hematopoietic stem cell (HSC) subsets in wildtype or CD41-KO mice

Project description:The hematopoietic stem cell (HSC) compartment is heterogeneous, yet our understanding of the identities of different HSC subtypes is limited. Here we show that platelet integrin CD41 (αIIb), currently thought to only transiently mark fetal HSCs, is expressed on an adult HSC subtype that accumulates with age. CD41+ HSCs were largely quiescent and exhibited myeloerythroid and megakaryocyte gene priming, governed by Gata1, whereas CD41- HSCs were more proliferative and exhibited lymphoid gene priming. When isolated without the use of blocking antibodies, CD41+ HSCs possessed long-term repopulation capacity upon serial transplantations and showed a marked myeloid-bias compared to CD41-HSCs, which yielded a more lymphoid-biased progeny. CD41-knockout mice displayed multilineage hematopoietic defects coupled with decreased quiescence and survival of HSCs, suggesting that CD41 is functionally relevant for HSC maintenance and hematopoietic homeostasis. Transplantation experiments indicated that CD41-KO associated defects are long-term transplantable and HSC-derived, and in part mediated through the loss of platelet mass leading to decreases in HSC exposure to important platelet released cytokines, such as TGFβ1. In summary, our data provide a novel marker to identify a myeloid-biased HSC subtype that becomes prevalent with age, and highlights the dogma of HSC regulation by their progeny.

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Single cell RNA sequencing of CD41+ and CD41- CD34+ HPC in model of RUNX1 insufficiency

Project description:Single cell RNA sequencing of CD41+ and CD41- CD34+ HPC in model of RUNX1 insufficiency

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Gene expression analyses of hematopoietic stem cell (HSC) subsets in wildtype or CD41-KO mice

Project description:The hematopoietic stem cell (HSC) compartment is heterogeneous, yet our understanding of the identities of different HSC subtypes is limited. Here we show that platelet integrin CD41 (M-NM-1IIb), currently thought to only transiently mark fetal HSCs, is expressed on an adult HSC subtype that accumulates with age. CD41+ HSCs were largely quiescent and exhibited myeloerythroid and megakaryocyte gene priming, governed by Gata1, whereas CD41- HSCs were more proliferative and exhibited lymphoid gene priming. When isolated without the use of blocking antibodies, CD41+ HSCs possessed long-term repopulation capacity upon serial transplantations and showed a marked myeloid-bias compared to CD41-HSCs, which yielded a more lymphoid-biased progeny. CD41-knockout mice displayed multilineage hematopoietic defects coupled with decreased quiescence and survival of HSCs, suggesting that CD41 is functionally relevant for HSC maintenance and hematopoietic homeostasis. Transplantation experiments indicated that CD41-KO associated defects are long-term transplantable and HSC-derived, and in part mediated through the loss of platelet mass leading to decreases in HSC exposure to important platelet released cytokines, such as TGFM-NM-21. In summary, our data provide a novel marker to identify a myeloid-biased HSC subtype that becomes prevalent with age, and highlights the dogma of HSC regulation by their progeny. For microarray analysis, 1000 HSCs were FACS sorted from pools of 4-5 mice directly into lysis buffer, RNA extracted and whole transcript amplification was performed as previously described (Gonzalez-Roca E, Garcia-Albeniz X, Rodriguez-Mulero S, Gomis RR, Kornacker K, Auer H. Accurate expression profiling of very small cell populations. PLoS One. 2010;5:e14418.)

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Project description:Analysis of single CD41 cell transcriptomes from Zebrafish

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Hematopoietic differentiation of human embryonic stem cells - timecourse and d7 CD34 and CD41 fractions

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