Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor [bulkRNAseq]

ABSTRACT: Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor. We characterized mPB CD34+ drug products and their ex-vivo expanded samples (4 and 7 days) cell populations (n=2 patients from 10.1056/NEJMoa2106596) and transduction efficency by single cell RNA sequencing (scRNAseq) using commercial serum-free media in the presence of the epigenetic modifier UM171 and early acting cytokines (DP: refers to 10.1056/NEJMoa2106596; for cultured samples at day4 and day 7: SFT6: stem cell factor, 100ng/mL; flt3 ligand, 50ng/mL). Cells of DP and its expanded samples were transduced with a lentiviral vector expressing the IDUA gene. WPRE transcript quantification was used as surrogate of LV IDUA expression to evaluated transduction efficiency.

ORGANISM(S): Homo sapiens

PROVIDER: GSE292605 | GEO | 2026/06/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	GSE292605_BulkRNAseq_matrix.txt.gz	Txt

Items per page:

1 - 2 of 2

Similar Datasets

Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor [MPS_scRNAseq]

Project description:Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor. We characterized mPB CD34+ drug products and their ex-vivo expanded samples (4 and 7 days) cell populations (n=2 patients from 10.1056/NEJMoa2106596) and transduction efficency by single cell RNA sequencing (scRNAseq) using commercial serum-free media in the presence of the epigenetic modifier UM171 and early acting cytokines (DP: refers to 10.1056/NEJMoa2106596; for cultured samples at day4 and day 7: SFT6: stem cell factor, 100ng/mL; flt3 ligand, 50ng/mL). Cells of DP and its expanded samples were transduced with a lentiviral vector expressing the IDUA gene. WPRE transcript quantification was used as surrogate of LV IDUA expression to evaluated transduction efficiency.

2026-06-10 | GSE292604 | GEO

Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor [scRNAseq]

Project description:Clonal analysis and transcriptional profiling of ex vivo expanded mobilized peripheral blood hematopoietic stem and progenitor We characterized mPB CD34+ cell population dynamics (n=2 donors) by single cell RNA sequencing (scRNAseq) during 8 days of expansion culture using commercial serum-free media (Miltenyi Bioscience) in the presence of the epigenetic modifier UM171 and early acting cytokines (SFT6: stem cell factor, 100ng/mL; flt3 ligand, 100ng/mL; thrombopoietin, 50ng/mL; interleukin 6, 50ng/mL). Cultured cells were transduced with a lentiviral vector expressing a marker gene, to simulate a gene therapy context. CD34+ cells from donor 1 were analyzed before culture, on day 4 and on day 8 of expansion. For donor 2, in addition to the CD34+ bulk expansion culture, part of the CD34+ cells were FACS-sorted into subpopulations enriched in primitive HSPC (CD34+CD38-), committed granulocyte-monocyte progenitors (GMP) or megakaryocyte-erythrocyte progenitors (MEP), and subsequently expanded for 7 days.

2026-06-10 | GSE292606 | GEO

RNA expression profiling of human mPB or CB-derived CD34+ cells treated with UM171 at different doses

Project description:RNASeq data for mPB or CB-derived CD34+ exposed to UM171 human mobilized peripheral blood or cord blood-derived CD34(+) cells were cultured for 16 hours with vehicle (DMSO), dose response of UM171 [11.9nM, 19nM, 30.5nM, 48.8nM, 78.1nM and 125nM], SR1 [500nM] and combination of( UM171 [48.8nM]+SR1 [500nM])

2014-10-21 | E-GEOD-57561 | biostudies-arrayexpress

RNA expression profiling of human mPB or CB-derived CD34+ cells treated with UM171 at different doses

Project description:RNASeq data for mPB or CB-derived CD34+ exposed to UM171

2014-10-21 | GSE57561 | GEO

Ex vivo long-term expansion of human hematopoietic stem and progenitor cells as a tool for modeling vector integration sites and clonality

Project description:The small molecules A83-01, pomalidomide, and UM171 (APU) were used for the ex vivo expansion, lentiviral transduction, and long-term cultivation of umbilical cord blood-derived HSPCs. We determined the influence of APU on the stemness of HSPCs and their differentiation capacity via single-cell RNA sequencing (scRNA seq). APU supported the expansion of CD34+CD38-CD45RA-CD90+EPCR+ HSPCs. scRNAseq confirmed the enrichment of HSC signature genes in 24-h, 7-day, and 14-day APU-expanded HSPCs compared to the clinically used medium SFT3 (SCF, FLT3-L, TPO, IL-3).

2026-02-11 | GSE318863 | GEO

Characterization of transcriptomic changes induced by a gene therapy cell culture protocol to single human bone marrow and mobilized peripheral blood hematopoietic stem and progenitor cells [BM_MPB]

Project description:Here we present the single cell transcriptomes of human adult mobilized peripheral blood (mPB) and bone marrow (BM) hematopoietic stem and progenitor cell (HSPC) subsets,: long-term haematopoietic stem cells (LT-HSCs), short-term HSCs (ST-HSCs) and CD34+ cells before (0 h) and after 62 hours (62 h) of culture in a conditions mimicking gene therapy protocols. The culture protocol includes two hits of lentiviral transduction (lentiviral vector contains a GFP construct) and media as previously published . The objectives of this study are to investigate the effects of lentiviral transduction and cell culture in gene therapy protocol conditions on human mPB and BM haematopoietic stem and progenitor cell (HSPC) subsets. In the present study we report that 62 h of culture in gene therapy media significantly alters the transcriptome of BM and mPB subsets. In contrast, lentiviral transduction alone has a minimal effect on the transcriptome of all tested subsets. T=transduced GFP+; NT=non transduced; GFP-= transduced GFP-

2022-11-19 | GSE213370 | GEO

Expression profiling of fresh, DMSO or UM171 expanded CD34+ cells by high throughput sequencing

Project description:Ex-vivo expansion of hematopoietic stem cells (HSCs) is gaining in importance for cell and gene therapy and requires a shift from dormancy state to activation and cycling. However, abnormal or excessive HSC activation results in reduced self-renewal ability and increased propensity for myeloid-biased differentiation. To date, the threshold of HSC activation that marks “the point of no return” is undetermined. Identifying the molecular determinants that restrain or control HSC activation is essential for preventing accelerated exhaustion of cultured-HSCs. We now report that activation of the E3 ligase complex CRL3KBTBD4 by UM171 not only induces epigenetic changes through CoREST1 degradation but also control chromatin bound MYC levels to prevent excessive activation and maintain lympho-myeloid potential of expanded populations. Furthermore, reconstitution activity and multipotency of UM171-treated HSC is specifically compromised when MYC levels are experimentally increased despite degradation of CoREST1.

2024-10-24 | GSE232227 | GEO

Aged, Young and Restored Samples from Mobilized Peripheral Blood [mRNA]

Project description:We report the gene expression changes in mobilized peripheral blood in aged, young, and aged/young samples cocultured in transwell. Restored samples refer to aged MPB co-cultured with young MPB in the transwell culture

2021-12-01 | GSE138563 | GEO

Aged, Young and Restored Samples from Mobilized Peripheral Blood [miRNA]

Project description:We report the miRNA expression in each CD34+ cells and their exosomes in mobilized peripheral blood in aged, young, and aged/young samples cocultured in transwell. Restored samples refer to aged MPB co-cultured with young MPB in the transwell culture.

2021-12-01 | GSE138564 | GEO

Deciphering the effect of UM171 on human hematopoietic progenitor cell fate through clonal analysis

Project description:Ex vivo expansion of hematopoietic stem cells (HSC) requires the maintenance of a stemness state while cells are proliferating. This can be achieved via exposure to UM171 which leads to the degradation of chromatin modifiers and prevents the loss of key epigenetic marks. However, the chromatin landscape varies across populations within the hematopoietic system and the effect of UM171 on self-renewal and differentiation potential of different hematopoietic progenitor cells is less characterized. To address this, we used the CellTag barcoding approach to track the fate of individual stem and progenitor cells during in vitro expansion. We showed that in addition to its HSC self-renewing property, UM171 specifically modulates cell fate of a precursor common to erythroid, megakaryocytic, and mast cells in favor of self-renewal and a mast-bias differentiation trajectory. This differentiation bias can be driven by pro-inflammatory signaling pathways that are activated downstream of UM171 and resulted in an abundant mast cell population that can be transplanted as part of the graft to populate mice tissues in xenotransplantation studies.

2024-11-12 | GSE264199 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data