Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT-CHILP/iR9-CHILP_SmartSeq2]

ABSTRACT: We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells (PSCs) gave rise to engraftable iHPC capable of developing into common helper innate lymphoid progenitors (CHILPs) in the Rag2-/-Il2rg-/- recipients. To assess the gene-expression pattern of the PSC-derived R9-iCHILPs, we performed single-cell RNA-seq on the regenerative CD45.2+GFP+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- R9-iCHILPs from the bone marrow of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- WT-CHILPs from the bone marrow of wild type mice (C57BL/6, CD45.2).

ORGANISM(S): Mus musculus

PROVIDER: GSE210861 | GEO | 2022/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT_ILC/R9_iILC_SmartSeq2]

Project description:We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. We performed single-cell RNA-seq on the entire regenerative CD45.2+GFP+Lin-CD127+ R9-ILC population from the intestine of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+ WT-ILC population from the intestine of wild type mice (C57BL/6, CD45.2). Single-cell transcriptome illustrated the transcriptome landscape of the R9-ILCs and wild type ILCs including ILC1, ILC2 and ILC3.

2022-09-30 | GSE186777 | GEO

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [R9_DAY7.5_10X_genomics]

Project description:We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. The regenerative ILCs were detected in multiple tissues including intestine, lung, liver, spleen and thymus. We performed single cell RNA-seq on the sorted GFP+CD45.2+Lin- cells from the bone marrow of recipients at day 7.5 after iHPC transplantation. Single-cell transcriptome illustrated the existence of regenerative ILC-related progenitors including iLP, iILCP, iILC1/3P and iILC2P, and the cellular trajectory of regenerative ILCs development in vivo was closely resembles the natural ILCs development.

2022-09-30 | GSE186776 | GEO

Transcriptional deregulation in EZH2-deficient lymphocyte progenitors

Project description:This goal of this study was to identify genes that are deregulated in the absence of EZH2 in early lymphocyte progenitors. We examined gene expression by RNA-sequencing in sorted CLPs (Lin-CD117int CD127+ CD135+), pro-B cells (B220+CD19+CD43+), DN3 cells (Lin- CD25+ CD117-), splenic NK cells (Lin-NK1.1+DX5+) and bone marrow ILC2 cells (Lin- Sca1+CD127+) from Ezh2fl/fl Il7racre/+ and Il7racre/+ control mice. Reads were aligned to the mm10 reference genome by Tophat2.1.0. Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78. Differential expression was calculated across 2-3 independent replicates by EdgeR. We found that CLPs, ILC2s, and splenic NK cells maintained their normal transcriptional programs despite loss of EZH2. In contrast, loss of EZH2 caused over 1000 genes to be deregulated in pro-B and DN3 cells indicating that EZH2 is required for transcriptomic stability in adaptive, but not innate lymphocyte progenitors.

2017-04-07 | GSE97462 | GEO

Transcriptomic analysis of femoral diaphysis and primary osteoprogenitor cells cultures from mouse strains with SHIP1 deficiency and controls

Project description:Investigation of the SHIP1 (Inpp5d)-dependent and Rag2/Il2rg-dependent transcriptional changes in bone and osteoprogenitor cells cultures from murine strains with SHIP1 deficiency (Inpp5dm1Btlr/ m1Btlr, http://www.informatics.jax.org/allele/key/65037) and controls. Specifically, transcriptomic analysis was performed from femoral diaphysis from SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+/styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype). Alternatively, osteoprogenitor cells isolated from bone marrow from the same genotypes as above were differentiated in vitro into primary osteoclasts in the presence or absence of RANKL. After 5 days, RNA was extracted from these cultures for transcriptomic analysis (n=3 for each genotype). Experimental Designs: Transcripts were analyzed in femoral diaphysis of SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype). Alternatively, transcripts were analyzed in primary osteoclast cultures from bone marrow cells isolated from SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype), which were supplemented or not with RANKL.

2024-02-21 | E-MTAB-13164 | biostudies-arrayexpress

Myeloid, B, and T lineage regeneration from pluripotent stem cells by defined transcription factors

Project description:We identified that synergistic and inducible expression of specific transcription factors in pluripotent stem cells gave rise to engraftable iHPC capable of developing into multiple lineages including myeloid cells, T cells, and B cells in the C57BL/6 recipients. The regenerative myeloid, T, and B cells were detected in multiple tissues including peripheral blood, bone marrow and spleen. We performed single cell RNA-seq on the sorted GFP+CD45.2+ cells from the peripheral blood of recipients at 16 weeks after iHPC transplantation. Single-cell transcriptome illustrated the existence of regenerative myeloid cells, T cells, and B cells. The cell hierarchy of regenerative myeloid cells, T cells, and B cells in vivo resembles those of natural counterparts.

2022-11-24 | GSE189736 | GEO

Gene expression of thymic settling progenitors from embryos at E13 compared to E18

Project description:We used whole genome transcriptome as gene discovery to further understand the differential behaviour of the first (embryonic) and second waves of thymic settling progenitors in the murine embryo. Mouse embryos at days 13 and 18 of gestation were isolated and the thymic lobes were dissected. Single cell suspension was prepared and treated with biotinilated antibodies to CD3, CD4, CD8, TER119, Gr1, CD25, CD19, NK1.1 and CD11c. Cell suspensions were then incubated with streptavidin Miltenyi Macs beads. Lineage negative thymocytes were recovered in Macs columns. Cell suspensions were then incubated with antibodies against CD135, CD117, CD44, CD24 and Streptavidin bound to PECy7. Lin-, CD117+, CD44+, CD24low, CD135+ cells were then isolated by cell sorting. 3 biological replicates of each sample were isolated with 104-3x104 cells

2013-09-17 | E-GEOD-50910 | biostudies-arrayexpress

Single cell transcriptomic analysis of human CD25+ CD127- CD4+ Treg cells and CD25- CD127+ CD4+ Tconv cells isolated from peripheral blood

Project description:Single cell transcriptomic analysis of human CD25+ CD127- CD4+ Treg cells and CD25- CD127+ CD4+ Tconv cells isolated from peripheral blood from two different donors

2018-03-15 | GSE111901 | GEO

Human Innate Lymphoid Cell Precursors Express CD48 that Modulates ILC Differentiation through 2B4 Signaling

Project description:Innate lymphoid cells (ILCs) develop from common lymphoid progenitors (CLP), which further differentiate into the common ILC progenitor (CILP) that can give rise to both ILCs and NK cells. Murine ILC intermediates have recently been characterized, but the human counterparts and their developmental trajectories have not yet been identified, largely due to the lack of homologous surface receptors in both organisms. Here, we show that human CILPs (CD34+CD117+α4β7+Lin-) acquire CD48 and CD52, which define NK progenitors (NKPs) and innate lymphoid cell precursors (ILCPs). Two distinct NK cell subsets were generated in vitro from CD34+CD117+α4β7+Lin-CD48-CD52+ and CD34+CD117+α4β7+Lin-CD48+CD52+ NKPs, respectively. Independent of NKPs, ILCPs exist in the CD34+CD117+α4β7+Lin-CD48+CD52+ subset and give rise to ILC1s, ILC2s and NCR+ ILC3s, whereas CD34+CD117+α4β7+Lin-CD48+CD52- ILCPs give rise to a distinct subset of ILC3s that have lymphoid tissue inducer (LTi)-like properties. Additionally, CD48 expressing CD34+CD117+α4β7+Lin- precursors give rise to tissue-associated ILCs in vivo. We also observed that the interaction of 2B4 with CD48 induced differentiation of ILC2s, and together these findings show that expression of CD48 by human ILCPs modulates ILC differentiation.

2020-11-20 | GSE160009 | GEO

Expression data from human effector CD4 T cells co-cultured with various Treg subsets sorted from human peripheral blood.

Project description:Teff cells (CD4+CD25-CD127+CD45RO+) were co-cultured with and without sorted Treg subsets plus dendritic cells for 18h. All the sorted Teff cells are gated on CD4+CD25-CD127(hi), and further sorted for CD45RO- and CD45RO+ phenotype.

2015-10-01 | GSE64180 | GEO

Expression data from Treg subsets sorted from healthy human peripheral blood

Project description:All the sorted Treg cells are gated on CD4+CD25+CD127(low), followed by gating on various subsets using markers indicated in the sample names. All the sorted Teff cells are gated on CD4+CD25-CD127(hi), and further sorted for CD45RO- and CD45RO+ phenotype.

2015-10-01 | GSE64176 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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