RNA-seq of mouse common lymphoid progenitors, innate lymphoid cell progenitors and NK cell progenitors
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40258 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4571560_1.fastq.gz | Fastqsanger.gz | |||
| ERR4571560_2.fastq.gz | Fastqsanger.gz | |||
| ERR4571561_1.fastq.gz | Fastqsanger.gz | |||
| ERR4571561_2.fastq.gz | Fastqsanger.gz | |||
| ERR4571552_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 28 |
Similar Datasets
Project description:Natural Killer (NK) cells at different developmental stages (common lymphoid progenitor (CLP), innate lymphoid cell progenitors (ILCP), and refined NK progenitor (NKP)) were collected from Vav1+iCre FOXO1,3flox/flox mice (C57BL/6 background). Total RNA was harvested and sequenced with a strand-specific paired-end RNA-seq protocol.
2022-02-06 | E-MTAB-9560 | biostudies-arrayexpress
Project description:Subtypes of innate lymphoid cells (ILC), defined by effector function and transcription factor expression, have recently been identified. In the adult, ILC derive from common lymphoid progenitors in bone marrow, although transcriptional regulation of the developmental pathways involved remains poorly defined. TOX is required for development of lymphoid tissue inducer cells, a type of ILC3 required for lymph node organogenesis, and NK cells, a type of ILC1. We show here that production of multiple ILC lineages requires TOX, as a result of TOX-dependent development of common ILC progenitors. Comparative transcriptome analysis demonstrated failure to induce various aspects of the ILC gene program in the absence of TOX, implicating this nuclear factor as a key early determinant of ILC lineage specification. TOX KO vs. wild tyype
2015-04-27 | E-GEOD-65850 | biostudies-arrayexpress
Project description:Subtypes of innate lymphoid cells (ILC), defined by effector function and transcription factor expression, have recently been identified. In the adult, ILC derive from common lymphoid progenitors in bone marrow, although transcriptional regulation of the developmental pathways involved remains poorly defined. TOX is required for development of lymphoid tissue inducer cells, a type of ILC3 required for lymph node organogenesis, and NK cells, a type of ILC1. We show here that production of multiple ILC lineages requires TOX, as a result of TOX-dependent development of common ILC progenitors. Comparative transcriptome analysis demonstrated failure to induce various aspects of the ILC gene program in the absence of TOX, implicating this nuclear factor as a key early determinant of ILC lineage specification.
2015-04-27 | GSE65850 | GEO
Project description:Natural killer (NK) cells represent one of three lymphoid lineages and play a vital role in controlling viral infections and cancer. In contrast to B and T lymphopoiesis where cellular and regulatory pathways have been extensively characterized, the cellular stages of early human NK-cell commitment remain poorly understood Here we described a novel NK-lineage restricted progenitor (NKP) in fetal development, umbilical cord blood and adult bone marrow. We used microarrays to detail the global programme of gene expression genes of this new progenitor. Global gene expression analysis was performed on the NKP, multipotent progenitors LMPP, common lymphoid progenitor candidate and mature NK cells purified from Cord blood CD34+ cells (3-4 replicates, 2 experiments)
2015-09-01 | E-GEOD-60448 | biostudies-arrayexpress
Project description:In order to investigate molecular events involved in the regulation of lymphoid lineage commitment, we crossed lamda5 reporter transgenic mice to mice where the GFP gene is inserted into the Rag1 locus. This allowed us to sub-fractionate common lymphoid progenitors (CLPs) and pre-pro-B cells into lamda5-Rag1low, lamda5-Rag1high and lamda5+Rag1high cells. Clonal in vitro differentiation analysis demonstrated that Rag1low cells gave rise to B/T and NK cells. Rag1high cells displayed reduced NK-cell potential with preserved capacity to generate B- and T-lineage cells while the lamda5+ cells were B-lineage restricted. Ebf1 and Pax5 expression was largely confined to the Rag1high populations. These cells also expressed a higher level of the surface protein LY6D providing an additional tool for the analysis of early lymphoid development. These data suggest that the classical CLP compartment composes a mixture of cells with more or less restricted lineage potentials opening new possibilities to investigate early hematopoiesis. Two newly identified subpopulations of common lymphoid progenitors (CLP), hereafter called CLP_RAGhigh and CLP_RAGlow, have been sorted in 2 replicates. RNA was extracted from 2,000 purified adult BM cells using the RNAeasy microkit. RNA was labeled and amplified by dual amplification and hybridized to Affymetrix microarray MOE430_2, according to AffymetrixTM GeneChip Expression Analysis Technical Manual. Probe level expression values were calculated using the RMA algorithm.
2009-11-24 | E-GEOD-19142 | biostudies-arrayexpress
Project description:We identified a new type of bone marrow progenitors termed early innate lymphoid cell progenitor (EILP) using TCF-1 GFP reporter mice. We compared the transcriptomes of early innate lymphoid cell progenitors (EILP) with other early progenitors, including HSC, LMPP, CMP, CLP, ETP and DN3.
2015-08-17 | GSE69789 | GEO
Project description:Innate lymphoid cells (ILCs) play strategic roles in tissue homeostasis and immunity. ILCs arise from lymphoid progenitors undergoing lineage restriction leading to the development of specialised ILC subsets. We generated ‘5x polychromILC’ compound transcription factor reporter mice to delineate ILC precursor states by revealing the multifaceted expression of key ILC-associated transcription factors (Id2, Bcl11b, Gata3, Rorc(γt) and Rora) during ILC development in the bone marrow. This approach allowed previously unattained enrichment of rare progenitor subsets and revealed hitherto unappreciated ILC precursor heterogeneity. In vivo and in vitro assays identified novel precursors with potential to generate all ILC subsets and natural killer cells, and also permitted discrimination of elusive ILC3 bone marrow antecedents. Single cell gene expression analysis identified a discrete ILC2-committed population and delineated transition states between early progenitors and a highly heterogeneous ILC1/3/NK precursor cell cluster. This diversity may facilitate greater lineage potential upon progenitor recruitment to peripheral tissues.
2019-05-11 | GSE131038 | GEO
Project description:Early innate lymphoid progenitors (EILP) have recently been identified in the mouse adult bone marrow as a multipotential progenitor population committed to ILC lineages, but their relationship with other described ILC progenitors is still unclear. In this study, we examine the progenitor-successor relationships between EILP, IL-7R+ common lymphoid progenitors (ALP), and ILC precursors (ILCp). Bioinformatic, phenotypical, functional, and genetic approaches collectively establish EILP as an intermediate progenitor between ALP and ILCp. Our work additionally provides new candidate regulators of ILC development and clearly defines the stage of requirement of transcription factors key for early ILC development.
2017-11-15 | GSE81530 | GEO
Project description:Common Lymphoid Progenitors (CLPs) have two subsets, Ly-6d- which are mutli-potent, and Ly-6d, which derive from Ly-6d- and are committeed to the B-cell fate. Treatment of a mouse with CpG DNA causes an inflammatory response that alters both subsets. We used expression data to understand the changes in transcription in the transition of Ly-6d- CLPs to Ly-6d+ CLPs ion the presence and absence of CpG induced inflammation. C57BL/6 mice were treated over 10 days with either PBS or 50 ug of CpG1826. On day 10, bone marrow was harvested and CLPs populations were sorted by flow cytometry directly into RNAeasy buffer (Qiagen).
2015-03-01 | E-GEOD-59762 | biostudies-arrayexpress
Project description:The transcription factor PU.1 is a central regulator of hematopoiesis, required for the normal differentiation of the myeloid and lymphoid lineages. Due to its essential role in early development and the importance of PU.1 in regulating several defining markers of lymphoid progenitors, its precise function in early lymphopoiesis has remained unclear. Using conditional mutagenesis and alternative lineage identification strategies, we demonstrate the developmental stage restricted function for PU.1 in early lymphopoiesis. PU.1 was required for efficient generation of “lymphoid primed multipotent progenitors (LMPPs)” from hematopoietic stem cells and was essential for the subsequent formation of “common lymphoid progenitors (CLPs)”. In contrast, further differentiation into the B cell lineage was independent of PU.1. The function of PU.1 was dosage sensitive as loss of one allele decreased all stages of early lymphopoiesis. PU.1 expression mirrored its functional role during lineage differentiation. PU.1 peaked at LMPPs and was maintained in CLPs, before being down regulated in committed pro-B cells. Examination of the transcriptional changes in PU.1 conditionally deficient LSK cells revealed that PU.1 activates lymphoid and dendritic cell associated genes in LMPPs, while repressing genes normally expressed in neutrophils. These data identify PU.1 as a critical regulator of lymphoid priming and the transition between LMPPs and CLPs.
2017-08-14 | GSE89642 | GEO