Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Understanding transcriptional identity in Innate Lymphoid Cells (ILC)

ABSTRACT: In order to determine the dependency of mature tissue-resident ILCs on combinations of synergistic and antagonising Transcription Factors (TFs), we generated mice with conditional deletions of RORc, RORa and Tbx21 driven from the Id2 allele, utilizing a tamoxifen inducible Cre-recombinase in combination with a tdRFP allele to report Cre-excision (Id2creERT2 x ROSAtdRFP). RFP+ small intestinal ILCs were sorted from the lamina propria digests (gated as CD45+, Lineage negative, CD90+ CD127+, tdRFP+ - see manuscript for full methodological details), from control mice or mice containing loxP flanked alleles for RORc, RORc and RORa or RORc and Tbx21. Four samples of sort-purified ILCs were then subjected to 10X single cell sequencing; - Id2creERT2 - Id2idRORc - Id2idRORc/RORa - Id2idRORc/Tbx21

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: David Withers

PROVIDER: E-MTAB-9795 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Systemic human ILC precursors provide a substrate for tissue ILC differentiation

Project description:Innate lymphoid cells (ILCs) represent innate versions of T helper and cytotoxic T cells that differentiate from committed ILC precursors (ILCP). Still, how ILCP relate to mature tissue-resident ILCs remains unclear. We identify ILCP that are present in the blood and all tested lymphoid and non-lymphoid human tissues. Human ILCP fail to express the signature transcription factors (TF) and cytokine outputs of mature NK cells and ILCs but are epigenetically poised to do so. Human ILCP robustly generate all ILC subsets in vitro and in vivo. While human ILCP express RAR related orphan receptor C (RORC), circulating ILCP can be found in RORC-deficient patients that retain potential for EOMES+ NK cells, T-BET+ ILC1, GATA-3+ ILC2 and for IL-22+ but not for IL-17A+ ILC3. We propose a model of tissue ILC differentiation (‘ILC-poiesis’) whereby diverse ILC subsets are generated in situ from ILCP in response to environmental stressors, inflammation and infection.

2017-03-19 | GSE90640 | GEO

Progression of adult diffuse hemispheric astrocytoma is associated with a gene network driven by the myeloid transcription factor SPI1

Project description:Glioma associated Macrophages (GAMs) are the most abundant immune cell type within diffuse gliomas and their density correlates with poorer prognosis. GAMs consist of resident microglia and bone marrow derived (BDM) cells and increased BDM infiltration is thought to be associated with disease progression however no definitive human marker of BDM exists. This is particularly true of LGGs, In this study we perform multicompartmental sampling and analyse GAMs from the perspective of gene regulatory networks. We show that GAMs and BDMs consist of distinct GRNs driven by the same master transcription factor SPI1, and that an increased activation of the blood derived SPI1 signature is associated with poorer prognosis in LGGs. Defining GAMs in terms of GRNs instead of marker genes alone permits a better understanding of the transcirptional programs that drive disease progression in diffuse gliomas.

2023-06-30 | E-MTAB-12528 | biostudies-arrayexpress

Single cell RNA-seq from 10X for a living biobank of ovarian cancer ex vivo models reveals profound mitotic heterogeneity

Project description:We validated fifteen models from “living biobank” to provide models that support interrogation of Chromosome Instability and to evaluate novel therapeutics. Single cell RNA-seq was performed on tumour and stromal cells from 4 patients with ovarian cancer to establish gene expression profile differences between the two cell types and also heterogeneity within the tumour population. The samples used were AS38b, AS59, AS74-1, AS79, they are grown in OCMI media supplemented with 5% hyclone serum (AS38, AS59) or 5% FBS (AS74, AS79) in 5% CO2 and 5% O2. At 37C

2020-01-23 | E-MTAB-8559 | biostudies-arrayexpress

Single cell RNA sequencing of chronic myelomonocytic leukemia stem cell

Project description:Chronic myelomonocyticleukemia (CMML) is a clinically heterogeneous stem cell malignancy with overlapping features of myelodysplasiaand myeloproliferation. CMML is further subclassified according to percentage of leukemic blasts present in blood or bone marrow, reflecting its intrinsic tendency to progression towards acute myeloid leukemia. Over 90% of CMML patients carry founding mutations in epigenetic and/or splicing genes, which typically involve the primitive stem cell compartment. Thus, transcriptional dysregulation at the stem cell level is likely fundamental to disease onset and progression. However, the critical early hematopoietic stem and progenitor cell (HSPC) subpopulation has not been studied in CMML. We performed single cell RNA sequencing on>6,800 Lin-CD34+CD38-primitive HSPCs from seven CMML patients and three healthy controls. We found substantial inter-and intra-patient heterogeneity, with CMML stem cells displaying distinct transcriptional programs, differentiation potential and cellular signaling pathway priming. Pseudotime analyses revealed that CMML-1/CMML-2 HSPCs have distinct cellular trajectories, indicating that transformation events initiate early within the hematopoietic hierarchy and suggesting against a simple linear clonal evolution dynamic in acute leukemic transformation. We further identified several transcription factors uniquely active in distinct sample subsets. Together our findings provide novel insights into the CMML stem cell compartment, revealing an unexpected degree of transcriptional and subclonal heterogeneity and highlighting early mediators of disease initiation and transformation, of potential translational importance

2020-08-03 | E-MTAB-8884 | biostudies-arrayexpress

Unravelling the heterogeneity of haemogenic endothelium in human pluripotent stem cell differentiation cultures

Project description:In embryo, few Endothelial cells from Aorta would be producing Haemogenic endothelium (HE) cells. These HE cells would then be progressing to take kind of a round shape and Undergo EHT. They then take a full round shape to make Intra-aortic haematopoietic clusters (IAHC) cells. These IAHC cells would then diassociate and turn into Hematopoitic Stem Cells (HSC) that ultimately would go to produce different lineage of hematopoitic (blood) cells. We wanted to study the heterogeneity of HE in human pluripotent stem cells.

2020-05-02 | E-MTAB-8271 | biostudies-arrayexpress

single cell RNAseq on isolated spinal cord cells before and 3 day post tail amputation in Xenopus tropicalis tadpoles at stage NF50

Project description:The tails of stage NF50 Xenopus tropicalis tadpoles were amputated and samples were collected at 0 and 3 days post amputation. 10 spinal cords were isolated for each time point. After cell dissociation, single cell RNAseq was performed using 10X Genomics platform

2021-05-21 | E-MTAB-8839 | biostudies-arrayexpress

Single-cell RNAseq of murine Bcl6-deficient ILC against wild-type controls

Project description:Innate lymphoid cells (ILC) are tissue-resident effector cells with important roles in tissue homeostasis, protective immunity and inflammatory disease. Here we investigated the role of the transcription factor Bcl6 in small intestinal innate lymphoid cells. Specifically, we performed single-cell RNA-seq on total small intestine lamina propria ILCs from tamoxifen-treated Id2-CreERT2 ROSA26-tdRFP Bcl6-fl/fl mice and Id2-CreERT2 ROSA26-tdRFP controls.

2023-10-31 | E-MTAB-12864 | biostudies-arrayexpress

Analyses of ILC3s from the mesenteric lymph nodes (LN)

Project description:Analyses of ILC3s in Rorc floxed control and Id2iÎ?RORÎ³t mice following daily treatments of tamoxifen for two weeks. Cells were sort purified as lineage negative, CD127+ CD90.2+ CCR6+ ST2- CCR6+ ILCs were sorted from the mesenteric LN of Rorc floxed control and Id2iÎ?RORÎ³t mice following daily treatments of tamoxifen for two weeks.

2016-02-15 | E-GEOD-76201 | biostudies-arrayexpress

Polychromic reporter mice reveal unappreciated innate lymphoid cell progenitor heterogeneity and elusive ILC3 progenitors in bone marrow

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

Gene expression profiling of small intestine (SI) NKp46+RORgt+ and NKp46+RORgt- Innate Lymphoid Cells (ILCs)

Project description:The aim of this study was to analyze the global transcriptional profiles of small intestine (SI) Innate Lymphoid Cells (ILCs) expressing the NK cell marker NKp46. Based on differential expression of the RORgt transcription factor SI NKp46+ ILCs can be divided in NKp46+RORgt- and NKp46+RORgt+ cells. While NKp46+RORgt- cells produce IFN-g, like conventional Natural Killer (NK) cells, NKp46+RORgt+ cells secrete IL-22, like Lymphoid Tissue inducer (LTi) cells. We compared the global transcriptional profiles of both NKp46+RORgt- and NKp46+RORgt+ cells to conventional splenic NK cells and to SI NKp46-RORgt+ cells, which contain adult LTi cells. By following this approach, we showed that SI NKp46+RORγt- ILCs correspond to SI NK cells. We also identified a transcriptional program conserved in adult SI NKp46+RORγt+, NKp46-RORγt+ ILCs and fetal LTi. The various ILC cell populations analyzed in this study were isolated from C57BL/6 RORc(gt)+/GFP reporter mice. SI NKp46+RORγt- (NKp46+GFP-) cells, SI NKp46+RORγt+ cells (NKp46+GFPlow and NKp46+GFPhigh cells) and NKp46-RORγt+ ILCs, including adult LTi cells , were sorted by flow cytometry from CD3- lamina propria cells of small intestine (SI) of RORc(γt)+/GFP reporter mice . Splenic NKp46+RORγt- (NKp46+GFP-) cells were also sorted as the reference for conventional NK cells. Two replicates of each populations were produced and analyzed.

2011-06-20 | E-GEOD-29777 | biostudies-arrayexpress

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