Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-sequencing data from Ctrl (Id2F/F or Id2F/FTcf7F/F), Ncr1Cre Id2F/F, Ncr1Cre Tcf7F/F and Ncr1Cre Id2F/F Tcf7F/F bone marrow NK cells.

ABSTRACT: RNA-sequencing data from Ctrl (Id2F/F or Id2F/FTcf7F/F), Ncr1Cre Id2F/F, Ncr1Cre Tcf7F/F and Ncr1Cre Id2F/F Tcf7F/F bone marrow NK cells.

PROVIDER: PRJNA656538 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12430506.fastq.gz	Fastqsanger.gz
	SRR12430507.fastq.gz	Fastqsanger.gz
	SRR12430508.fastq.gz	Fastqsanger.gz
	SRR12430509.fastq.gz	Fastqsanger.gz
	SRR12430510.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

RNA-sequencing data from Ctrl (Id2F/F or Id2F/FTcf7F/F), Ncr1Cre Id2F/F, Ncr1Cre Tcf7F/F and Ncr1Cre Id2F/F Tcf7F/F bone marrow NK cells.

Project description:The goal of this study was to determine how gene expression changes when Id2 and Tcf7 are deleted in bone marrow natural killer cells as compared to NK cells in which only Id2 or Tcf7 are deleted. We sorted NK1.1+CD49b+ cells from the bone marrow of mice with each of the indicated genotypes. 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 3 independent replicates by EdgeR. We found that NK cells lacking Id2 had reduced expression of mature NK cell genes and increased expression of immature genes and known E protein target genes. Deletion of Tcf7 in ID2-deficient NK cells partially restored expression of maturation associated genes and decreased immature genes bringing their gene expression profiles closer to that of Ncr1Cre Tcf7F/F or Ctrl NK cells.

2020-08-12 | GSE156046 | GEO

TGF-β1 induces bone marrow NK cells dysfunction

Project description:TGF-β1 induces bone marrow NK cells dysfunction

| PRJNA787546 | ENA

scRNAseq for bone marrow cells from Cebpαcre/+ R26EYFP/+ SbdsF/F (neutropenia) mice vs Cebpαcre/+ R26EYFP/+ Sbds+/+ (Ctrl) mice

Project description:To delineate the potential molecular mechanisms underlying the communication between neutrophils and NK cells, we performed scRNAseq of the neutropenic bone marrow (12 months after transplantation of Cebpacre/+ Sbds +/+ or F/F cells). To this end, bone marrow cells were subsorted into HSC+MPP (LKS CD48-), HPC1 (LKS CD48+CD150-), B and T cells (B220+, CD3+), NK cells (NK1.1+ NKp46+) and a myeloid ‘rest’ fraction (B220-,CD3-,NKp46- and NK1.1-) and sorted fractions pooled together to obtain robust representation of all bone marrow cell types in the scRNAseq data

2022-12-31 | E-MTAB-12428 | biostudies-arrayexpress

Single-cell transcriptomics in bone marrow delineates CD56dimGranzymeK+ subset as intermediate stage in NK cell differentiation

Project description:In this study we performed single-cell RNA sequencing on 7000 negatively enriched fresh NK and progenitor cells from one healthy bone marrow donor, that were pre-labeled with oligonucleotide-conjugated antibodies against CD34, CD117, CD56 and CXCR6. A new CD56dimGzmK+ subset was identified that shared features with CD56bright and CD56dimGzmK- NK cells based on transcriptome, phenotype (NKG2AhighCD16lowKLRG1highTIGIThigh) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56bright, CD56dimGzmK+ and CD56dimGzmK- cells in one differentiation trajectory, while ltNK cells were separated in a distinct lineage. Integrative analysis with bone marrow cells from the human cell atlas did not demonstrate a developmental connection between CD34+ progenitor and NK cells, implicating that bone marrow is not a site of active NK cell development.

2022-10-01 | GSE199411 | GEO

Expression data of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors

Project description:Expression profiling of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors, WT T cells, and WT Pro B cells WT Hematopoietic progenitors, CD4 T cells, Pro B cells, and WT and Ets1-deficient NK cells were FACs sorted. RNA was subsequently extracted, labelled, and hybridized to Affymetrix microarrays. The goal if this experiment was to identify Ets1 dependent genes in NK cells

2012-08-09 | E-GEOD-37301 | biostudies-arrayexpress

Eomes expression identifies the early bone marrow precursor to classical NK cells

Project description:Classical NK cells are the prototypical type 1 innate lymphocytes mounting cytolytic and IFNg responses to intracellular pathogens and tumors. A similar but distinct population termed ILC1 was recently described, differing from NK cells in multiple though relatively subtle ways, including tissue residency vs recirculation, and levels of NK receptors. Whether the differences reflect distinct lineages or mere variations in program expression is not fully understood. Here, using transcription factor reporter mice and cell transfers of bone marrow precursors, we found that, upon transfer in vivo, Eomes-expressing, lineage-negative, NK receptor-negative cells acquired properties typically associated with classical NK cells including the capacity to prevent metatstatic disease. In contrast, as previously reported, PLZFhigh cells mostly generated ILC1, ILC2, or ILC3. These findings identify the Eomes-expressing NK precursor as the long-elusive bone marrow precursor to classical NK cells, and demonstrate that the NK and ILC1 lineages diverge early during development.

2024-05-20 | GSE256395 | GEO

Eomes expression identifies the early bone marrow precursor to classical NK cells

Project description:Classical NK cells are the prototypical type 1 innate lymphocytes mounting cytolytic and IFNγ responses to intracellular pathogens and tumors. A similar but distinct population termed ILC1 was recently described, differing from NK cells in multiple though relatively subtle ways, including tissue residency vs recirculation, and levels of NK receptors. Whether the differences reflect distinct lineages or mere variations in program expression is not fully understood. Here, using transcription factor reporter mice and cell transfers of bone marrow precursors, we found that, upon transfer in vivo, Eomes-expressing, lineage-negative, NK receptor-negative cells acquired properties typically associated with classical NK cells including the capacity to prevent metatstatic disease. In contrast, as previously reported, PLZF-expressing cells mostly gave rise to ILC1 cells. These findings identify the Eomes-expressing NK precursor as the long-elusive bone marrow precursor to classical NK cells, and demonstrate that the NK and ILC1 lineages diverge early during development.

2024-12-31 | GSE245062 | GEO

Expression data of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors

Project description:Expression profiling of Rag2-deficient Ets1++ and Rag2-deficient Ets1-- mature NK cells and WT bone marrow progenitors, WT T cells, and WT Pro B cells

2012-08-10 | GSE37301 | GEO

Bone Marrow - scRNA-sequencing

Project description:Bone Marrow - scRNA-sequencing

| PRJNA790965 | ENA

Expression data from miR-142 WT and KO spleen and bone marrow

Project description:miR-142 is critical for the presence of NK cells in the periphery. Global gene expression analysis of bone marrow and splenic NK cells

2018-11-01 | GSE85476 | 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