GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

60 Samples

Download data

(Submitter supplied) T-BET and EOMES are key transcription factors in the development of mature NK cells in mice. However, the role of these transcription factors during human NK cell development is less well understood. Therefore, we overexpressed T-BET or EOMES in human umbilical cord blood-derived hematopoietic progenitor cells (HPC) and cultured them in vitro in an NK cell differentiation model. On day 21 of culture mature stage 4 (CD56+CD94+CD16-) and stage 5 (CD56+CD94+CD16+) NK cells from T-BET or EOMES overexpression and control cultures were sorted, whereafter mRNA was isolated and transcriptome analysis was performed by RNA sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: TXT

(Submitter supplied) T-BET and EOMES are key transcription factors in the development of mature Natural Killer (NK) cells in mice. However, the role of these transcription factors during human NK cell development is less well understood. Therefore, we overexpressed T-BET or EOMES in human umbilical cord blood-derived HPC and cultured them in vitro in an NK cell differentiation model. To evaluate the effect of early overexpression of T-BET and EOMES in HPC, transcriptome profiling was performed on T-BET and EOMES overexpressing HPC and compared to control transduced HPC by RNA sequencing on day 0 of culture.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: TXT

(Submitter supplied) T-BET and EOMES are key transcription factors in the development of mature NK cells in mice. However, the role of these transcription factors during human NK cell development is less well understood. Therefore, we overexpressed T-BET or EOMES in human umbilical cord blood-derived hematopoietic progenitor cells (HPC) and cultured them in vitro in an NK cell differentiation model. On day 21 of culture mature stage 4 (CD56+CD94+CD16-) and stage 5 (CD56+CD94+CD16+) NK cells from T-BET or EOMES overexpression and control cultures were sorted, whereafter genomic DNA was isolated and the chromatin accessibility landscape was determined by assay for transposase-accessible chromatin (ATAC) sequencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: BED, TXT

(Submitter supplied) T-BET and EOMES are key transcription factors in the development of mature Natural Killer (NK) cells in mice. However, the role of these transcription factors during human NK cell development is less well understood. Therefore, we overexpressed T-BET or EOMES in human umbilical cord blood-derived HPC and cultured them in vitro in an NK cell differentiation model. To evaluate the effect of early overexpression of T-BET and EOMES in HPC, the chromatin landscape was uncovered using assay for transposase-accessible chromatin (ATAC) sequencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: BED, TXT

(Submitter supplied) This study shows that liver Eomes- NK cells are not precursors of classical Eomes+ NK cells but rather constitute a distinct lineage of innate lymphoid cells. Gene profile analyses show that Eomes- NK cells share part of their transcriptional program with NKT cells that includes genes involved in liver homing, NK cell receptors, and several cytokines and cytokine receptors.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18098

11 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

30 Samples

Download data: WIG

(Submitter supplied) This project aims at understanding the role of T-bet and Eomes in the differentiation of Natural Killer (NK) cells. NK cells are innate cytotoxic lymphocytes that play an important role in the early control of viral infections and in immune surveillance of cancers. T-bet and Eomes are related T-box factors that are co-expressed by NK cells and are supposed to bind to similar DNA motifs. Their role in NK cell differentiation are not very well understood, in part because their direct target genes are unknown. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: WIG

(Submitter supplied) T-bet and Eomes are related T-box transcription factors that control NK cell development. This study was designed to understand the specific roles of Eomes and T-bet in regulating gene expression. RNAseq data were generated for immature (CD11b- CD27+) and mature (CD11b+ CD27-) NK cells from T-bet KO (Tbet Ho) or control mice (Tbet WT) or from Eomes KO (Eomes Ho) or control mice (NK-Cre). Three samples were generated for each condition (Tri 1, 2, 3).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

24 Samples

Download data: TXT

(Submitter supplied) ATAC-seq was performed on peripheral blood NK cells that were CRISPR-edited to knock-out expression of T-BET and EOMES. The following samples were analyzed to elucidate the role of T-BET and EOMES in regulating mature human NK cell chromatin accessibility.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: NARROWPEAK

(Submitter supplied) Peripheral blood NK cells that were CRISPR-edited to knock-out expression of T-BET or EOMES were prepared for scRNA-sequencing(10X Genomics). The following samples were analyzed to elucidate the role of T-BET and EOMES in regulating mature human NK cell transcriptional profiles.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: MTX, TSV

(Submitter supplied) ChIP-seq analysis of Eomes in murine NK cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21493

6 Samples

Download data: TXT

(Submitter supplied) Gene expression profiling of EomesΔ/Δ and Wild Type Murine NK cells sorted into specific maturaion stages

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT

(Submitter supplied) E4bp4 is essential for the development of natural killer (NK) cells. We sought to identify downstream targets of E4bp4 by comparing mRNA expression in wild type vs. E4bp4 knockout Lineage-depleted bone marrow, which is enriched for haematopoietic progenitor cells. We then went on to validate these targets using real time PCR, genetic complementation assays and ChIP

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5220

Platform:

GPL6246

12 Samples

Download data: CEL

Analysis of wild-type and E4bp4-knockout lineage-depleted bone marrow which is enriched for hematopoietic progenitor cells. Transcription factor E4bp4 (Nfil3) is essential for natural killer (NK) cell development. Results provide insight into downstream targets of E4bp4 in early NK development.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 genotype/variation sets

Platform:

GPL6246

Series:

GSE55014

12 Samples

Download data: CEL

(Submitter supplied) We compared transcriptome of different types of NK cells including obtained from peripheral Blood (PB-NK), derived from human ES cell, H9-NK, derived from human iPSC (iPSC-NK), derived from CD34+ cells from umbilical cord blood (UCB-NK), NKcell line (NK92) and 3 cancer cell lines (K562, Raji and Jurkat). When comparing the similarity of the NK cells populations by the number of differentially expressed genes to iPSC NK cells, there were the fewest differentially expressed genes in the comparison with the UCB NK cells, followed by the PB-NK cells, followed by the H9 embryonic stem cell derived-NK cells and lastly by the NK92 cell line.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: XLSX

(Submitter supplied) We compared transcriptome of different types of NK cells including obtained from Umbilical Blood (UCB-NK) from 3 donors, both UCB56 NK cells that were isolated from the UCB unit as well as UCB34 NK cells that were differentiated from CD34+ cells, and derived from human iPSC (iPSC-NK), pre and post antigen presenting cell expansion. When comparing the similarity of the NK cells populations by the number of differentially expressed genes to iPSC NK cells, there were the pre and post expansion cells clustered together

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) Using scRNAseq, we identified five distinct NK cell clusters and define their relative developmental maturity in the murine bone marrow of WT mice. Transcriptome-based machine-learning classifiers revealed that half of the mTORC2-deficient NK cells belongs to the least mature NK cluster. Mechanistically, loss of mTORC2 results in an increased expression of signature genes representing immature NK cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV, MTX, TSV, XLSX

(Submitter supplied) Epigenetic landscapes can provide insight into regulation of gene expression and cellular diversity. Here, we examined the transcriptional and epigenetic profiles of seven human blood NK cell populations, including adaptive NK cells. The BCL11B gene, encoding a transcription factor (TF) essential for T cell development and function, was the most extensively regulated, with expression increasing throughout NK cell differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) Natural killer (NK) cells are innate lymphocytes that possess features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin (IL)-12 signaling through its downstream transcription factor STAT4 is required for the generation of memory NK cells following expansion, while type I interferon through STAT1 is important for NK cell expansion. Here, we identify gene loci that are highly enriched for STAT4 binding using ChIP-seq for STAT4 and the permissive histone mark H3K4me3 in activated NK cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

28 Samples

Download data: BED, BIGWIG, BW