GEO DataSets

(Submitter supplied) Gamma delta T (gdT) cells with distinct properties develop in the embryonic and adult thymus and have been identified as critical players in a broad range of infections, antitumor surveillance, autoimmune diseases and tissue homeostasis. Despite their potential value for immunotherapy, differentiation of gdT cells in the thymus is incompletely understood. Here, we establish a high-resolution map of gdT cell differentiation from the fetal and adult thymus using single-cell RNA-sequencing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21493

333 Samples

Download data: CSV, TXT

(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

Platforms:

GPL19057 GPL13112 GPL21103

16 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) IL-17-producing gd T (Tgd17) cells are early mediators of immunity and autoimmunity that undergo effector programming in the thymus. While Vg subset-restricted regulators of Tgd17 specialization are known, a universal type 17 commitment factor for all gd T cells remains undefined. In this study, we identify the transcription factor c-Maf as an essential and uniform regulator of Tgd17 differentiation and maintenance. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) IL-17-producing gd T (Tgd17) cells are early mediators of immunity and autoimmunity that undergo effector programming in the thymus. While Vg subset-restricted regulators of Tgd17 specialization are known, a universal type 17 commitment factor for all gd T cells remains undefined. In this study, we identify the transcription factor c-Maf as an essential and uniform regulator of Tgd17 differentiation and maintenance. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL21103

12 Samples

Download data: TXT

(Submitter supplied) Tgd17 cells are critical immune effector cells that exit the thymus committed to peripheral IL-17 responses, but whether the development of cells into this lineage is pre-programmed or driven by instructive TCR signals is unresolved. Using newly generated reporter mice for a gene necessary for Tgd17 cell development, Sox13, we identified progenitor cells (known as DN1d cells) that expressed high levels of Sox13 prior to expression of the TCR. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: XLSX

(Submitter supplied) The indicated thymic progenitor population was sorted via FACS and then loaded into a Fluidigm C1 small cell capture chip for single-cell capture, lysis, reverse transcription, and preamplification. Preamplified products were analyzed on a BioMark HD with EvaGreen chemistry. The genes analyzed were selected based on bulk RNA sequencing data and/or prior publications, including genes relevant for gamma/delta T cells and T cell progenitors. more...

Organism:

Mus musculus

Type:

Expression profiling by RT-PCR

Platform:

GPL25465

610 Samples

Download data: TXT

(Submitter supplied) Gene-expression microarray datasets generated as part of the Immunological Genome Project (ImmGen). Primary cells from multiple immune lineages are isolated ex-vivo, primarily from young adult B6 male mice, and double-sorted to >99% purity. RNA is extracted from cells in a centralized manner, amplified and hybridized to Affymetrix 1.0 ST MuGene arrays. Protocols are rigorously standardized for all sorting and RNA preparation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

653 Samples

Download data: CEL

(Submitter supplied) Murine γδ T cells include several effector subsets that fulfil distinct functional roles. In pathological conditions, such as cancer, some γδ T cell subsets are highly protective whereas other subsets may exacerbate disease. γδ T cells are programmed for their effector function during their development in the thymus. Investigations of γδ T cell development have been hampered by the scarcity of surface markers distinguishing different development stages. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

28 Samples

Download data: CSV

(Submitter supplied) Until now, the systematic and comprehensive deciphering of γδ T heterogeneity and the extrathymic developmental pathway of liver γδ T cells remains largely unsolved. In this study, we performed single cell RNA sequencing to comprehensively identify the heterogeneity of γδ T cells from murine liver and thymus. We further revealed the developmental trajectory of γδ T cells and found that liver contains γδ T precursors.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: MTX, TSV

(Submitter supplied) The murine thymus produces discrete γδ T cell subsets making either IFN-γ or IL-17, but the role of the TCR in this developmental process remains controversial. Here we generated a non-transgenic and polyclonal model of reduced TCR expression and signal strength selectively on γδ T cells. Mice haploinsufficient for both CD3γ and CD3δ (CD3DH) showed normal αβ thymocyte subsets but specific defects in γδ T cell development, namely impaired differentiation of IL-17-producing embryonic Vγ6+ (but not adult Vγ4+) γδ T cells and a marked depletion of IFN-γ-producing CD122+ NK1.1+ (Vγ1-biased) γδ T cells throughout life. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17400

4 Samples

Download data: CEL

(Submitter supplied) To investigate the human γδT17 cells from oral cancers, we performed sc-RNAseq of two pairs of oral cancers with normal tissues.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: MTX, TSV

(Submitter supplied) Developmental thymic waves of innate-like and adaptive-like gd T cells have been described, but the current understanding of γδ T cell development is mainly limited to mouse models. Here, we combined single cell (sc) RNA gene expression and sc γδ T cell receptor (TCR) sequencing on fetal and pediatric γδ thymocytes in order to understand the ontogeny of human γδ T cells. Mature fetal γδ thymocytes were committed to either a type 1, a type 3 or type 2-like effector fate, independent from γδ T cell subset type (Vγ9Vδ2 vs nonVγ9Vδ2), and were enriched for public CDR3 features upon maturation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL15520

60 Samples

Download data: CSV, MTX, RDS, TSV

(Submitter supplied) In the mouse thymus, invariant γδ T cells are generated at well-defined times during development and acquire effector functions before exiting the thymus. However, whether such thymic programming can occur in human is not known. Here we analyzed human fetal and post-natal γδ thymocytes and investigated the role of hematopoietic-stem-and-precursor-cells (HSPC) in the generation of human γδ T cells. Unlike post-natal γδ thymocytes, fetal γδ thymocytes were functionally programmed (e.g. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: CSV

(Submitter supplied) ab and gd T cells originate from a common, multi-potential precursor population in the thymus, but the molecular mechanisms regulating this lineage fate decision process are unknown. We have identified Sox13 as a gd-specific gene in the immune system. Using Sox13 transgenic mice, we show that SOX13 promotes gd T cell development while opposing ab T cell differentiation. Conversely, mice deficient in Sox13 expression exhibited impaired development of gd T cells, but not ab T cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL76 GPL75 GPL81

6 Samples

Download data: CEL, EXP

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the difference of NGS-derived transcriptome profiling between DN thymocytes from Toxf/f and Toxf/fPdcd1Cre mice. Methods: mRNA profiles of DN thymocytes sorted by FACS from 3-4-week-old Toxf/f and Toxf/fPdcd1Cre mice were generated by deep sequencing, in triplicate, using Illumina Novaseq6000. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) STAT3 has a more profound effect on chromatin accessibility regulation than RORgt during Th17 cell differentiation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: BW

(Submitter supplied) We performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) for ICN1 in thymic gd T cells from neonates of C57BL/6 mice. Sequence reads for ICN1 and Input were aligned with the mouse reference genome (mm10) by bowtie program (v1.0.0), and peak detection and identification of ICN1 binding sites were obtained with MACS program (v1.4.2). ChIP-seq data revealed that 12%, 6% and 47% of ICN1 binding sites were within -10kb upstream of transcription start site, +10kb downstream of 3'end and the bodies of genes, respectively. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

2 Samples

Download data: BED

(Submitter supplied) gd T cells are major innate sources of interleukin-17 (IL-17) and interferon-g (IFN-g), which are differentially produced by two thymically-derived subsets segregated on CD27 expression. However, the molecular mechanisms that program the functional differentiation of gd cells remain incompletely understood. Here we show that CD27+ gd cells are epigenetically committed to express Ifng but not Il17, whereas CD27- gd cells spontaneously make IL-17 but can be induced to produce IFN-g under specific inflammatory conditions. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

8 Samples

Download data: BEDGRAPH