GEO DataSets

Analysis of T-regulatory cells (Treg) from various organs (small intestine, spleen, mesenteric lymph node) of polyp-ridden Foxp3-GFPxAPCΔ468 reporter males. Tregs from the polyposis model promote cancer. Results provide insight into molecular mechanisms underlying these pathogenic Tregs.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 cell type, 2 genotype/variation, 5 tissue sets

Platform:

GPL6246

Series:

GSE41229

44 Samples

Download data: CEL

(Submitter supplied) The DNA binding factor Tcf-1 is one of the most prominently expressed genes in thymocytes yet its global DNA binding pattern remained unknown. Here we have assessed by ChIP-seq the Tcf-1 binding pattern in murine thymocytes in WT B6 mice and in mice expressing a stabilized form of the Tcf-1 binding partner beta-Catenin (CAT mice).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: WIG

(Submitter supplied) There is much controversy about the role of T-regulatory cells (Treg) in human colon cancer. High densities of tumor-infiltrating Treg can correlate with better or worse clinical outcomes depending on the sutdy. Treg have potent anti-inflammatory functions that have been shown to control cancer progression. However, Treg isolated from patient with colon cancer or in mouse models of polyposis do not have the ability to suppress inflammation and instead promote cancer. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4588

Platform:

GPL6246

44 Samples

Download data: CEL

(Submitter supplied) Activation of b-catenin has been causatively linked to the etiology of colon cancer. Conditional stabilization of this molecule in pro-T-cells promotes thymocyte development without the requirement for preTCR signaling. We show here that activated b-catenin stalls the developmental transition from the double-positive (DP) to the single-positive (SP) thymocyte stage and predisposes DP thymocytes to transformation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

18 Samples

Download data: CEL

(Submitter supplied) Previous work indicated that β-catenin/TCF-1 occupy DNA together with Foxp3. Thus, we anticipated that precise mapping of TCF-1 and Foxp3 co-binding in Tregs, could provide a molecular explanation for our phenotypic observations. To address this, we analyzed TCF-1 DNA binding in Tregs through chromatin immunoprecipitation and deep sequencing (ChIPseq) in Foxp3YFP-Cre WT Tregs. Furthermore, we assessed regions of accessible chromatin in Tregs via transposase-accessible chromatin approach and deep sequencing (ATAC-seq). more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

13 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) Interleukin 33 (IL33) is an inflammatory cytokine released during necrotic cell death. The epithelium and stroma of the intestine express large amounts of IL33 and its receptor St2. IL33 is therefore continuously released during homeostatic turnover of the intestinal mucosa. Although IL33 can prevent colon cancer associated with inflammatory colitis, the contribution of IL33 signaling to sporadic colon cancer remains unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TSV

(Submitter supplied) The aim of this study is to identify EBP50 binding sequence.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL8169 GPL8170

2 Samples

Download data: TXT

(Submitter supplied) Both TCF-1 and its coactivator β-catenin are known to be required for supporting normal double positive (DP) thymocyte survival through upregulating Bcl-xL. However, the downstream factors mediating this effect remained unknown. We used microarray to compare the global expression difference among WT, TCF-1-deficient, and β-catenin transgenic thymocytes to search for the genes that are down-regulated and up-regulated in TCF-1-deficient and β-catenin transgenic thymocytes, respectively.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

3 Samples

Download data: CEL

(Submitter supplied) The colonic lamina propria contains a distinct population of Foxp3+ T regulatory cells (Tregs) that modulate responses to commensal microbes. Analysis of gene expression revealed that the transcriptome of colonic Tregs is distinct from splenic and other tissue Tregs. Rorγ and Helios in colonic Tregs mark distinct populations: Rorγ+Helios- or Rorγ-Helios+ Tregs. We uncovered an unanticipated role for Rorγ, a transcription factor generally considered to be antagonistic to Foxp3. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

13 Samples

Download data: CEL

(Submitter supplied) To investigate the detailed molecular mechanisms for the regulatory role of HIF-1α in colon, microarray gene expression analysis was performed on colon RNA isolated from 6- to 8-week-old Hif-1α+/+, Hif-1αLSL/LSL mice. Background & Aims: The progression and growth of solid tumors leads to a state where tumors outgrow their capacity for efficient oxygenation and nutrient uptake and an increase in tumor hypoxia. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

2 Samples

Download data: CEL

(Submitter supplied) To identify the target genes of transcription factor zinc finger protein (ZNF) 277, we performed RNAseq experiments using RNAs from human colon cancer cell line HT29 and its clones with ZNF277 knockout by CRISPR.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) Th17 cells are potent mediators in autoimmune diseases and RORγt is required for their development. Recent studies have shown that RORγt+ Treg cells in the gut regulate intestinal inflammation by inhibiting effector T cell function. In the current study, we report that RORγt+ Treg cells were also found in lymph nodes following immunization. Not only distinct from intestinal RORγt+ Treg in their transcriptomes, peripheral RORγt+ Treg cells were derived from Foxp3+ thymic Treg cells, in an antigen-specific manner. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14602

5 Samples

Download data: TXT

(Submitter supplied) Tcf1, the DNA-binding partner of β-catenin, is essential for the development and function of T regulatory cells (Tregs). However, how Tcf1 regulates Treg functional specification is less understood. Here, we ablated Tcf1 in Tregs to elucidate its role in Treg specification in healthy mice and mice with colon cancer. RNAseq and single-cell RNAseq revealed that Tcf1 deficient Tregs maintain their core transcriptional signature and diversity, but promote T-cell receptor, Tgfβ receptor, TH17, and Wnt/β-catenin signaling pathways. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

14 Samples

Download data: CSV, H5, LOOM, RDS, TXT

(Submitter supplied) Analyses of ILC3s in Rorc floxed control and Id2iΔRORγt mice following daily treatments of tamoxifen for two weeks. Cells were sort purified as lineage negative, CD127+ CD90.2+ CCR6+ ST2-

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

4 Samples

Download data: CEL, CHP

(Submitter supplied) The aim of this study was to identify differential gene expression resulting from the inhibition of RORgt in human CD4+ T cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

20 Samples

Download data: CEL

(Submitter supplied) Deregulation of canonical Wnt/beta-catenin pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 (beta-catenin gene) are highly frequent in colon cancer and cause aberrant stabilization of b-catenin, which activates the transcription of Wnt target genes by binding to chromatin via the TCF/LEF transcription factors. Here we report an integrative analysis of genome-wide chromatin occupancy of b-catenin by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and gene expression profiling by microarray analysis upon RNAi-mediated knockdown of beta-catenin in colon cancer cells (GSE53656).

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: BED, WIG

(Submitter supplied) Deregulation of the canonical Wnt/beta-catenin pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 are frequent in colon cancer and cause aberrant stabilization of beta-catenin, which activates Wnt target genes by binding to chromatin via TCF/LEF transcription factors. In a comprehensive study, we conducted an integrative analysis of genome-wide chromatin occupancy of beta-catenin by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) along with gene expression profiling changes resulting from RNAi-mediated knockdown of beta-catenin in colon cancer cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4372

2 Samples

Download data

(Submitter supplied) Interleukin 17 (IL-17)-producing gamma delta T (gdT17) cells are one of the major cellular sources of IL-17 under the steady state and in disease. However, gdT17 cell metabolism and its role in tissue homeostasis remain poorly understood. Here, we show that the tissue milieu shapes splenic and intestinal gdT17 cell gene signatures. Conditional deletion of mitochondrial transcription factor A (Tfam) in gdT17 cells significantly affected gdT17 cell maintenance systemically. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

24 Samples

Download data: TXT

(Submitter supplied) The goals of this study were to assess the differentially expressed transcripts in CD4+ cell isolated from the ileal lamina propria of germ-free (GF) and E. lenta strain 2243 monocolonized mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: CSV, RMD

(Submitter supplied) T cell factor 1 (TCF1; encoded by Tcf7) plays a critical role in T cell development and functions as a tumor suppressor by repressing the expression of LEF1 in the thymus. Here we reported the stage-specific regulation of TCF1 in early T cell differentiation and T cell malignancy despite the broad understand on the functions of TCF1. To illustrate the stage-specific functions of Tcf7 in T cell development and tumorigenesis, we applied single-cell transcriptional analysis to identify the precise trajectory of gene expression changes between the surface receptor-defined stages of T cell development.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

768 Samples

Download data: CSV, XLSX