GEO DataSets

(Submitter supplied) Comparison of transcriptome between control, Tcf1 long isoform (p45)-deficient, complete Tcf1-deficient DN3 thymoctyes

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: CSV

(Submitter supplied) Comparison of the transcriptome between control Tfh and Tcf1 long isoform-deficient Tfh cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: WIG, XLS

(Submitter supplied) The HMG-box factor Tcf1 is required during T-cell development in the thymus and mediates the nuclear response to Wnt signals. Tcf1−/− mice have previously been characterized and show developmental blocks at the CD4−CD8− double negative (DN) to CD4+CD8+ double positive transition. Due to the blocks in T-cell development, Tcf1−/− mice normally have a very small thymus. Unexpectedly, a large proportion of Tcf1−/− mice spontaneously develop thymic lymphomas with 50% of mice developing a thymic lymphoma/leukemia at the age of 16 wk. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4867

Platform:

GPL1261

17 Samples

Download data: CEL

Analysis of thymocytes collected from Tcf1-/- animals with thymic lymphoma. Tcf1-/- animals of similar age without tumors and Tcf1+/- animals were also examined. Tcf1 is a Wnt-responsive transcription factor. Results provide insight into the role of Tcf1 in the development of thymic lymphomas.

Organism:

Mus musculus

Type:

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

Platform:

GPL1261

Series:

GSE54976

17 Samples

Download data: CEL

(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 aim of this study is to evaluate the effect of Autoimmune regulator (Aire) gene disruption in a murine medullary thymic epithelial cells (mTEC 3.10 cell line) on the transcriptome of these cells during its adhesion with thymocytes. The mTEC-thymocyte adhesion is a crucial step for the negative selection of autoreactive thymocytes and prevention of autoimmune diseases. To generate Aire mutant cell clones, a total of 5x10^5 mTEC 3.10 cells were electro-transfected (Lonza Nucleofector) with CRISPR-Cas9 plasmid targeting the Aire Exon 3 (plasmid "all in one" encoding Aire Exon 3 gRNA + Cas9 + GFP, from Sigma-Aldrich). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(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) NFATc1 plays a critical role in double-negative thymocyte survival and differentiation. However, the signals that regulate Nfatc1 expression are unknown. Here we show a developmental stage-specific differential expression pattern of Nfatc1 driven by the distal (P1) or proximal (P2) promoters in thymocytes. Whereas, preTCR-negative thymocytes exhibited only P2 promoter-derived Nfatc1b expression, preTCR-positive thymocytes expressed both Nfatc1b and P1 promoter-derived Nfatc1a transcripts. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

2 Samples

Download data: WIG

(Submitter supplied) We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene expression microarray analysis in CD4+ CD8+ DP thymocytes. Overall, we find a key role for the transcription factor Ets1, contributing towards alpha beta T cell lineage commitment via differential transactivation of stage-specific genes orchestrated by dynamic, co-association -mediated chromatin remodeling, as well as transcription dependent generation of a specialized chromatin structure at the TCR beta locus.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

20 Samples

Download data: WIG

(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) 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; Other

Platforms:

GPL13112 GPL17021 GPL21103

26 Samples

Download data: HIC

(Submitter supplied) Comparison of transcriptomes between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: DIFF

(Submitter supplied) Comparison of H3K27ac profiles ibetween WT and Tcf1/Lef1-deficient naïve CD8+ T cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL21103

9 Samples

Download data: BED

(Submitter supplied) Comparison of global genome organization between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

4 Samples

Download data: HIC

(Submitter supplied) Comparison of chromatin accessibility profiles between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: XLS

(Submitter supplied) Determine genome-wide binding locations by Tcf1 in naive CD8+ T cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

2 Samples

Download data: XLS

(Submitter supplied) T cell factor 1 (Tcf1) is the first T cell‒specific protein induced in multipotent progenitors following Notch signaling in the thymus, leading to the activation of two major target genes, Gata3 and Bcl11b. Tcf1 deficiency results in partial arrests in T cell development high apoptosis, and increased development of B cells and myeloid cells. Phenotypically, fully T cell‒committed, Tcf1-deficient thymocytes have promiscuous gene expression, an altered epigenetic profile and can de-differentiate into more immature thymocytes and non-T cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: BW