GEO DataSets

(Submitter supplied) T cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy strongly affected by the abnormal activity of transcription factors. Here we report a high expression of developmental transcription factor SIX6 in TAL1 subtype of T-ALL. Our data indicates that this high expression is directly regulated by binding of TAL1 and GATA3 transcription factors into an upstream enhancer element. We also looked into the potential targets of SIX6 in T-ALL and Crispr-cas9 mediated knockout of SIX6 in Jurkat cells caused significant changes in the expression of multiple genes, including genes related to mTOR signaling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) miRNA profiling of Jurkat T-ALL cells after knockdown with two control shRNAs and two shRNAs targeting TAL1 to identify miRNAs that are regulated by TAL1

Organism:

human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Mus musculus cytomegalovirus 2; Betapolyomavirus macacae; Homo sapiens; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1; Rattus norvegicus; Human alphaherpesvirus 2; Merkel cell polyomavirus

Type:

Non-coding RNA profiling by array

Platform:

GPL11432

8 Samples

Download data: TXT

(Submitter supplied) The transcriptional status of genes can be determined from the enrichment pattern of RNA polymerase at the transcription start site (TSS) and across the body of the gene. Active elongating genes are enriched for H3K79me2, and Polycomb paused genes are marked by H3K27me3.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

4 Samples

Download data: TXT, WIG

(Submitter supplied) The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

22 Samples

Download data: WIG, YLF

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL9115 GPL13232

64 Samples

Download data: CEL, WIG, YLF

(Submitter supplied) The oncogenic transcription factor TAL1/SCL is aberrantly expressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing its importance in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, LMO1, LMO2, GATA3 and RUNX1 in T-ALL cells. We show that TAL1 forms an interconnected auto-regulatory loop with its partners, and that the TAL1 complex directly activates the MYB oncogene, forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

10 Samples

Download data: WIG, YLF

(Submitter supplied) The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13232

32 Samples

Download data: CEL

(Submitter supplied) We performed microarray gene expression profiling in 16 T-ALL cell lines

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

16 Samples

Download data: CEL

(Submitter supplied) RNA-seq analysis was performed in Jurkat cells (T-cell lymphoblastic leukemia cell line).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: BW

(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; Third-party reanalysis

Platform:

GPL11154

17 Samples

Download data: BED, BW

(Submitter supplied) T-cell Acute Lymphoblastic Leukemia (T-ALL) is a heterogeneous group of hematological tumors composed of distinct subtypes that vary in their genetic abnormalities, gene expression signatures and prognoses. However, it remains unclear whether T-ALL subtypes differ at the functional level, and as such T-ALL treatments are uniformly applied across subtypes leading to variable responses between patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: R, TXT

(Submitter supplied) T-cell Acute Lymphoblastic Leukemia (T-ALL) is a heterogeneous group of hematological tumors composed of distinct subtypes that vary in their genetic abnormalities, gene expression signatures and prognoses. However, it remains unclear whether T-ALL subtypes differ at the functional level, and as such T-ALL treatments are uniformly applied across subtypes leading to variable responses between patients. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: BED

(Submitter supplied) We performed ChIP-Seq in Jurkat T-ALL cells to identify UTX binding sites across the genome. We then compared UTX binding sites (this study) with TAL1 binding sites (Data from Palii, 2011 GSE25000), and found a high degree of overlap between TAL1 and UTX in Jurkat T-All cells. Indeed, over 80% of TAL1 binding sites overlap with UTX.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL11154

2 Samples

Download data: BED, BW

(Submitter supplied) TAL1/SCL is a master regulator of hematopoiesis whose expression promotes opposite outcomes depending on the cell type - differentiation in the erythroid lineage or oncogenesis in the T-cell lineage. Here we used a combination of ChIP-sequencing and gene expression profiling to compare the function of TAL1 in normal erythroid and leukemic T-cells. Analysis of the genome-wide binding properties of TAL1 in these two hematopoietic lineages revealed new insight into the mechanism by which transcription factors select their binding sites in alternate lineages. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

3 Samples

Download data: BED, MAP

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL28038 GPL24676

34 Samples

Download data: BED, BEDPE, BW, NARROWPEAK, TXT

(Submitter supplied) Cut&Run analysis was performed in RPMI-8402 cells to analyze binding regions of MYC, MYCN and various histone modifications in normal culture conditions

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

10 Samples

Download data: BED, BW

(Submitter supplied) RNA-seq analysis was performed in a RPMI-8402 T-ALL cell stably expressing Cas9 aafter knockout of both MYC and MYCN

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

6 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis was performed in a RPMI-8402 T-ALL cell stably expressing Cas9 after knockout of MYC

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

6 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis was performed in a RPMI-8402 T-ALL cell stably expressing Cas9 after knockout of MYCN

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

6 Samples

Download data: TXT

(Submitter supplied) H3K27ac Hi-ChIP analysis was performed in Jurkat and RPMI-8402 stably expressing dCAR9-KRAB after treatment with DMSO (Control) or Doxycycline to induce sgRNA expression to block MYCN enhnacer region

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28038

4 Samples

Download data: BED, BEDPE, TXT