GEO DataSets

(Submitter supplied) The neural transcription factor SOX11 is overexpressed in aggressive lymphoid neoplasms mainly in mantle cell lymphoma (MCL), but its functional role in malignant B-cells is unknown. To identify target genes transcriptionally regulated by SOX11 in malignant lymphoid cells, we have used Gene Expression Profiling (GEP) after SOX11 silencing in MCL cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4801

Platform:

GPL570

4 Samples

Download data: CEL

(Submitter supplied) The neural transcription factor SOX11 is overexpressed in aggressive lymphoid neoplasms mainly in mantle cell lymphoma (MCL). We have recently demonstrated SOX11 tumorigenic potential in vivo by showing a significant reduction on tumor growth of SOX11-knockdown MCL cells in xenograft experiments, confirming the clinical observations that SOX11 may play an important role in the aggressive behavior of MCL (Vegliante et al., 2013). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

14 Samples

Download data: CEL

(Submitter supplied) Gene expression analyis of primary MCL including IGHV mutated and unmutated cases Gene set analysis was perfomed in MCL samples, comparing IGHV mutated cases vs. IGHV unmutated cases

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4984

Platform:

GPL570

38 Samples

Download data: CEL

(Submitter supplied) To determine the role of SOX11 in aggressive lymphoid neoplasm, we first investigated direct target genes of this transcription factor using chromatin immunoprecipitation and DNA microarrays (ChIP-chip) in MCL cell lines. Analysis of the exact location of SOX11 binding elements showed that SOX11 interacts with DNA predominantly in the enhancer regions (in 40% of the enriched regions) and intron segments (in 33% of the enriched regions), suggesting that in these genes SOX11 may interact with the general transcriptional machinery and transcriptional co-regulators.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15114

4 Samples

Download data: PAIR, TXT

Analysis of B cell lymphocytes from Mantle Cell Lymphoma (MCL) patients with unmutated or mutated immunoglobulin heavy chain variable (IGHV) genes. Results provide insight into the effect of IGHV mutational status on MCL clinical features.

Organism:

Homo sapiens

Type:

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

Platform:

GPL570

Series:

GSE36000

38 Samples

Download data: CEL

Analysis of Z138 mantle cell lymphoma (MCL) cells depleted for the neural transcription factor SOX11. SOX11 is overexpressed in aggressive lymphoid neoplasms mainly in MCL. Results provide insight into the role of SOX11 in the pathogenesis of MCL.

Organism:

Homo sapiens

Type:

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

Platform:

GPL570

Series:

GSE34763

4 Samples

Download data: CEL

(Submitter supplied) The genes regulated by SOX11 in MCL was investigated in MCL cell line Granta 519 by siRNA knock down system. Cells were transfected using the LONZA electroporation system. Results represent cells harvested after 20 hours. Details of the experiment is published in PMID 21124928.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

12 Samples

Download data: CEL, TXT

(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

Platforms:

GPL9052 GPL11154

10 Samples

Download data: BIGBED

(Submitter supplied) SOX11 (Sex determining region Y-box 11) expression is specific for MCL as compared to other Non-Hodgkin’s lymphomas. However, the function and direct binding targets of SOX11 in MCL are largely unknown. We used high-resolution ChIP-Seq to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11 target genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) SOX11 (Sex determining region Y-box 11) expression is specific for MCL as compared to other Non-Hodgkin’s lymphomas. However, the function and direct binding targets of SOX11 in MCL are largely unknown. We used high-resolution ChIP-Seq to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11 target genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

4 Samples

Download data: BIGBED

(Submitter supplied) Gene expression profiles were obtained via Nanostring nCounter Expression Assay (PanCancer Immune Profiling Panel, Nanostring Technologies, Hamburg, Germany). We aimed to obtain the differential immune gene expression comparing the lymph node microenvironment of SOX11-positive and SOX11-negative MCL primary samples and non-neoplastic nodal samples (RLN).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL25262

20 Samples

Download data: RCC

(Submitter supplied) Mantle cell lymphoma (MCL) is an aggressive neoplasm with poor outcome. However, some patients have an indolent disease (iMCL) and may not require intensive treatment at initial diagnosis. Diagnostic criteria to recognize these patients are not available. We hypothesized that the analysis of the genetic and expression features of the tumors may help to identify patients with an indolent clinical evolution and provide biomarkers that could be used in the clinical setting.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

55 Samples

Download data: CEL

(Submitter supplied) Treatment with the monoclonal Notch1-antibody OMP-52M51 prevented DLL4-dependent activation of Notch1 and suppressed induction of Notch target genes in NOTCH1 mutated cell lines

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

8 Samples

Download data: CEL, XLSX

(Submitter supplied) DNA from four 29 cases, 38 tumor samples (23 PB, 12 LN, 1 Tonsil, 1 colonic biopsy, 1 spleen) and 29 normal DNA from the same patients were analyzed with Affymetrix SNP 6.0 platform for copy number alterations study. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples, lymph nodes and other tissues like spleen, tonsil and colonic biopsy

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

67 Samples

Download data: CEL, CNCHP

(Submitter supplied) Hypomorphic mutations of the transcription factor PAX5 occur in one third of B-progenitor acute lymphoblastic leukemias (B-ALLs). To identify PAX5-regulated genes in B-ALL, here we employ inducible expression of PAX5 in a human B-ALL cell line (REH) that harbors a loss-of-function mutation in PAX5. In this model, inducing PAX5 expression is associated with competitive disadvantage.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) Hypomorphic mutations of PAX5 occur in one third of B-progenitor acute lymphoblastic leukemias (B-ALLs), however their functional consequences remain undefined. Here we employ advanced transgenic RNAi in mice to suppress endogenous Pax5 expression in the hematopoietic compartment in vivo, which co-operates with activated STAT5 to induce B-ALL. In this model, restoring endogenous Pax5 expression in established B-ALL induces transcriptional and immunophenotypic changes reminiscent of normal B cell differentiation, disabling leukemia-initiating capacity and ultimately causing leukemia clearance.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) Triplicate RNA-seq expression analysis of bone marrow pre-B cells isolated from mice, to demonstrate repertoire at the IgH locus

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: TXT

(Submitter supplied) Hi-C was used to examine long range chromatin interactions in B cell progenitors in the presence and absence of the Erg transcription factor. Specifically, OP9 cultured B220+ B-cell progenitors derived from the bone marrow of Rag1CreT/+;ErgΔ/Δ mice and from Rag1CreT/+ and Rag1Cre+/+;Erg fl/fl control mice were isolated and DNA interactions were profiled by in situ Hi-C.

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

6 Samples

Download data: BED, MTX

(Submitter supplied) RNA-seq of pre-proB, proB and preB populations from Ergfl/fl bone marrow, pre-proB cell population from Rag1CreT/+;ErgΔ/Δ bone marrow

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: TXT

(Submitter supplied) ChIP-seq of B-cell progenitors and Rag1CreT/+;ErgΔ/Δ thymocytes for Erg transcription factor

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: NARROWPEAK