GEO DataSets

(Submitter supplied) Human hypopharygeal squamous cell carcinoma (HSCC) is a common head and neck cancer with a poor prognosis in advanced stages. Determining genes associated with transferring in HSCC could provide new targets and therapeutic strategies. We performed single-cell RNA sequencing of hypopharyngeal carcinoma and lymphoid metastases from five patients with hypopharyngeal squamous cell carcinoma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: TAR

(Submitter supplied) Despite the progress in immunotherapies, leading immune checkpoint inhibitors are only effective in a subset of patients. The efficacy of atezolizumab, an anti-PD-L1 antibody, in triple negative breast cancer (TNBC) is limited for unknown reasons. We utilized single-cell RNA- and ATAC-sequencing to examine the dynamics of immune cells in metastatic TNBC patients treated with paclitaxel or its combination with atezolizumab. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20795

83 Samples

Download data: MTX, TSV

(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; Genome variation profiling by SNP array; Expression profiling by array

Platforms:

GPL6801 GPL11154 GPL16686

301 Samples

Download data: CEL, CHP, NARROWPEAK, TXT

(Submitter supplied) Dynamic changes to the epigenome are essential regulators of B cell differentiation and, when perturbed, can lead to cancer. We compared three types of mature B cell lymphoma/leukemia (BCL) and normal lymphocytes to identify common and distinct epigenetic perturbations that promote oncogenesis. Purified malignant B cells from 52 patients (18 Follicular, 11 Diffuse Large B Cell, 23 Chronic Lymphocytic Lymphomas) and normal B cell subsets from 28 donor tonsils were subjected to chromatin immunoprecipitation and sequencing (ChIP-seq) for H3K4me1, H3K9/14ac, and H3K27ac; FAIRE-seq for open chromatin; RNA-seq; and genome copy number arrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

29 Samples

Download data: TXT

(Submitter supplied) Gastric cancer (GC) is a leading cause of cancer-induced mortality with poor prognosis with metastasis. However, the mechanism of gastric carcinoma lymph node metastasis remains unknown due to traditional bulk-leveled approaches mask roles of subpopulations. To answer questions from the gastric carcinoma intratumoral perspective in the metastasis, we performed single-cell level analysis on three gastric cancer patients with primary cancer and paired metastatic lymph node cancer tissues using scRNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

94 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

134 Samples

Download data: CEL, CHP

(Submitter supplied) Biopsies (lymph nodes, ascites or hydrothorax) from 60 patients with cancer of unknown primary origin were analyzed. Results provide insight into the molecular pathogenesis of CUP.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

74 Samples

Download data: CEL, CHP

(Submitter supplied) The cellular microenvironment in classical Hodgkin lymphoma (cHL) is dominated by a mixed infiltrate of inflammatory cells with typically only about 1% Hodgkin and Reed/Sternberg (HRS) tumor cells. T cells are usually the largest population of cells in the cHL microenvironment, encompassing T helper (Th) cells, regulatory T (Treg) cells and cytotoxic T cells. Th and Treg cells presumably provide essential survival signals for HRS cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

19 Samples

Download data: CEL

(Submitter supplied) Peripheral T-cell lymphoma (PTCL) encompasses a heterogeneous group of neoplasms with generally poor clinical outcome. Currently 50% of PTCL cases are not classifiable: PTCL-not otherwise specified (NOS). Gene-expression profiles on 372 PTCL cases were analyzed and robust molecular classifiers and oncogenic pathways that reflect the pathobiology of tumor cells and their microenvironment were identified for major PTCL-entities, including 114 angioimmunoblastic T-cell lymphoma (AITL), 31 anaplastic lymphoma kinase (ALK)-positive and 48 ALK-negative anaplastic large cell lymphoma, 14 adult T-cell leukemia/lymphoma and 44 extranodal NK/T-cell lymphoma that were further separated into NK-cell and gdT-cell lymphomas. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

193 Samples

Download data: CEL

(Submitter supplied) The identification of genes that contribute to the biological basis for clinical heterogeneity and progression of prostate cancer is critical to accurate classification and appropriate therapy. We performed a comprehensive gene expression analysis of prostate cancer using oligonucleotide arrays with 63,175 probe sets to identify genes and expressed sequences with strong and uniform differential expression between nonrecurrent primary prostate cancers and metastatic prostate cancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL91

35 Samples

Download data: CEL, RPT, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10558 GPL96 GPL570

55 Samples

Download data: CEL

(Submitter supplied) We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen, and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content, and closely related cell types. CIBERSORT should enable large-scale analysis of RNA specimens for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

28 Samples

Download data: CEL

(Submitter supplied) The assignment of diffuse large B-cell lymphoma into cell-of-origin (COO) groups is becoming increasingly important with the emergence of novel therapies that have selective biological activity in germinal center B-cell-like (GCB) or activated B-cell-like (ABC) groups. The LLMPP's Lymph2Cx assay is a parsimonious digital gene-expression (NanoString) based test for COO assignment in formalin-fixed paraffin-embedded tissue (FFPET) routinely produced in standard diagnostic processes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

119 Samples

Download data: CEL, TXT

(Submitter supplied) Biopsies (lymph nodes, ascites or hydrothorax) from 60 patients with cancer of unknown primary origin were analyzed. Results provide insight into the molecular pathogenesis of CUP.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

60 Samples

Download data: CEL, CHP

(Submitter supplied) Pulmonary metastasis continues to be the most common cause of death in osteosarcoma. Indeed, the 5-year survival for newly diagnosed osteosarcoma patients has not significantly changed in over 20 years. Further understanding of the mechanisms of metastasis and resistance for this aggressive pediatric cancer is necessary. Pet dogs naturally develop osteosarcoma providing a novel opportunity to model metastasis development and progression. more...

Organism:

Homo sapiens; Canis lupus familiaris

Type:

Expression profiling by array

Platforms:

GPL3979 GPL96

80 Samples

Download data: CEL

(Submitter supplied) Follicular lymphoma (FL) is genetically characterized by the presence of the t(14;18)(q32;q21) chromosomal translocation in approximately 90% of cases. In contrast to FL carrying the t(14;18), their t(14;18)-negative counterparts are less well studied regarding their immunohistochemical, genetic, molecular and clinical features. Within a previously published series of 184 FL grade 1-3A with available gene expression data, we identified 17 FL lacking the t(14;18). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL96 GPL97

368 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling of DLBCL patient samples was performed to investigate, whether molecular gene expression signatures retain their prognostic significance in patients treated with chemotherapy plus Rituximab. The lymphnode, germinal center signature and a new angiogenesis signature were combined to a final multivariate model which defined quartile groups among Rituximab-CHOP-treated patients with distinct 3-year overall survival rates. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

420 Samples

Download data: CEL, TXT

(Submitter supplied) We performed array comparative genomic hybridization (aCGH) and gene expression profiling in 203 samples of diffuse large B cell lymphoma (DLBCL). By gene expression, at least three molecular subtypes of DLBCL termed as germinal center B cell-like (GCB) DLBCL, activated B cell-like (ABC) DLBCL, and primary mediastinal B cell lymphoma (PMBL) can be distinguished. Combining gene expression profiling and aCGH, revealed copy number abnormalities that had strikingly different frequencies in the three molecular DLBCL subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL570 GPL6400

406 Samples

Download data: CEL, TXT

(Submitter supplied) Burkitt Lymphoma patient samples using gene expression to create a molecular definition of the disease. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Keywords: clinical history design

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3706

303 Samples

Download data