GEO DataSets

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

57 Samples

Download data

(Submitter supplied) Microbes are an integral component of the tumor microenvironment (TME). However, mechanisms that direct microbial recruitment into tumors and the spatial relationship between intratumoral microbes and host cells remain poorly understood. Here, we show that microbes and immune cells have parallel spatial distribution and that the presence of intratumoral microbes is dependent on T cells. Analysis of human pancreatic ductal adenocarcinomas (PDAC) and lung adenocarcinomas (LUAD) revealed a spatially heterogeneous distribution of lipopolysaccharide (LPS) that is associated with T cell infiltration. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Growing evidence shows that intratumoral microbes are associated with immune microenvironments in cancer. However, mechanisms that direct the recruitment of microbes to tumors remain poorly understood. Here, we show that intratumoral infiltration of immune cells and microbes are heterogeneous, and the distribution of microbes within tumors are orchestrated by the spatial heterogeneity of intratumoral lymphoid populations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: TXT

(Submitter supplied) We examined the effects of an oral small molecule DPP inhibitor (BXCL701) on PDAC tumor growth and tumor immune landscape using mT3-2D and Pan02 subcutaneous syngeneic murine models in C57BL/6 mice

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

42 Samples

Download data: CSV, XLSX

(Submitter supplied) As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient survival. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

8 Samples

Download data: MTX, TSV

(Submitter supplied) As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. Using a spatially-resolved multimodal single cell approach we unveil a detailed view of the immune micromilieu in PDAC with specific emphasis on the correlation of immune subtypes with patient prognosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

18 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Despite the uniform mortality in pancreatic adenocarcinoma (PDAC), clinical disease heterogeneity exists with limited genomic differences. A highly aggressive tumor subtype termed basal-like was identified to show worse outcomes and higher inflammatory responses. Here, we focus on the microbial effect in PDAC progression and present a comprehensive analysis of the tumor microbiome in different PDAC subtypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

62 Samples

Download data: TXT

(Submitter supplied) The single-cell RNA profiles of dissociated 10 pancreatic primary tumors and 6 metastatic biopsies were obtained using the 10x Genomics Chromium platform

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

16 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) The aim of this study is to identify by Next Generation Sequencing - RNA-seq profiling a molecular signature of Hepatocellular Carcinoma samples that correlates with survival. The samples were retrospectively derived from hepatocellular carcinoma tissue as well as non-tumor tissue from the livers of the same patients. The bioinformatical analysis of 32 pairs RNA-seq datasets were obtained from human RNAs on Illumina Hiseq-PE150. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

64 Samples

Download data: XLS

(Submitter supplied) Significant gut microbiota heterogeneity exists amongst UC patients though the clinical implications of this variance are unknown. European and South Asian UC patients exhibit distinct disease risk alleles, many of which regulate immune function and relate to variation in gut microbiota β-diversity. We hypothesized ethnically distinct UC patients exhibit discrete gut microbiotas with unique luminal metabolic programming that influence adaptive immune responses and relate to clinical status. more...

Organism:

Bacteria; human gut metagenome; Archaea

Type:

Other

Platform:

GPL21523

34 Samples

Download data: CEL

(Submitter supplied) Purpose: Use RNA-seq strategy to characterize the differentially expressed genes in T cell low and high mouse pancreatic tumors in order to identify factors contributing to the differential abundance of tumor infiltrating T cells. Methods: Subcutaneously implanted T cell low and high pancreatic tumors were utilized for the preparation of RNA-seq libraries from both bulk tumors.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

37 Samples

Download data: TXT

(Submitter supplied) Purpose: Use ATAC-seq strategy to characterize the differentially openned chromatin region in T cell low and high mouse pancreatic tumors in order to identify factors contributing to the differential abundance of tumor infiltrating T cells. Methods: Subcutaneously implanted T cell low and high pancreatic tumors were utilized for the preparation of ATAC-seq libraries from sorted tumor cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

15 Samples

Download data: TXT

(Submitter supplied) Purpose: Use RNA-seq strategy to characterize the differentially expressed genes in T cell low and high mouse pancreatic tumors in order to identify factors contributing to the differential abundance of tumor infiltrating T cells. Methods: Subcutaneously implanted T cell low and high pancreatic tumors were utilized for the preparation of RNA-seq libraries from sorted tumor cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

39 Samples

Download data: TXT

(Submitter supplied) Cancer immunotherapies utilize distinct mechanisms to harness the power of the immune system to eradicate cancer cells. Therapeutic vaccines, aimed at inducing active immune responses against an existing cancer, are highly dependent on the immunological microenvironment, where many immune cell types display high levels of plasticity and, depending on the context, promote very different immunological outcomes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

14 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30172 GPL24247

22 Samples

Download data: MTX, TSV

(Submitter supplied) The composition of the gut microbiome controls innate and adaptive immunity and has emerged as a key regulator of tumor growth and the success of immune checkpoint blockade (ICB) therapy. However, the underlying mechanisms remain unclear. Pancreatic ductal adenocarcinoma (PDAC) tends to be refractory to therapy, including ICB. We found that the gut microbe-derived metabolite trimethylamine N-oxide (TMAO) enhances anti-tumor immunity to PDAC. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

2 Samples

Download data: MTX, TSV

(Submitter supplied) The composition of the gut microbiome controls innate and adaptive immunity and has emerged as a key regulator of tumor growth and the success of immune checkpoint blockade (ICB) therapy. However, the underlying mechanisms remain unclear. Pancreatic ductal adenocarcinoma (PDAC) tends to be refractory to therapy, including ICB. We found that the gut microbe-derived metabolite trimethylamine N-oxide (TMAO) enhances anti-tumor immunity to PDAC. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

20 Samples

Download data: TXT