GEO DataSets

(Submitter supplied) Two orthotopic pancreatic tumor mouse models were used for ChIP-Seq and RNA-Seq to identify genome-wide dysfunction of H3K4me3 and gene expression. Mouse pancreatic tumors have a genome-wide increase in H3K4me3 deposition as compared to normal pancreas. Osteopontin (OPN) and its receptor CD44 were identified being up-regulated in pancreatic tumors by their promoter H3K4me3 deposition. OPN protein is increased in both tumor cells and tumor-infiltrating immune cells in human pancreatic carcinoma and is inversely correlated with pancreatic cancer patient survival. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: CSV, TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL17021

12 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Total RNA was isolated from normal C57BL/6 mouse pancreas, PANC02-H7, and UN-KC-6141 tumors from tumor-bearing mice. The RNA was used for RNA-Seq. The gene expression profiles between normal mouse pancreas and orthotopic pancreatic tumors were compared, and differentially expressed genes were identified.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: BIGWIG

(Submitter supplied) To explore the molecular mechanism underlying OICR-9429-induced WDR5 inhibition in BCa cells, a genome-wide RNA-sequencing was conducted to compare gene expression profiles between OICR-9429 treated T24, UM-UC-3 cells and their control cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: XLSX

(Submitter supplied) Our data showed that ENT broadly impacted multiple populations of immune cells within the TME. Thus, we performed general immune transcriptome profiling on whole tumors isolated from the neu-N model using a PanCancer immune-profiling gene panel for the NanoString platform.

Organism:

Mus musculus

Type:

Other

Platform:

GPL25652

24 Samples

Download data: CSV, RCC

(Submitter supplied) Immune checkpoint inhibition (ICI) has revolutionized treatment in cancers that are naturally immunogenic by enabling infiltration of T cells into the tumor microenvironment (TME) and promoting cytotoxic signaling pathways. Tumors possessing complex immunosuppressive TME’s such as breast and pancreatic cancers present unique therapeutic obstacles as response rates to ICI remain low. Such tumors often recruit myeloid-derived suppressor cells (MDSCs) whose functioning prohibits both T-cell activation and infiltration. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL25266

22 Samples

Download data: CSV, RCC

(Submitter supplied) In order to study the difference between high tumor burden and low tumor burden, we established MC38 tumor-bearing mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: TXT

(Submitter supplied) MMTV-neu cells consist of epithelial-like and mesenchymal-like cell populations with distinct genetic signatures.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1 Sample

Download data: MTX, TSV

(Submitter supplied) The incidence of TP53 loss-of-function in hepatocellular carcinoma is very high. In order to clarify the gene expression differences induced by the changes of TP53 gene, we used two human hepatocellular carcinoma cell lines, SK-HEP-1 and Hep 3B with TP53 knockdown or overexpression for RNA sequencing . SK-HEP-1 is a TP53 wild-type hepatocellular carcinoma cell line. Thus, we knockdown TP53 in SK-HEP-1. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

14 Samples

Download data: TXT

(Submitter supplied) The openness of chromatin affects the expression and regulation of genes. In order to figure out the changes of transcriptional factors after sirolimus treatment in hepatocellular carcinoma, ATAC-seq was performed for human hepatocellular carcinoma cell line SK-HEP-1. Here, we found that a series of transcriptional factors, including E2F1, SP1, M2F1, etc. enhanced binding to DNA after sirolimus treatment.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: BED

(Submitter supplied) Aberrant expression of immune checkpoint protein programmed death ligand-1 (PD-L1) promotes immune tolerance in cancer. RB is a tumor suppressor known to regulate the cell cycle, DNA damage response, and differentiation. Here, we demonstrate transient knockdown or homozygous deletion of RB markedly induces PD-L1 mRNA expression. RB binds to NFκB protein p65 and serine-249/threonine-252 (S249/T252) phosphorylation of RB is important for its interaction with p65 and suppression of PD-L1 expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: XLS

(Submitter supplied) ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To explore global transcriptional activity, we performed chromatin immunoprecipitation followed by high throughput sequencing (ChIP–seq) to investigate H3K27ac histone modification of ARID1A knockout and control MDA-MB-231 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: BW, TXT

(Submitter supplied) ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To explore global transcriptional activity, we performed chromatin immunoprecipitation followed by high throughput sequencing (ChIP–seq) to investigate H3K4me1 histone modification of ARID1A knockout and control MDA-MB-231 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: BW, TXT

(Submitter supplied) ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To investigate global chromatin remodeling, we performed ATAC–seq in ARID1A knockout and control MDA-MB-231 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: BW, 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:

GPL11154 GPL24676

36 Samples

Download data: BW

(Submitter supplied) ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. To explore global transcriptional activity, we performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–seq) to investigate H3K4me3 histone modification of ARID1A knockout and control MDA-MB-231 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TXT

(Submitter supplied) ARID1A has been suggested as a key regulator for anti-tumor immunity. In the present study, we evaluated the role of ARID1A deficiency in inducing adaptive immune resistance in triple negative breast cancer. Next-generation sequencing analysis was performed in control and ARID1A knockout MDA-MB-231 cells to investigate global gene expression changes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) An autochthonous model of pancreatic ductal adenocarcinoma (PDA) permitted the analysis of why immunotherapy is ineffective in this human disease. Despite finding that PDA-bearing mice had cancer cell-specific CD8+ T cells, the mice, like human PDA patients, did not respond to two immunological checkpoint antagonists that promote the function of T cells, α-CTLA-4 and α-PD-L1. Immune control of PDA growth was achieved, however, by depleting carcinoma-associated fibroblasts (CAFs) that express Fibroblast Activation Protein (FAP). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: TXT

(Submitter supplied) Tumor cells modulate host immunity by secreting extracellular vesicles (EV) and soluble factors in circulation. Their interactions with myeloid cells could lead to the generation of myeloid-derived suppressor cells (MDSC), which strongly inhibit the anti-tumor function of T and NK cells. We demonstrated previously that EV derived from mouse and human melanoma cells induced such immunosuppressive activity via upregulating the expression of programmed cell death ligand 1 (PD-L1) on myeloid cells that was dependent on the heat-shock protein 90a (HSP90a) in EV and on the toll-like receptor (TLR) on myeloid cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

14 Samples

Download data: CEL

(Submitter supplied) Background: Previous studies have shown that EZH2 regulates tumor PD-L1 expression at the transcriptional level and has an impact on tumor immune environment and prognosis. However, whether EZH2 can regulate PD-L1 expression at the post-translational level remains unclear. Therefore, this study aims to investigate the effects of EZH2 inhibition on PD-L1 expression and protein stability in colorectal cancer cells, uncover its underlying mechanisms, and provide new therapeutic strategies for anti-tumor immune therapy. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT