GEO DataSets

(Submitter supplied) We sorted GFP-labeled 4T1 cells from primary tumors and lung metastases and performed methylation-seq.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) We sorted GFP-labeled 4T1 cells from primary tumor and lung metastases and performed mRNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) We sorted GFP-labeled 4T1 cells from lung metastases and performed DNMT3B ChIP-seq.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: TXT

(Submitter supplied) Massive accumulation of myeloid-derived suppressor cells (MDSCs) is a hallmark of cancer. It is well-known that proinflammatory mediators induce MDSC accumulation. However, the functions of cell death pathways in MDSC survival and the mechanism underlying regulation of cell death pathways in MDSCs are still elusive. Herein, we determined that DNA methylation sustains MDSC accumulation in tumor-bearing mice since pharmacological inhibition of DNMTs with Dacitabine abolished MDSC accumulation and activated antigen-specific cytotoxic T lymphocytes in tumor-bearing mice. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: BW

(Submitter supplied) DNA methylation has suppressive effects on gene transcription and it is involved in a variety of physiologic processes, including development and cancer. As we and others demonstrated, Dnmt3b is a tumor suppressor in oncogene-driven lymphoid and myeloid malignancies in mice. Due to numerous activities such as methylation-dependent and independent repression and accessory functions, it is difficult to pinpoint physiological processes solely dependent on catalytic activity of Dnmt3b. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL24247 GPL24676

31 Samples

Download data: BIGWIG, TXT

(Submitter supplied) The findings indicate that EZH2 may act as a important therapeutic target for treatment of EAC. Furherly, EZH2 knockdown couldinduce G2/M phase arrest and resulted in cell proliferation inhibition. To further investigate how EZH2 overexpression impacted cell proliferation of EAC, Microarray gene expression profiling was performed on ISK cell line with or without EZH2 knockdown.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

6 Samples

Download data: CEL

(Submitter supplied) The seed-and-soil hypothesis was described over a century ago to describe why cancer cells (seeds) grow in certain organs (soil). Since then, the genetic properties that define the cancer cells have been heavily investigated, however, the genetic mediators within the organ microenvironment that mediate successful metastatic growth are less understood. In these studies, a set of human breast cancer patient-derived xenograft (PDX) metastasis models were utilized. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL22245

128 Samples

Download data: TXT

(Submitter supplied) RNA-sequencing analysis of control (shCon) and NSD3-knockdown (shNSD3) MDA-MB-231 cell lines. NSD3 (also known as WHSC1L1), a histone H3 lysine K36methyltransferase, is highly amplificated in several human cancers, including breast carcinomas. Results provide insight into the transcriptional regulation of NSD3 in breast cancer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of human breast cancer cell lines, lowly invasive MCF10CA1h and highly invasive MCF10CA1a, treated with vehicle control (ethanol) and with RSV (resveratrol). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human cell lines exposed to described treatments. Samples included biological triplicate of MCF10CA1h control (ethanol treated), biological triplicate of MCF10CA1h treated with RSV, biological triplicate of MCF10CA1a control (ethanol treated), biological triplicate of MCF10CA1a treated with RSV.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

12 Samples

Download data: IDAT, XLSX

(Submitter supplied) Inhibition of estrogen related receptor alpha (ERRa) with C29 decreases global levels of DNA methylation and sensitizes breast cancer cells to the cytostatic effect of the DNMT inhibitor 5-aza-2'-deoxycytidine. We performed RRBS to understand the mechanisms behind the tumor suppression effect observed upon cotreatment with C29 and 5-azadC . We observed distinct patterns of differentially methylated regions in promoters for each condition and discovered that IRF4 was hypomethylated specifically in the condition with drug combination. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TSV

(Submitter supplied) We investigated if Overexpression of ANG in UROtsaANG and RT112Scr could cause epigenetic changes, comparing to UROtsaEmpty and RT112KD-ANG, respectively . The alteration of genome-wide DNA methylation in these cells was analyzed using Illumina whole genome methylation array. Specifically, methylated DNAs with 5-mC were amplified using nonbiased conditions, labeled and hybridized to a BeadChip array covering over >450,000 methylation sites. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

8 Samples

Download data: TXT, XLSX

(Submitter supplied) Dnmt3b is a DNA methytransferase which is an enzyme that methylated genomic DNA which contributes to genomic stability and transcriptional regulation.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9250

16 Samples

Download data

(Submitter supplied) Dnmt3b is a DNA methytransferase which is an enzyme that methylated genomic DNA which contributes to genomic stability and transcriptional regulation.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

11 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL16686 GPL6244

12 Samples

Download data: CEL

(Submitter supplied) Nuclear LASP-1 has a direct correlation with the overall survival of breast cancer patients. Gene expression analysis of MDA-MB-231S (sorted for high surface expression of CXCR4) and MDA-Bone-Un (Mouse bone metastasized MDA-MB-231 cells) human basal-like breast cancer cells cultured in 3D-Matrigel was performed. Changes in transcript levels of key microRNAs 29B1 and 29B2, miRLet7F1, miR519A1, MMP9, MMP1, FAM75D4, Interferons a7 and a17, Glycine receptor a3, CADM2 and claudin12

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

4 Samples

Download data: CEL, TXT

(Submitter supplied) Nuclear LASP-1 has a direct correlation with the overall survival of breast cancer patients. Gene expression analysis of MCF7 human breast cancer cells cultured in 3D-Matrigel was performed. Up regulation of cell junction proteins, extracellular matrix proteins and down regulation of MMP 9 and 2 were observed. This corroborates well with the involvement of LASP-1 in cell migration and chemotaxis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL, TXT

(Submitter supplied) Despite substantial progress in lung cancer immunotherapy, the overall response rate in KRAS-mutant lung adenocarcinoma (ADC) patients remains low. Combining standard immunotherapy with adjuvant approaches that enhance adaptive immune responses—such as epigenetic modulation of anti-tumor immunity—is therefore an attractive strategy. To identify epigenetic regulators of tumor immunity, we constructed an epigenetic-focused sgRNA library, and performed an in vivo CRISPR screen in KrasG12D/P53-/- (KP) lung ADC model. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL21103

10 Samples

Download data: BW

(Submitter supplied) We performed single-cell RNA sequencing (scRNAseq) analysis on the mouse lung tissues from KP tumor-bearing mice treated with tumor cell intrinsic Asf1a KO, anti-PD-1 or combination treatment

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: MTX, TSV

(Submitter supplied) To systematically study the functions of epigenetic genes in controlling tumor progression and regulating anti-tumor immunity, we performed a series of in vitro and in vivo epigenome-wide CRISPR screens in mouse KP lung adenocarcinoma model. We constructed an epigenetic-focused sgRNA library, established KP-Cas9-library pools, and then performed in vitro and in vivo CRISPR screens. For in vitro screens, we compared the cell pools harvested at week 4 with the cells pools harvested at week 2 to check the functions of epigenetic genes in tumor cell proliferation. more...

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL19604 GPL17021

54 Samples

Download data: TXT

(Submitter supplied) KrasG12D/P53-/-(KP)-Cas9 single clone was transfected with ctrl vector, ctrl sgRNA-1, ctrl-sgRNA-2 or ctrl-sgRNA-3 and then selected by using 5ug/ml Blasticidin, to get the 4 ctrl lines; KP-Cas9 single clone was transfected with Asf1a sgRNA-1, sgRNA-2, sgRNA-3 and new sgRNA-1 and then selected by using 5ug/ml Blasticidin, and then picked up single clones with Asf1a KO. For each Asf1a sgRNA, we selected one clone for RNA seq, so totally we have 4 Asf1a KO clones for RNA seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT