GEO DataSets

(Submitter supplied) MMTV-PyMT late carcinomas, orthotopically injected in syngeneic RANK+/+ mice were digested until single cells and cultured over Matrigel in the prescence or abscence of RANKL for 24 hours.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

3 Samples

Download data: TXT

(Submitter supplied) Transcriptional profile of either RANK+/+ or RANK-/- MMTV-PyMT late carcinomas, orthotopically injected in syngeneic RANK+/+ mice. Once host mice developed tumors, CD45- tumor cells were sorted by flow cytometry in order to compare changes on tumor gene expression caused by the absence of RANK protein.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

6 Samples

Download data: TXT

(Submitter supplied) RANK-positive and RANK-negative luminal progenitor cells were isolated by FACS from histologically normal human breast tissue from wild-type human donors. RNA-seq gene expression profiling was used to find differentially expressed genes between the RANK-positive and RANK-negative cell populations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Combinational blockade of B7S1 and PD-1 exhibits stronger anti-tumor efficacy than monotherapies. In order to further understand the mechanisms whereby blockade of B7S1 or PD-1 inhibits tumor growth, we conducted ATAC-seq analysis of OVA-specific CD8+ TILs from E.G7-bearing mice treated with control antibodies, anti-B7S1, anti-PD-1 monotherapy or combinational therapy.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: BW

(Submitter supplied) B7S1 negatively regulates T cells and its expression correlates with poor prognosis of cancer patients. In order to understand how B7S1 signaling contributes to dysfunction of CD8+ T cell in the TME, we conducted transcriptional analysis of OVA-specific CD8+ TILs and different TIL subsets from E.G7-bearing WT and B7S1 KO mice (Day 21).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL21103

15 Samples

Download data: TXT

(Submitter supplied) Transcriptional profile of MMTV-PyMT late carcinomas after adjuvant or neoadjuvant treatment with RANK-Fc (receptor activator of NF-kB) cells isolated from one single MMTV-PyMT carcinoma were orthotopically injected in syngeneic WT mice, which were randomized 1:1 for neoadjuvant RANK-Fc or mock treatment (passage 1) for 4 weeks. Cells isolated from both treatment arms were pooled and injected into the fat pad of FvB recipients (passage 2) in limiting dilutions (mimicking occult disease) and again randomized 1:1 for additional RANK-Fc (adjuvant) or mock treatment

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

8 Samples

Download data: TXT

(Submitter supplied) Differential gene expression analysis between Vehicle and Trametininb treatment in 4T1Ch9 in vivo. GSEA analysis between Vehicle and Trametininb treatment in 4T1Ch9 in vivo.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11180

4 Samples

Download data: CEL

(Submitter supplied) During early tumorigenesis tumors edit their gene expression to evade immune surveillance. Because of difficulty capturing early tumors, studies of gene editing have to date mostly investigated changes in expression of candidate genes involved in activating adaptive immunity, such as those needed for antigen presentation and processing. Here we took advantage of an aggressive genetically engineered mouse model (GEMM) of breast cancer that expresses inducible oncogenic HER2 to identify tumor edited genes without bias.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TAR

(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; Methylation profiling by high throughput sequencing

Platforms:

GPL21103 GPL24247

36 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) We report genomewide methylation levels on CpG sites and segments before and after Decitabine treatment

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) The goal of RNA-seq is to identify the differential expressed genes in the B16F10 and 4T1 cells after Decitabine treatment. Three biological replicates were assigned for each group and in total 12 groups were prepared for RNA-seq libraries with 300 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped over 60 million reads per sample to mouse genome (mm10) with RSEM workflow. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL21103

12 Samples

Download data: XLSX

(Submitter supplied) The goal of ATAC-seq is to identify the open chromatin regions in the B16 and 4T1 cells after Decitabine treatment. Three biological replicates were assigned for each group and in total 12 groups were prepared for ATAC-seq libraries. We mapped about 30-100 million reads per sample to M.musculus (mm10) with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL24247

12 Samples

Download data: NARROWPEAK

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL20301 GPL21103 GPL24676

16 Samples

Download data: BW, MTX, NARROWPEAK, TSV, TXT

(Submitter supplied) The transcription factor SOX9 can act as a pioneering factor in driving lineage dedifferentiation and tumor progression for breast cancer. To unbiasedly understand how committed luminal stem progenitor cells dedifferentiate into embryonic multipotent progenitor-like cells, we performed scRNA-seq in luminal cells FACS sorted from WT control mice and Sox9-GFP;C3-TAg mice at the age of 3.5 months when C3-TAg mice have developed extensive hyperplastic lesions but not yet malignant tumors.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: MTX, TSV

(Submitter supplied) The transcription factor SOX9 can act as a pioneering factor in driving lineage dedifferentiation and tumor progression for breast cancer. To investigate downstream pathways mediating SOX9 function and identify the direct gene targets of SOX9, we performed RNA-seq and SOX9 ChIP-seq on human breast cancer cell line MCF7ras ctrl and SOX9-overexpressing (SOX9OE) cells.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL20301

14 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) NMU-induced sprague dawley rat model of breast cancer treated with immunotherapy to prevent tumor progression

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25947 GPL20084

115 Samples

Download data: CSV

(Submitter supplied) As a hallmark of cancer, altered metabolisms induce the suppression of anti-tumor immunity, contributing to immunotherapy resistance. Tumor metabolic reprogramming decreases immune effector cell infiltration, inhibits antigen priming and arrests expansion of effector cells. Therefore, we analyzed metabolism-related gene expression of tumors on a single-cell level using 3 tumor samples from breast cancer patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TAR, TSV

(Submitter supplied) Tumors employ various strategies to evade immune surveillance. Central nervous system (CNS) has multiple features to restrain immune response，because cranial inflammation can rapidly develop into lethal brain edema. However, whether tumors and CNS share similar programs of immune tolerance is elusive. Here, we analyzed transcriptomic and metabolomic profiles of tumors from patients with HER2+ breast cancer, who received trastuzumab, anti-PD-L1 antibodies and docetaxel (KN035-TH-HER2 study). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 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:

GPL21273 GPL19057

19 Samples

Download data

(Submitter supplied) We performed transcriptional profiling of tumor cells from indolent and aggressive lesions isolated from a mouse model of breast cancer. To initiate formation of mammary lesions, we delivered lentiviral particles carrying constitutively-activated Erbb2 tagged with HA and GFP (caErbB2) through the lactiferous glands of adult virgin female. Mammary glands bearing lesions were visualized under a fluorescence stereoscope, and regions harboring aggressive (>2mm, comprised of invasive lesions) and indolent (<2mm, enriched for in situ lesions) lesions were dissected away from each other. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

15 Samples

Download data: TSV