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Links from GEO DataSets

Items: 20

1.

Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing

(Submitter supplied) Although metastasis remains the cause of most cancer-related mortality, mechanisms governing seeding in distal tissues are poorly understood. Here we establish a robust method for identification of global transcriptomic changes in rare metastatic cells during seeding using single-cell RNA-sequencing and patient-derived xenograft (PDX) models of breast cancer. We find that both primary tumours and micrometastases display transcriptional heterogeneity, but micrometastases harbor a distinct transcriptome program conserved across PDX models that is highly predictive of poor survival in patients. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
1707 Samples
Download data: TXT
Series
Accession:
GSE123837
ID:
200123837
2.

Single-cell analysis reveals a stem cell program in human metastatic breast cancer cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by RT-PCR
Platform:
GPL20665
1293 Samples
Download data
Series
Accession:
GSE70555
ID:
200070555
3.

Single-cell analysis reveals a stem cell program in human metastatic breast cancer cells (Human patients - mammary cells)

(Submitter supplied) Despite major advances in understanding the molecular and genetic basis of cancer, metastasis remains the cause of >90% of cancer-related mortality1. Understanding metastasis initiation and progression is critical to develop new therapeutic strategies to treat and prevent metastatic disease. Prevailing theories hypothesize that metastases are seeded by rare tumor cells with unique properties, which may function like stem cells in their ability to initiate and propagate metastatic tumors.2 3-5 However, the identity of metastasis-initiating cells in human breast cancer remains elusive, and whether metastases are hierarchically organized is unknown.2 Here we show at the single-cell level that early stage metastatic cells possess a distinct stem-like gene expression signature. more...
Organism:
Homo sapiens
Type:
Expression profiling by RT-PCR
Platform:
GPL20665
271 Samples
Download data: TXT
Series
Accession:
GSE70554
ID:
200070554
4.

Single-cell analysis reveals a stem cell program in human metastatic breast cancer cells (PDX mice - cancer cells)

(Submitter supplied) Despite major advances in understanding the molecular and genetic basis of cancer, metastasis remains the cause of >90% of cancer-related mortality1. Understanding metastasis initiation and progression is critical to develop new therapeutic strategies to treat and prevent metastatic disease. Prevailing theories hypothesize that metastases are seeded by rare tumor cells with unique properties, which may function like stem cells in their ability to initiate and propagate metastatic tumors.2 3-5 However, the identity of metastasis-initiating cells in human breast cancer remains elusive, and whether metastases are hierarchically organized is unknown.2 Here we show at the single-cell level that early stage metastatic cells possess a distinct stem-like gene expression signature. more...
Organism:
Homo sapiens
Type:
Expression profiling by RT-PCR
Platform:
GPL20665
1022 Samples
Download data: TXT
Series
Accession:
GSE70552
ID:
200070552
5.

PGC-1α mediates mitochondrial biogenesis and oxidative phosphorylation in cancer cells to promote metastasis

(Submitter supplied) The study aimed to analyse the transcriptome of mouse cancer cells while in primary tumor, in circulation and after homing to metastatic site. The model used here is the 4T1 cancer cell orthotopic model.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
3 Samples
Download data: TXT
Series
Accession:
GSE37344
ID:
200037344
6.

RNA sequencing of siSNRNP40 in breast cancer cells

(Submitter supplied) To identify gene expression profile changes upon SNRNP40 depletion, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting SNRNP40.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
4 Samples
Download data: TXT
Series
Accession:
GSE78527
ID:
200078527
7.

Genome-wide mapping of SRC-3 binding in the liver at CT4.

(Submitter supplied) We reported the cistrome of steroid receptor co-activator SRC-3 in the liver at CT4
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
1 Sample
Download data: BW
Series
Accession:
GSE110462
ID:
200110462
8.

Coactivator-Dependent Oscillation of Chromatin Accessibility Dictates Circadian Gene Amplitude through REV-ERB Loading

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057 GPL9185
12 Samples
Download data: BIGWIG, BW
Series
Accession:
GSE67860
ID:
200067860
9.

Detection of chromatin accessibility in WT and SRC-2-/- mice in liver

(Submitter supplied) We futher characterized genome-wide chromatin accessibility of WT and SRC-2-/- mouse liver at CT10 through DNase-Seq. In addition,chromatin accessibility was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
4 Samples
Download data: BIGWIG
Series
Accession:
GSE67859
ID:
200067859
10.

Genome-wide maps of BAF180 and REV-ERBα binding

(Submitter supplied) We generated genome-wide cistromes of BAF180 subunit of the SWI-SNF chromatin remodeling complex in mouse liver at CT10 and CT22. In addition, we performed ChIP-Seq analysis on REV-ERBα in WT and SRC-2-/- mouse liver at CT10. We found circadian oscilation of BAF180 chromatin recruitment in mouse liver with peak recruitment at CT22 and nadir at CT10. Further,REV-ERBα chromatin recruitment was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057
7 Samples
Download data: BIGWIG, BW
Series
Accession:
GSE67852
ID:
200067852
11.

ChIP-seq and mRNA-seq experiment to find the direct target genes of ATF4 and CHOP

(Submitter supplied) We report the direct target genes of ATF4 and CHOP in response to endoplasim reticulum stress through next generation sequencing. By obtaining genowide sequence from chromatin immunoprecipitated DNA with anti-CHOP and anit-ATF4, we identified direct binding sites of ATF4 and CHOP in promoter regions of their target genes in mouse embrynic fibroblasts (MEFs) in response to ER stress. In addition, we obtained list of genes which are differentially regulated in Atf4 or Chop-deficient MEFs compared to the wild-type MEFs in response to ER stress. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
10 Samples
Download data: BEDGRAPH, RPKM
Series
Accession:
GSE35681
ID:
200035681
12.

Transcriptome determinants of lung seeding by mammary tumor cells

(Submitter supplied) Metastasis accounts for most of cancer-related deaths. Paracrine signaling between tumor cells and the stroma induces changes in the tumor microenvironment required for metastasis. Transcription factor c-Myb was associated with breast cancer (BC) progression but its role in metastasis remains unclear. Here we show that increased c-Myb expression in BC cells inhibits spontaneous lung metastasis through impaired tumor cell extravasation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
12 Samples
Download data: TXT
Series
Accession:
GSE104264
ID:
200104264
13.

BHLHE40 modulates gene transcription in breast cancer cells exposed to hypoxia and low glucose

(Submitter supplied) Knockdown of BHLHE40 expression significantly reduced primary tumor growth and spontaneous lung metastasis in an orthotopic xenograft model of human breast cancer. Gene expression analysis implicated a role of BHLHE40 in hypoxia-induced exosomic secretion of Heparin Binding Epidermal Growth Factor HBEGF, which promotes cell survival and invasion. BHLHE40 induces HBEGF transcription by blocking DNA binding of HDAC1 and HDAC2.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
12 Samples
Download data: TXT
Series
Accession:
GSE107300
ID:
200107300
14.

Expression data from a lung metastatic cell line or metastatic explants in mouse and human

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by array
Platforms:
GPL23038 GPL23159
40 Samples
Download data: CEL
Series
Accession:
GSE99557
ID:
200099557
15.

Expression data from lung metastatic explants

(Submitter supplied) The role of PGC1alpha in breast cancer lung metastasis is largely unknown. We used expression data from lung metastatic explants overexpressing PGC1alpha or control, treated with phenformin to understand global gene expression changes which occur in a PGC1alpha context and under phenformin treatment. We used expression data to understand the pathways and genes that may lead to lung metastasis in a PGC1alpha overexpression setting.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL23038
12 Samples
Download data: CEL, TXT
Series
Accession:
GSE99556
ID:
200099556
16.

Expression data from lung metastasis

(Submitter supplied) The role of PGC1alpha in breast cancer lung metastasis is largely unknown. We used expression data from lung metastasis of mice injected with PGC1alpha overexpression or control cells to understand global changes that occur upon overexpression of PGC1alpha that lead to lung metastasis. We used expression data to understand the pathways and genes that may lead to lung metastasis in a PGC1alpha overexpression setting.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL23038
22 Samples
Download data: CEL, TXT
Series
Accession:
GSE99555
ID:
200099555
17.

Expression data from a human lung metastatic cell line treated with siPGC1alpha or siControl

(Submitter supplied) To understand global expression changes in a knockdown of PGC1alpha (siPGC1alpha) vs control (siControl) in a lung metastatic cell line (4175) Metabolic adaptations play a key role in fuelling tumour growth. However, less is known regarding the metabolic changes that promote cancer progression to metastatic disease. Herein, we reveal that PGC-1a expression and activity are differentially regulated depending on breast cancer metastatic sites. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL23159
6 Samples
Download data: CEL, TXT
Series
Accession:
GSE99554
ID:
200099554
18.

Circulating Tumor Cell Clusters are Oligoclonal Precursors of Breast Cancer Metastasis

(Submitter supplied) Clusters of circulating tumor cells (CTC-clusters) are present in the blood of patients with cancer but their contribution to metastasis is not well defined. Here, we first use mouse models to demonstrate that breast cancer cells injected intravascularly as clusters are more prone to survive and colonize the lungs than single cells. Primary mammary tumors comprised of tagged cells give rise to oligoclonal CTC-clusters, with 50-fold increased metastatic potential, compared with single CTCs. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16288
29 Samples
Download data: XLS
Series
Accession:
GSE51827
ID:
200051827
19.

RNA-seq expression profiling of individual clones sorted from mouse mammary tumors

(Submitter supplied) Breast tumors are characterized by inherent heterogeneity but the evolving cellular organization of breast tumors through progression remains poorly understood. Individual clones were tracked by combining mouse models of breast cancer with Confetti reporter strains. Expression profiling of individual clones sorted from tumors arising in K5- and Elf5-driven Pten/p53-deficient mice revealed distinct molecular signatures.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
38 Samples
Download data: TXT
Series
Accession:
GSE120816
ID:
200120816
20.

Targeting IL13Ralpha2 activates STAT6-TP63 pathway to suppress breast cancer lung metastasis

(Submitter supplied) IL13Rα2 overexpression promotes metastasis of basal-like breast cancers IL13Rα2 depletion in highly metastatic breast cancer cells suppresses lung metastases formation by upregulating TP63 and decreasing their migratory potential
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
8 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE57677
ID:
200057677
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