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Items: 1 to 20 of 48

1.

Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [scRNA-seq]

(Submitter supplied) We analyzed chromatin accessibility, scATAC-seq and RNA-seq across neuroendocrine carcinomas from distinct anatomic origins including Merkel cell carcinomas, neuroendocrine prostate cancer, small cell lung cancer and gastrointestinal NECs.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
1 Sample
Download data: H5
Series
Accession:
GSE262624
ID:
200262624
2.

Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [scATAC-seq]

(Submitter supplied) We analyzed chromatin accessibility, scATAC-seq and RNA-seq across neuroendocrine carcinomas from distinct anatomic origins including Merkel cell carcinomas, neuroendocrine prostate cancer, small cell lung cancer and gastrointestinal NECs.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
5 Samples
Download data: TSV
Series
Accession:
GSE262623
ID:
200262623
3.

Pyrvinium pamoate targets to multiple vulnerabilities of Merkel cell carcinoma

(Submitter supplied) Among several WNT signaling perturbagens, we identified pyrvinium pamoate, an FDA-approved anthelminthic drug that exhibits anti-tumor abilities in multiple cancers. Through the integration of transcriptomic, network, and molecular analyses, we discovered that pyrvinium is broadly effective against Merkel cell carcinoma cell lines, and it targets multiple proposed MCC tumorigenesis pathways. Our study revealed that pyrvinium exerts anti-tumor activity in MCC not only through perturbing the canonical and non-canonical WNT signaling pathway but also non-specifically inhibiting cell growth - via the activation of the p53-mediated apoptosis pathway, modulation of mitochondrial function, and induction of endoplasmic reticulum (ER) stress.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
30 Samples
Download data: CSV, TXT
Series
Accession:
GSE229701
ID:
200229701
4.

Dynamics of host response to Merkel cell polyomavirus oncogenes

(Submitter supplied) Merkel cell polyomavirus (MCPyV) small tumor antigen (ST), truncated large tumor antigen (TLT), early region (ER), and GFP control inducible vectors were introduced into IMR90 human lung embryonic fibrobrasts. After induction, cells were extracted and sequenced in triplicate every 4 hours for the first 24 hours, then every 8 hours until 48 hours. The purpose of this experiment was to identify the dynamic host response to MCPyV oncogenes, using both differential expression analysis and transcriptional network reconstruction, and to provide a systems-level understanding of the initial steps toward Merkel cell carcinoma.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
115 Samples
Download data: TXT
5.

Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling

(Submitter supplied) While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL24676
1539 Samples
Download data: BED
Series
Accession:
GSE243474
ID:
200243474
6.

Next-generation mRNA sequencing of MKL-1 Merkel cell carcinoma cells expressing wild-type or mutant YAP or TAZ

(Submitter supplied) The overarching goal of this study was to characterize TEAD-dependent transcriptional effects of YAP and TAZ in Merkel cell carcinoma cells. To that end, transcriptional profiling was performed on MKL-1 cells induced to express GFP, wild-type YAP or TAZ, or YAP S94A or TAZ F52A for 3 days.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
15 Samples
Download data: TXT
7.

MKL-1 Merkel cell carcinoma cells treated with EPZ011989

(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
Platform:
GPL24676
24 Samples
Download data: BROADPEAK, BW, NARROWPEAK, TXT
Series
Accession:
GSE186899
ID:
200186899
8.

Next-generation sequencing of CUT&RUN of MKL-1 Merkel cell carcinoma cells treated with EPZ011989

(Submitter supplied) The overarching goal of this study was to characterize mechanisms of sensitivity to EZH2 inhibitors in Merkel cell carcinoma cell lines. To that end, CUT&RUN for H3K27me3 and H3K4me3 histone marks was performed in MKL-1 cells treated with the EZH2 inhibitor EPZ011989 for 6 days.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24676
12 Samples
Download data: BROADPEAK, BW, NARROWPEAK
Series
Accession:
GSE186897
ID:
200186897
9.

Next-generation mRNA sequencing of MKL-1 Merkel cell carcinoma cells treated with EPZ011989

(Submitter supplied) The overarching goal of this study was to characterize mechanisms of sensitivity to EZH2 inhibitors in Merkel cell carcinoma cell lines. To that end, early and late transcriptional changes were profiled in MKL-1 cells treated with the EZH2 inhibitor EPZ011989 for 6 or 12 days.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
12 Samples
Download data: TXT
10.

Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer

(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:
GPL18573 GPL20301 GPL24676
79 Samples
Download data: BW, H5, TSV
Series
Accession:
GSE156292
ID:
200156292
11.

Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [ATAC-seq]

(Submitter supplied) We analyzed chromatin accessibility, ChIP-seq and RNA-seq across neuroendocrine carcinomas from distinct anatomic origins including Merkel cell carcinomas, neuroendocrine prostate cancer, small cell lung cancer and gastrointestinal NECs.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
27 Samples
Download data: BW
Series
Accession:
GSE156291
ID:
200156291
12.

Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [ChIP-seq]

(Submitter supplied) We analyzed chromatin accessibility, ChIP-seq and RNA-seq across neuroendocrine carcinomas from distinct anatomic origins including Merkel cell carcinomas, neuroendocrine prostate cancer, small cell lung cancer and gastrointestinal NECs.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20301 GPL18573
11 Samples
Download data: BW
Series
Accession:
GSE156290
ID:
200156290
13.

Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [RNA-seq]

(Submitter supplied) We analyzed chromatin accessibility, ChIP-seq and RNA-seq across neuroendocrine carcinomas from distinct anatomic origins including Merkel cell carcinomas, neuroendocrine prostate cancer, small cell lung cancer and gastrointestinal NECs.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
35 Samples
Download data: BW
14.

ADDICTION OF MERKEL CELL CARCINOMA TO MUC1-C IDENTIFIES A POTENTIAL NEW TARGET FOR TREATMENT OF THIS RECALCITRANT MALIGNANCY [MCC26]

(Submitter supplied) MCCP and MCCN cells are addicted to the oncogenic MUC1-C protein. MUC1-C is a druggable target that may provide new opportunities for advancing MCC treatment.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
6 Samples
Download data: CSV
15.

ADDICTION OF MERKEL CELL CARCINOMA TO MUC1-C IDENTIFIES A POTENTIAL NEW TARGET FOR TREATMENT OF THIS RECALCITRANT MALIGNANCY [MKL1]

(Submitter supplied) MCCP and MCCN cells are addicted to the oncogenic MUC1-C protein. MUC1-C is a druggable target that may provide new opportunities for advancing MCC treatment.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
12 Samples
Download data: CSV
16.

ADDICTION OF MERKEL CELL CARCINOMA TO MUC1-C IDENTIFIES A POTENTIAL NEW TARGET FOR TREATMENT OF THIS RECALCITRANT MALIGNANCY

(Submitter supplied) MCCP and MCCN cells are addicted to the oncogenic MUC1-C protein. MUC1-C is a druggable target that may provide new opportunities for advancing MCC treatment.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: CSV
17.

RNA-seq profiling of A549 cells with sgRNA knockouts that confer prexasertib resistance

(Submitter supplied) A549 cells with FOXM1 or LIN54 sgRNA knockout, which confers resistance to the CHK1 inhibitor prexasertib, were generated. These cells and control (empty vector) cells were synchronized in S phase, released for 1 hour and treated with 100 nM prexasertib or DMSO (vehicle) for 2 hours. RNA-seq profiling was performed to identify drug-induced perturbations in gene expression in these cells.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
12 Samples
Download data: TXT
18.

CHK1 Inhibitor Blocks Phosphorylation of FAM122A and Promotes Replication Stress

(Submitter supplied) While effective anti-cancer drugs targeting the CHK1 kinase are advancing in the clinic, drug resistance is rapidly emerging. Here, we demonstrate that CRISPR-mediated knockout of the little-known gene FAM122A confers cellular resistance to CHK1 inhibitors and cross-resistance to ATR inhibitors. Knockout of FAM122A results in activation of PP2A-B55α, a phosphatase which dephosphorylates the WEE1 protein and rescues WEE1 from Ubiquitin-mediated degradation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
4 Samples
Download data: CSV
Series
Accession:
GSE158338
ID:
200158338
19.

Profiling chromatin accessible regions in Merkel cell carcinoma cells

(Submitter supplied) Merkel cell carcinoma (MCC) is an aggressive neuroendocrine cancer of the skin, caused by either excessive UV damage or integration of the Merkel cell polyomavirus (MCV) genome. Here, we report that virally encoded MCV small T antigen (ST) establishes dependence on the LSD1 transcriptional repressor. Inhibition of LSD1 reduces growth of MCV-positive MCC and suppresses ST’s transformation capacity in vitro and in vivo. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
8 Samples
Download data: BED
Series
Accession:
GSE140505
ID:
200140505
20.

LSD1-RCOR2 binding and LSD1 and BRD9 transcriptome analysis in Merkel cell carcinoma cells

(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
Platform:
GPL18573
66 Samples
Download data: BED, TXT
Series
Accession:
GSE124864
ID:
200124864
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