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Links from GEO DataSets

Items: 18

1.

MMRC aCGH reference collection

(Submitter supplied) The MMRC reference collection is a dataset of gene expression profiling, array comparative genomic hybridization, and re-sequencing created as a resource for the Multiple Myeloma research community.
Organism:
Homo sapiens
Type:
Genome variation profiling by array
Platform:
GPL9128
254 Samples
Download data: TXT
Series
Accession:
GSE26849
ID:
200026849
2.

MMRC expression and aCGH reference collection

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome variation profiling by array
Platforms:
GPL9128 GPL570
558 Samples
Download data: CEL, TXT
Series
Accession:
GSE26863
ID:
200026863
3.

MMRC expression reference collection

(Submitter supplied) The MMRC reference collection is a dataset of gene expression profiling, array comparative genomic hybridization, and re-sequencing created as a resource for the Multiple Myeloma research community.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
304 Samples
Download data: CEL
Series
Accession:
GSE26760
ID:
200026760
4.

Highly Recurrent MYD88 Mutations That Promote Human Lymphoma Cell Survival

(Submitter supplied) The ABC subtype of diffuse large B cell lymphoma (DLBCL) remains the least curable form of this lymphoma despite recent advances in therapy. We have combined structural and functional genomics to triangulate on new oncogenic mechanisms and devise new therapeutic strategies. RNA interference screen revealed a dependence of ABC DLBCL cell lines on MYD88 and IRAK1. High throughput resequencing of RNA (RNA-Seq) revealed frequent somatic mutations in MYD88 that preferentially occurred in the ABC DLBCL subtype. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL4133
16 Samples
Download data: TXT
Series
Accession:
GSE22900
ID:
200022900
5.

Assessment of MEK-ERK pathway targeting by BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL19824
146 Samples
Download data: CEL
Series
Accession:
GSE66293
ID:
200066293
6.

Assessment of MEK-ERK pathway targeting by BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias [U266 human myeloma cell line]

(Submitter supplied) Multiple myeloma (MM) is a malignant disorder characterized by the clonal proliferation of plasma cells (PCs) in the bone marrow (BM). The genetic background and clinical course of the disease are largely heterogeneous, and MM pathophysiology ranges from the premalignant condition of monoclonal gammopathy of undetermined significance (MGUS) to smoldering MM, symptomatic MM, and extramedullary MM/plasma cell leukemia (PCL). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL19824
4 Samples
Download data: CEL
Series
Accession:
GSE66292
ID:
200066292
7.

Assessment of MEK-ERK pathway targeting by BRAF, NRAS and KRAS gene mutations in plasma cell dyscrasias [Patient samples]

(Submitter supplied) Multiple myeloma (MM) is a malignant disorder characterized by the clonal proliferation of plasma cells (PCs) in the bone marrow (BM). The genetic background and clinical course of the disease are largely heterogeneous, and MM pathophysiology ranges from the premalignant condition of monoclonal gammopathy of undetermined significance (MGUS) to smoldering MM, symptomatic MM, and extramedullary MM/plasma cell leukemia (PCL). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL19824
142 Samples
Download data: CEL
Series
Accession:
GSE66291
ID:
200066291
8.

Genome-wide copy number aberrations and methylation profiles in human colorectal lesions

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array
Platforms:
GPL10123 GPL15182
172 Samples
Download data: TXT
Series
Accession:
GSE35534
ID:
200035534
9.

Methylated CpG island amplification (MCA) microarray analysis of human colorectal tumors

(Submitter supplied) The concept of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects are not fully understood. Our aim in this study was to unravel the molecular development of CIMP cancers by dissecting their genetic and epigenetic signatures in precancerous and malignant colorectal lesions.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL15182
88 Samples
Download data: TXT
Series
Accession:
GSE35508
ID:
200035508
10.

Array CGH analysis of human colorectal tumors

(Submitter supplied) The concept of the CpG island methylator phenotype (CIMP) in colorectal cancers (CRCs) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects early during carcinogenesis remains largely unknown. Our aim was to uncover the molecular evolution of CIMP CRCs through integrative analysis of endoscopic, histological and molecular signatures in precancerous and malignant colorectal lesions.
Organism:
Homo sapiens
Type:
Genome variation profiling by genome tiling array
Platform:
GPL10123
84 Samples
Download data: TXT
Series
Accession:
GSE35476
ID:
200035476
11.

methylatedDNA_peripheralBlood

(Submitter supplied) The goal of the experiment – genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters Keywords: DNA methylation, Methylated CpG island amplification coupled with promoter arrays, normal tissue
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
4 related Platforms
4 Samples
Download data
Series
Accession:
GSE8810
ID:
200008810
12.

Nucleosome deposition and DNA methylation at coding region boundaries

(Submitter supplied) We profiled CpG methylation for human T cells and compared this pattern with public T cell nucleosome (H2A.Z) and polymerase II profiles (SRA000234). Focusing on DNA regions surrounding the start codon and stop codon, instead of the transcription start and end sites, we discovered a very intriguing pattern, namely methylation and nucleosomal peaks at those regions, more prominent than peaks near transcript boundaries. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL9052
1 Sample
Download data: BED
Series
Accession:
GSE17554
ID:
200017554
13.

Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL570 GPL11154
7 Samples
Download data: BW, CEL, GTF
Series
Accession:
GSE37169
ID:
200037169
14.

Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [Affymetrix]

(Submitter supplied) Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncogenic BRAF to catalog transcriptome remodeling. We discovered that BRAF regulates expression of 1027 protein coding transcripts, 39 annotated lncRNAs and 70 novel transcripts. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
3 Samples
Download data: CEL
Series
Accession:
GSE37132
ID:
200037132
15.

Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [HT-seq]

(Submitter supplied) Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncogenic BRAF to catalog transcriptome remodeling. We discovered that BRAF regulates expression of 1027 protein coding transcripts, 39 annotated lncRNAs and 70 novel transcripts. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11154
4 Samples
Download data: BW, GTF
Series
Accession:
GSE33092
ID:
200033092
16.

Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL16558 GPL17586
22 Samples
Download data: BED, CEL, TAB
Series
Accession:
GSE69253
ID:
200069253
17.

Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target [Affymetrix]

(Submitter supplied) in this study we define an epigenomic profile of PRC2 (H3K27me3 and bivalent) tragets in four newly diagnosed MM patients. Using Oncomine database we demonstarte that PRC2 targets are underexpressed with advanced ISS stages and correlated to poor outcome. Pharmacological inhibition of UNC1999 showed anti-myeloma potential in vitro by activating the expression genes related to apoptosis and cell differenatiation.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL17586
6 Samples
Download data: CEL
Series
Accession:
GSE69251
ID:
200069251
18.

Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target [Seq]

(Submitter supplied) Multiple myeloma (MM) is a hematopoietic malignancy characterised by the accumulation of neoplastic post-germinal centre, isotype-switched, long-lived plasma cell within the bone marrow. In genetic and clinical terms MM is highly heterogeneous and remains fatal. Here we present the first epigenomic map of MM derived from freshly isolated bone marrow plasma cells from four patients. Using ChIP- and RNA-sequencing we define a set of silent H3K27me3 targets, active genes bearing H3K4me3, and bivalent genes.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL16558
16 Samples
Download data: BED, TAB
Series
Accession:
GSE53215
ID:
200053215
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