Similar studies for GEO DataSets (Select 200213685) - GEO DataSets

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Items: 20

Select item 2002136851.

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. [methylation]

(Submitter supplied) Aberrant DNA-methylation at CpG dinucleotides is a hallmark of cancer and is associated with the emergence of resistance to anti-cancer treatment, though molecular mechanisms and biological signifi- cance remain elusive. Genome-scale methylation maps by currently used methods are based on chemical modification of DNA and are best suited for analyses of methylation at CpG-rich regions (CpG islands). more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL28975
6 Samples

Download data: TSV

Series

Accession:: GSE213685

ID:: 200213685

PubMed Full text in PMC Similar studies

Select item 2002136862.

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias.

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

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:: GPL28975 GPL24676
23 Samples

Download data: TSV

Series

Accession:: GSE213686

ID:: 200213686

PubMed Full text in PMC Similar studies

Select item 2002136843.

High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias.[RNA-Seq]

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
17 Samples

Download data: XLSX

Series

Accession:: GSE213684

ID:: 200213684

PubMed Full text in PMC Similar studies

Select item 2000374544.

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia

(Submitter supplied) Here we used Illumina NGS for high-throughput profiling of the DNA methylome in two human colon cancer derived cell lines, two human normal bone marrow CD34+ controls and in five human Acutre Myeloid Leukeima patient samples. These data can be used to determine the CpG cytosine methylation pattern at base pair resolution in each sample and to determine differentially methylated cytosines and regions between samples

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platforms:: GPL11154 GPL10999
19 Samples

Download data: TXT

Series

Accession:: GSE37454

ID:: 200037454

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000762705.

DNA methylome analysis of pediatric acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.

(Submitter supplied) We used whole genome bisulfite sequencing (WGBS) to determine the DNA methylation levels at single base-pair resolution of four patients with different subtypes of pediatric ALL together with RNA-sequencing to increase our understanding of the leukemic transformation in ALL.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:: GPL10999
49 Samples

Download data: BED, BEDGRAPH, TXT

Series

Accession:: GSE76270

ID:: 200076270

PubMed Full text in PMC Similar studies

Select item 2000286486.

Genome-wide methylation and expression profiling study identifies candidate DNA methylation drivers of acquired cisplatin resistance in ovarian cancer.

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

Organism:: Homo sapiens

Type:: Expression profiling by array; Methylation profiling by array

Platforms:: GPL570 GPL8490
46 Samples

Download data: CEL

Series

Accession:: GSE28648

ID:: 200028648

Select item 2000286477.

Genome-wide Methylation Profiling Identifies Candidate DNA Methylation Drivers of Acquired Cisplatin Resistance in Ovarian Cancer.

(Submitter supplied) Multiple DNA methylation changes have been associated with the acquisition of drug resistance; however it remains uncertain how many of these changes may represent critical DNA methylation drivers of chemoresistance. Using genome-wide DNA methylation profiling across 27,578 CpG sites on Illumina HumanMethylation27 bead array we identified loci at 4092 genes becoming hypermethylated in the chemoresistant A2780/cp70 ovarian tumour cell line compared to the parental sensitive A2780 line. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL8490
31 Samples

Download data: TXT

Series

Accession:: GSE28647

ID:: 200028647

Select item 2000286468.

Gene expression profiling in A2780, CP70 and CP70 following Decitabine and/or PXD101 treatment

(Submitter supplied) Multiple DNA methylation changes have been associated with the acquisition of drug resistance; however it remains uncertain how many of these changes may represent critical DNA methylation drivers of chemoresistance. Using gene expression profiling method on HGU133plus2 array, we identified a total of 1370 genes showing significant gene expression changes with 687 genes going up and 683 genes going down in the resistant (cp70) versus sensitive cell lines (A2780) by Rank Product (FDR<5%). more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL570
15 Samples

Download data: CEL

Series

Accession:: GSE28646

ID:: 200028646

Select item 2002130299.

Aerobic Exercise Training Rejuvenates the Human Skeletal Muscle Methylome Ten years after Breast Cancer Treatment and Survival

(Submitter supplied) Many cancer survivors suffer from impairments in skeletal muscle (SkM), both in terms of reduced mass and function. Interestingly, human SkM possesses an epigenetic memory of earlier stimuli, such as exercise. Long-term retention of epigenetic changes in SkM following cancer survival and/or exercise training have not yet been studied. We therefore investigated genome-wide DNA methylation (the methylome) in SkM following a 5-month, 3/week treadmill-based aerobic training intervention in breast cancer survivors 10-14 years after diagnosis and treatment. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL21145
32 Samples

Download data: IDAT, TXT

Series

Accession:: GSE213029

ID:: 200213029

Select item 20002904710.

CpG methylation patterns and decitabine treatment response in acute myeloid leukemia cells and normal hematopoietic precursors

(Submitter supplied) The DNA hypomethylating drug decitabine maintains normal hematopoietic stem and progenitor cell (HSPC) self-renewal but induces terminal differentiation in acute myeloid leukemia (AML) cells. To better understand the basis for this contrasting treatment effect, the baseline expression of key lineage-specifying transcription factor (TF) (eg., CEBPa) and key late differentiation TF (CEBPe), was examined in normal, myelodysplastic (MDS) and AML primary cells and cell lines. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL9183
208 Samples

Download data: TXT

Series

Accession:: GSE29047

ID:: 200029047

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001751211.

Detection of aberrant DNA methylation in colorectal carcinoma samples compared to normal human colon

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in colorectal carcinoma we analyzed the methylation status of 23,000 CpG islands of the human genome in ten coleorectal carcinoma samples as well as normal colon using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array

Platform:: GPL8544
10 Samples

Download data: TXT

Series

Accession:: GSE17512

ID:: 200017512

Select item 20001751012.

Detection of aberrant DNA methylation in acute leukemia samples compared to normal human monocytes

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in eight acute leukemia samples as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array; Genome variation profiling by genome tiling array

Platform:: GPL8544
8 Samples

Download data: TXT

Series

Accession:: GSE17510

ID:: 200017510

Select item 20001745513.

Detection of aberrant DNA methylation in AML cell lines compared to normal human monocytes

(Submitter supplied) To globally define methylation-’prone’ and -’protected’ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in two acute leukemia cell lines as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL8544
6 Samples

Download data: TXT

Series

Accession:: GSE17455

ID:: 200017455

Select item 20001607814.

Detection of transcription factor NRF1, YY1 and SP1 bound regions in human peripheral blood monocytes

(Submitter supplied) To study the correlation between sequence motif appearance, transcription factor binding and aberrant hypermethylation in the cell lines, we performed ChIP-on-chip analyses (on CpG island microarrays) for the transcription factors Sp1, NRF1 and YY1 in normal peripheral blood monocytes. Keywords: ChIP-on-Chip; comparative genomic hybridization

Organism:: Homo sapiens

Type:: Genome variation profiling by genome tiling array

Platform:: GPL8544
6 Samples

Download data: TXT

Series

Accession:: GSE16078

ID:: 200016078

Select item 20001607615.

Transcriptome analysis of myelid cell types (normal and leukemic)

(Submitter supplied) Transcriptome analysis of freshly sorted human CD34+ hematopoietic progenitor cells, human CD14+ peripheral blood monocytes and the human cell line U937 Keywords: one-color based gene expression

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6480
6 Samples

Download data: TXT

Series

Accession:: GSE16076

ID:: 200016076

Select item 20006262916.

Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases

(Submitter supplied) The most common congenital heart disease (CHD) is the ventricular septal defect (VSD), which is also a subfeature of Tetralogy of Fallot (TOF) representing the most common form of cyanotic CHD. The underlying causes for the majority of CHDs are still unclear and most probably consist of combinations of genetic, epigenetic and environmental factors. DNA methylation is the most widely studied epigenetic modification and several cardiac regulators have already been shown to be differentially methylated in CHD patients. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL11154
23 Samples

Download data: TXT

Series

Accession:: GSE62629

ID:: 200062629

PubMed Similar studies SRA Run Selector

Select item 20003676117.

mRNA expression profiling in patients with Tetralogy of Fallot and healthy unaffected individuals

(Submitter supplied) Right ventricular mRNA profiles from 22 patients with Tetralogy of Fallot (TOF) and mRNA-seq profiles from the left and right ventricle (LV and RV, respectively) of 4 healthy unaffected individuals (NH) were generated. The total RNA was isolated from the 30 human heart samples using TRIzol. mRNAs were isolated from total RNA and prepared for sequencing using Illumina Kit RS-100-0801 according to the manufacturer's protocol (Preparing Samples for Sequencing of mRNA Sept 2008). more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9052
30 Samples

Download data: TXT

Series

Accession:: GSE36761

ID:: 200036761

Select item 20020328918.

LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic 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; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL21697
25 Samples

Download data: BW, TXT

Series

Accession:: GSE203289

ID:: 200203289

PubMed Full text in PMC Similar studies

Select item 20020328819.

LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [small RNA-seq]

(Submitter supplied) LINE1s are abundant retroelements comprising 17% of human genome. Naturally, genomic LINE1s are tightly repressed by epigenetic mechanism; however, if relieved, they can be detrimental to genome stability by their transposition capability. So, a supervising mechanism that quickly re-represses the leaky LINE1s is demanded. Here we show that de-repressed LINE1s generate small RNAs, L1-siRNAs, which SETDB1 and AGO2 recognize, then move into searching for a transcript with sequence complementarity, and ultimately re-install a repression mechanism at LINE1 5’-untranslated region (5’UTR) by depositing trimethyl-H3K9 (H3K9me3). more...