Similar studies for GEO DataSets (Select 200116229) - GEO DataSets

Select item 2001162291.

DNA Methylation Potential Energy Landscape Analysis of Pediatric Pre-B cell Acute Lymphoblastic Leukemia (ALL) and Normal B cells and precursors

(Submitter supplied) Acute lymphoblastic leukemia (ALL) is the most common cancer in children. We applied WGBS and the informME analysis pipeline to investigate the role of DNA methylation stochasticity in pre-B cell ALL.

Organism:: Homo sapiens

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

Platform:: GPL20301
53 Samples

Download data: BW, XLSX

Series

Accession:: GSE116229

ID:: 200116229

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001136642.

Analysis of gene expression in colorectal cancer RKO cells with UHRF1 depletion and HDAC inhibition

(Submitter supplied) UHRF1 is a major regulator of epigenetic mechanism and is overexpressed in various human malignancies. In this study, we examined the involvement of UHRF1 in aberrant DNA methylation in colorectal cancer (CRC). In CRC cells, transient UHRF1 knockdown rapidly induced DNA demethylation across entire genomic regions, including CpG islands, gene bodies and repetitive elements. Nonetheless, UHRF1 depletion only minimally reversed CpG island hypermethylation-associated gene silencing. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL16699
9 Samples

Download data: TXT

Series

Accession:: GSE113664

ID:: 200113664

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001064393.

UHRF1 depletion and HDAC inhibition synergistically reactivate epigenetically silenced genes in colorectal cancer cells

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

Organism:: Homo sapiens

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

Platforms:: GPL13534 GPL16699
23 Samples

Download data: TXT

Series

Accession:: GSE106439

ID:: 200106439

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001064384.

Analysis of DNA methylation in colorectal cancer RKO cells with UHRF1 depletion and HDAC inhibition

(Submitter supplied) UHRF1 is a major regulator of epigenetic mechanism and is overexpressed in various human malignancies. In this study, we examined the involvement of UHRF1 in aberrant DNA methylation in colorectal cancer (CRC). In CRC cells, transient UHRF1 knockdown rapidly induced DNA demethylation across entire genomic regions, including CpG islands, gene bodies and repetitive elements. Nonetheless, UHRF1 depletion only minimally reversed CpG island hypermethylation-associated gene silencing. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
3 Samples

Download data: IDAT, TXT

Series

Accession:: GSE106438

ID:: 200106438

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001064375.

Analysis of DNA methylation in colorectal cancer DLD1 cells with UHRF1 depletion and HDAC inhibition

(Submitter supplied) UHRF1 is a major regulator of epigenetic mechanism and is overexpressed in various human malignancies. In this study, we examined the involvement of UHRF1 in aberrant DNA methylation in colorectal cancer (CRC). In CRC cells, transient UHRF1 knockdown rapidly induced DNA demethylation across entire genomic regions, including CpG islands, gene bodies and repetitive elements. Nonetheless, UHRF1 depletion only minimally reversed CpG island hypermethylation-associated gene silencing. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
3 Samples

Download data: IDAT, TXT

Series

Accession:: GSE106437

ID:: 200106437

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001064026.

Analysis of gene expression in colorectal cancer DLD1 cells with UHRF1 depletion and HDAC inhibition

(Submitter supplied) UHRF1 is a major regulator of epigenetic mechanism and is overexpressed in various human malignancies. In this study, we examined the involvement of UHRF1 in aberrant DNA methylation in colorectal cancer (CRC). In CRC cells, transient UHRF1 knockdown rapidly induced DNA demethylation across entire genomic regions, including CpG islands, gene bodies and repetitive elements. Nonetheless, UHRF1 depletion only minimally reversed CpG island hypermethylation-associated gene silencing. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL16699
8 Samples

Download data: TXT

Series

Accession:: GSE106402

ID:: 200106402

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000692297.

Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia

(Submitter supplied) We analyzed 52 Diagnostic samples from childhood Acute lymphoblastic leukemia samples

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
52 Samples

Download data: CSV

Series

Accession:: GSE69229

ID:: 200069229

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000576338.

Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigatoing molecular mechanisms of drug resistance

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

Organism:: Homo sapiens

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

Platforms:: GPL8490 GPL6884
38 Samples

Download data

Series

Accession:: GSE57633

ID:: 200057633

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000575819.

Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigatoing molecular mechanisms of drug resistance (methylation)

(Submitter supplied) Background: Patient-derived tumour xenografts are an attractive model for preclinical testing of anti-cancer drugs. Insights into tumour biology and biomarkers predictive of responses to chemotherapeutic drugs can also be gained from investigating xenograft models. As a first step towards examining the equivalence of epigenetic profiles between xenografts and primary tumours in paediatric leukaemia, we performed genome-scale DNA methylation and gene expression profiling on a panel of 10 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) tumours that were stratified by prednisolone response. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL8490
20 Samples

Download data: TXT

Series

Accession:: GSE57581

ID:: 200057581

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005749110.

Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigatoing molecular mechanisms of drug resistance (expression)

(Submitter supplied) Background: Patient-derived tumour xenografts are an attractive model for preclinical testing of anti-cancer drugs. Insights into tumour biology and biomarkers predictive of responses to chemotherapeutic drugs can also be gained from investigating xenograft models. As a first step towards examining the equivalence of epigenetic profiles between xenografts and primary tumours in paediatric leukaemia, we performed genome-scale DNA methylation and gene expression profiling on a panel of 10 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) tumours that were stratified by prednisolone response. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6884
18 Samples

Download data: TXT

Series

Accession:: GSE57491

ID:: 200057491

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004486211.

Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype

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

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL6604
380 Samples

Download data: PAIR

Series

Accession:: GSE44862

ID:: 200044862

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004486012.

Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype [194 samples]

(Submitter supplied) Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL6604
194 Samples

Download data: PAIR

Series

Accession:: GSE44860

ID:: 200044860

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20003829513.

Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype [186 samples]

(Submitter supplied) Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL6604
186 Samples

Download data: PAIR

Series

Accession:: GSE38295

ID:: 200038295

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002628114.

Integrated Genetic and Epigenetic Analysis of Childhood Acute Lymphoblastic Leukemia Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype

(Submitter supplied) Acute lymphoblastic leukemia (ALL), the commonest childhood malignancy, is characterized by recurring gross and submicroscopic structural genetic alterations that contribute to leukemogenesis. Disordered epigenetic regulation is a hallmark of many tumors, and while analysis of DNA methylation of limited numbers of genes or ALL samples suggests epigenetic alterations may also be important, a large-scale integrative genome-wide analysis evaluating DNA methylation in ALL has not been performed. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL96
154 Samples

Download data: CEL

Series

Accession:: GSE26281

ID:: 200026281

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20003823515.

Integration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia

(Submitter supplied) B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic origin of the disease remains unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. We assessed the DNA methylation status of 402,842 CpG-sites across the genome (Illumina 450k array) in tumor and remission samples of 46 pre-B ALL patients, thus generating the most comprehensive single CpG-site resolution pre-B ALL methylomes so far. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
92 Samples

Download data: TXT

Series

Accession:: GSE38235

ID:: 200038235

Select item 20011897216.

Defining UHRF1 Domains That Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties

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

Organism:: Homo sapiens

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

Platforms:: GPL21145 GPL10332
50 Samples

Download data: IDAT, TXT

Series

Accession:: GSE118972

ID:: 200118972

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20011897117.

Defining UHRF1 Domains That Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties [expression]

(Submitter supplied) UHRF1 is essential for targeting DNA methyltransferases (DNMT’s) to replicating DNA to establish de novo DNA methylation and maintain it. While, UHRF1 domains are defined, including requirement for an E3 ligase region, for de novo methylation, those essential for maintenance have been difficult to outline. Herein, via a new assay, chromatin histone-binding and a hemimethylated DNA reader domains, but not the ligase domain are found essential for cancer-specific DNA methylation maintenance in human colorectal cancer (CRC) cells. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10332
20 Samples

Download data: TXT

Series

Accession:: GSE118971

ID:: 200118971

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20011897018.

Defining UHRF1 Domains That Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties [methylation]

(Submitter supplied) UHRF1 is essential for targeting DNA methyltransferases (DNMT’s) to replicating DNA to establish de novo DNA methylation and maintain it. While, UHRF1 domains are defined, including requirement for an E3 ligase region, for de novo methylation, those essential for maintenance have been difficult to outline. Herein, via a new assay, chromatin histone-binding and a hemimethylated DNA reader domains, but not the ligase domain are found essential for cancer-specific DNA methylation maintenance in human colorectal cancer (CRC) cells. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL21145
30 Samples

Download data: IDAT, TXT

Series

Accession:: GSE118970

ID:: 200118970

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20014808619.

DNA methylation analysis of HCT116 after disruption of methyllysine reading and writing.

(Submitter supplied) The chromatin-binding E3 ubiquitin ligase Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) maintains DNA methylation patterning in cancer cells through multivalent histone and DNA recognition. The tandem Tudor domain (TTD) of UHRF1 is well-characterized as a reader of lysine 9 di- and tri-methylation on histone H3 (H3K9me2/me3) and, more recently, lysine 126 di- and tri- methylation on DNA ligase 1 (LIG1K126me2/me3). more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platforms:: GPL23976 GPL21145
10 Samples

Download data: IDAT

Series

Accession:: GSE148086

ID:: 200148086

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20014751820.

DNA methylation analysis of HCT116 after knockdown of LIG1, UHRF1, or luciferase (control)

(Submitter supplied) In HCT116 colorectal cancer cells, UHRF1, LIG1, or luciferase was knocked down by shRNA followed by selection with puromycin for 2 days. DNA was analyzed 12 days after viral transduction.

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL21145
3 Samples

Download data: IDAT

Series

Accession:: GSE147518

ID:: 200147518

PubMed Full text in PMC Similar studies Analyze with GEO2R

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