Similar studies for GEO DataSets (Select 200042119) - GEO DataSets

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Items: 20

Select item 2000421191.

DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding

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

Organism:: Mus musculus; Homo sapiens

Type:: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by genome tiling array

4 related Platforms
61 Samples

Download data: TXT

Series

Accession:: GSE42119

ID:: 200042119

Select item 2000421182.

DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding (Illumina Methylation)

(Submitter supplied) The origin of aberrant DNA methylation in cancer remains largely unknown. In this study, we elucidated the DNA methylome in primary Acute Promyelocytic Leukemia (APL) and the role of PML-RARa in establishing these patterns. APL patients showed increased genome-wide DNA methylation with higher variability than healthy CD34+ cells, promyelocytes and remission bone marrow. A core set of differentially methylated regions in APL was identified. more...

Organism:: Homo sapiens

Type:: Methylation profiling by genome tiling array

Platform:: GPL13534
10 Samples

Download data: TSV

Series

Accession:: GSE42118

ID:: 200042118

Select item 2000420443.

DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding (sequencing)

Organism:: Homo sapiens; Mus musculus

Type:: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL15456 GPL11154 GPL16173
51 Samples

Download data: TXT

Series

Accession:: GSE42044

ID:: 200042044

PubMed Similar studies SRA Run Selector

Select item 2001267204.

Genome-wide studies identify genes directly regulated by PML/RARα fusion protein

(Submitter supplied) Acute promyelocytic leukemia (APL) is characterized by a specific t(15;17) chromosome translocation that generates the promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion gene. However, the global association between PML/RARα and transcriptional co-regulators, and the rules of their association in governing the key processes during the leukemogenesis remain obscure. Here, we performed the genome-wide binding profiling of PML/RARα, HDAC1 and P300, in NB4, an APL patient-derived cell line. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL16791 GPL11154
10 Samples

Download data: TXT, XLS

Series

Accession:: GSE126720

ID:: 200126720

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2000188865.

PML-RARa/RXR alters the epigenetic landscape in Acute Promyelocytic Leukemia

(Submitter supplied) Many different molecular mechanisms have been suggested to be associated with PML-RAR dependent transformation of haematopoietic progenitors. Here, we investigated the role of PML-RAR and RXR in the organization of epigenetic structures at a genome-wide level. We identified 2722 high confidence PML-RAR binding sites in the leukemic model cell line NB4 and found PML-RAR colocalization with RXR to the vast majority of these binding regions. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9052
40 Samples

Download data: BED, TXT, WIG

Series

Accession:: GSE18886

ID:: 200018886

PubMed Similar studies SRA Run Selector

Select item 2001518376.

PML-RARa induces dynamic changes in genome architecture during leukemic transformation

(Submitter supplied) Acute Promyelocytic Leukemia (APL) is a fatal subtype of leukemia driven by the translocation between genes encoding the Promyelocytic Leukemia (PML) protein and the Retinoic Acid Receptor alpha (RARa) protein. We use mouse hematopoietic progenitor cells expressing PML-RARa and dissect the dynamic changes in the epigenome, transcriptome and genome architecture triggered by the expression of this oncogenic transcription factor during leukemic transformation. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL13112
51 Samples

Download data: BED, BEDGRAPH, TSV

Series

Accession:: GSE151837

ID:: 200151837

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000956377.

Expression data from NB4 control shRNA cells and NB4 TRIB3 shRNA cells

(Submitter supplied) To identify the top 20 up-regulated genes in NB4 TRIB3 shRNA cells in comparison with NB4 control shRNA cells, we examined the microarray gene expression profile of these groups above. Despite the fact that combined therapy of all-trans retinoic acid (ATRA) with arsenic trioxide (ATO) or chemotherapy dramatically improves the prognosis of patients with acute promyelocytic leukemia (APL), these regimens can cause systemic infections and secondary leukemias. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL18943
6 Samples

Download data: PAIR

Series

Accession:: GSE95637

ID:: 200095637

Select item 2000900628.

Expression data from healthy donors and AML patients

(Submitter supplied) To identify the top 20 up-regulated genes in CD34+ cells from AML patients in comparison with healthy donors, we examined the microarray gene expression profile of CD34+ blasts from patients with newly diagnosed AML vs CD34+ normal cells from healthy donors. Despite the fact that combined therapy of all-trans retinoic acid (ATRA) with arsenic trioxide (ATO) or chemotherapy dramatically improves the prognosis of patients with APL, these regimens can cause systemic infections and secondary leukemias. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL15207
6 Samples

Download data: CEL

Series

Accession:: GSE90062

ID:: 200090062

Select item 2000594319.

Effect of PML/RARA on the transcriptome of preleukemic early promyelocytes vs PML/RARA-Flt3ITD leukemic promyelocytes

(Submitter supplied) Transcriptional profiling of murine cells expressing PML/RARA at the early promyelocyte stage (4 weeks old, preleukemic) and in full blown PML/RARA leukemia generated by transducing PML/RARA bone marrow with a Flt3-ITD retroviral vector

Organism:: Mus musculus

Type:: Expression profiling by array

Platforms:: GPL18090 GPL7202
8 Samples

Download data: TXT

Series

Accession:: GSE59431

ID:: 200059431

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005447410.

Effect of PML/RARa on the transcriptome of maturing myeloid populations in vivo

(Submitter supplied) Transcriptional profiling of murine cells at the GMP, Early promyelocyte (Early Pros) and Late promyelocyte (Late Pros) stages, isolated from Wt or MRP8-PML/RARa transgenics after 2 rounds of sorting.

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL18090
20 Samples

Download data: TXT

Series

Accession:: GSE54474

ID:: 200054474

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20005403811.

The ability of PML/RARα to initiate leukemia is associated with markedly increased proliferation of promyelocytes despite minor changes in the transcriptome and epigenome.

(Submitter supplied) Acute Promyelocytic Leukemia is characterized by the accumulation in the blood and bone marrow of promyelocytes. The PML/RARα fusion protein is identified as the primary abnormality implicated in the pathology, and is believed to prevent transcription of genes necessary for normal myeloid development and differentiation. Identifying its targets is critical to comprehend the road to pathogenesis. To understand how PML/RARα, in the absence of secondary lesions, alters gene expression, DNA methylation and proliferation we used a novel experimental and sorting strategy to study normal versus preleukemic promyelocytes in vivo. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL13112
20 Samples

Download data: TXT

Series

Accession:: GSE54038

ID:: 200054038

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20001847612.

Gene Expression Data from U937T:PLZF-RARa Inducible Cells

(Submitter supplied) The PLZF-RARa fusion oncoprotein is overexpressed in the t(11;17) subtype of acute promyelocytic leukemia. Gene expression microarrays were used to identify genes involved in leukemic transformation. We used microarray to detect gene expression changes induced by the PLZF-RARa fusion oncoprotein in the U937 cell line

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL570
6 Samples

Download data: CEL

Series

Accession:: GSE18476

ID:: 200018476

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001920313.

PML-RARa binding sites and their correlation with the gene expression in ATRA treated NB4 cells

(Submitter supplied) PML-RARa contributes to the development of APL through repression of genes important in myeloid development. Through a global approach, we have identified 2,979 high quality PML-RARa binding sites in ZnSO4 induced PR9 cells. By integration the gene expression data, we found that PML/RARa target genes are transcriptionally suppressed in primary APL cells and re-activated in ATRA treated NB4 cells. This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:: GPL570 GPL5082
7 Samples

Download data: BAR, BED, CEL, TXT

Series

Accession:: GSE19203

ID:: 200019203

Select item 20001920214.

Genome-wide recognition of PML/RARa binding sites

(Submitter supplied) PML/RARa is of crucial importance in acute promyelocytic leukemia (APL) both pathologically and therapeutically. Using a genome-wide approach, we identified in vivo PML/RARa binding sites in ZnSO4 treated PR9 cells. A total of 2,979 high quality binding sites were identified, representing 1,981 unique RefSeq genes. The supplementary bed file contains all 2,979 high quality PML-RARa binding sites reported in the paper.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by genome tiling array

Platform:: GPL5082
1 Sample

Download data: BAR, BED, CEL, TXT

Series

Accession:: GSE19202

ID:: 200019202

PubMed Similar studies

Select item 20001920115.

Expression profiling of ATRA treated NB4 cells

(Submitter supplied) NB4 is an APL derived cell line, carrying the t(15;17) translocation and expressing the PML/RARa fusion protein. Still, an important question that remains to be addressed is whether PML/RARa target genes are transcriptionally suppressed in primary APL cells and re-activated in all-trans retinoic acid (ATRA) treated NB4 cells. Gene expression of NB4 cells treated with ATRA at different time points were analyzed.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL570
6 Samples

Download data: CEL

Series

Accession:: GSE19201

ID:: 200019201

Select item 20017424716.

Transcriptomic analysis (RNA-seq) of Lin- BM cells from wild type C57 BM mice and GFP+ BM cells from TBLR1-RARa mice

(Submitter supplied) Purpose: The goal of this study is to decipher the molecular basis of TBLR1-RARa-expressing APL and to explore potential treatment target based on NGS-derived transcriptome profiling (RNA-seq) Methods: RNA-seq was performed to analyze differential gene expression between GFP+ cells from BM of TBLR1-RARa mice (TR1 and TR9) and lin- cells from BM of control mice (Control). Results: Transcriptome profiling associates with leukemic phenotype and predicts HDACi response in TR-induced APL. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
3 Samples

Download data: TXT

Series

Accession:: GSE174247

ID:: 200174247

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20004934417.

The induced APL cells generated by the transplantation of PML-RARA-transduced human CD34+ hematopoietic cells into immunodeficient mice

(Submitter supplied) A humanized in vivo APL model has been established utilizing the retroviral transduction of PML-RARA into human CD34+ hematopoietic cells and the transplantation of these cells into immunodeficient mice. The resultant leukemia recapitulated human APL phenotypically, and was clustered in the same category as human APL samples in the gene expression analysis.

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL570
5 Samples

Download data: CEL

Series

Accession:: GSE49344

ID:: 200049344

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004254318.

Loss of imprinting at the CTCF binding sites in the DLK1-DIO3 domain reactivates microRNA expression in acute promyelocytic leukaemia

(Submitter supplied) We report the DNA-methylation profiling of 10 regions selected from the DLK1-DIO3 domain on chromosome 14q32 in BM/PB samples from patients with acute promyelocytic leukaemia (APL), other subclasses of acute myeloid leukaemia and healthy donors, using high-throughput amplicon bisulfite sequencing with Roche 454 technology. We identify monoallelic-hypermethylation in APL only at the differentially methylated region (DMR) located upstream from the MEG3 gene (MEG3-DMR), whereas no changes in the DNA methylation profile were detected at the imprinting control region of the domain (IG-DMR) among the samples analysed. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL14603
47 Samples

Download data: TXT, WIG

Series

Accession:: GSE42543

ID:: 200042543

PubMed Similar studies SRA Run Selector

Select item 20014219819.

Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid Leukemia (RNA-seq)

(Submitter supplied) Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML/RARα, a major etiological agent in APL. Although PML/RARα is critical, the molecular mechanisms remains largely unknown. Here, using an inducible system, we comprehensively analyzed the 3D genome organization in myloid cells and its reorganizationn after PML/RARα induction, and performed additional analysis in patient-derived APL cells with native PML/RARα. more...