Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v2]

ABSTRACT: Genome-wide profiling of histone 3 lysine 4 trimethylation is used for identification of microRNA transcriptional start sites. Various cell types allow a broad range detection of putative promoters rather independent of tissue specific expression patterns. These data are used for identification of aberrant epigenetic regulation at the respective regions. 5 samples total: 1 primary CLL sample, 1 CLL related cell line -/+ 5-aza-2M-bM-^@M-^Y-deoxycytidine (DAC) treatment (Granta-519), myeloid cell line Kasumi-1 (-/+ 5-aza-2M-bM-^@M-^Y-deoxycytidine treatment); H3K4me3 enriched vs. Input

ORGANISM(S): Homo sapiens

SUBMITTER: Constance Baer

PROVIDER: E-GEOD-33304 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v3b]

Project description:Genome-wide profiling of histone 3 lysine 4 trimethylation is used for identification of microRNA transcriptional start sites. Various cell types allow a broad range detection of putative promoters rather independent of tissue specific expression patterns. These data are used for identification of aberrant epigenetic regulation at the respective regions. 11 samples total: 3 primary B-cell samples (1 chronic lymphocytic leukemia [CLL] and 2 healthy controls), 2 CLL related cell lines -/+ 5-aza-2M-bM-^@M-^Y-deoxycytidine (DAC) treatment (Mec-1, EHEB), T-lymphoid cell line JURKAT, myeloid cell line HL-60, colon cancer cell line HCT-116 wild type and double knock out; H3K4me3 enriched vs. input

2012-05-30 | E-GEOD-33305 | biostudies-arrayexpress

Epigenetic regulation of miRNA in CLL

Project description:This SuperSeries is composed of the following subset Series: GSE33304: Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v2] GSE33305: Epigenetic regulation of miRNA in CLL [ChIP_hsa_miRNA_v3b] GSE33623: Epigenetic regulation of miRNA in CLL [MCIp_hsa_miRNA_v3b] Refer to individual Series

2012-05-30 | E-GEOD-33347 | biostudies-arrayexpress

Genome-wide identification and DNA methylation of human full-length LINE-1 (L1) retrotransposons in HCT116 cells treated with 5-aza-2’-deoxycytidine.

Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1). The approach is focused on the youngest family (L1HS), but it also catches a significant fraction of L1PA2 to L1PA8 elements. This was performed in HCT116 cells treated by the DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza) or in mock-treated cells (DMSO).

2023-09-22 | E-MTAB-12240 | biostudies-arrayexpress

Expression data from paediatric ependymoma short-term cell cultures

Project description:Promoter hypermethylation and transcriptional silencing is a common epigenetic mechanism of tumour suppressor inactivation in cancer, including malignant brain tumours. To identify targets of epigenetic silencing mediated by CpG island methylation in paediatric ependymoma, we used a pharmacological unmasking approach through treatment with the demethylating agent 5-Aza-2M-bM-^@M-^Y-deoxycytidine followed by global expression microarray analysis. Three short-term ependymoma cell cultures were used for whole genome expression analysis following treatment with the demethylating agent 5-Aza-dC (5 M-BM-5mol/L) or mock-treated with DMSO (M-bM-^IM-$0.1% v/v) for 96-hrs.

2013-12-02 | E-GEOD-45437 | biostudies-arrayexpress

RNA-seq of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine

Project description:We performed poly(A)+ stranded RNA-seq of a panel of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine. In parallel, we determined the genomic location and DNA methylation levels of human full-length LINE-1 elements (L1) from the same samples using bs-ATLAS-seq (E-MTAB-12240). To link DNA methylation and L1 expression, we used cell pellets from the same cell culture to perform both RNA-seq and bs-ATLAS-seq.

2023-09-21 | E-MTAB-12245 | biostudies-arrayexpress

Transcription profiling of human neuroblastoma cells lines following DAC and ATRA treatment

Project description:Following treatment with the de-methylating agent 5-aza-deoxycytidine (DAC), the gene expression profiles of neuroblastoma cell lines Kelly, SK-N-AS and NGP were analysed in order to examine the relationship between transcriptional re-activation and promoter region DNA methylation.<br>In addition, the neuroblastoma cell line SK-N-BE was treated with all-trans-retinoic acid (ATRA) in order to examine the impact this differentiation agent has on DNA methylation status.

2010-11-03 | E-MEXP-2557 | biostudies-arrayexpress

Analysis of DNA methylation profiles in colorectal cancer cells treated with boswellic acids

Project description:Genome wide DNA methylation profiling of colorectal cancer cell lines treated with acetyl-11-keto-β-boswellic acid (AKBA) or 5-aza-2’-deoxycytidine (DAC). The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in the colorectal cancer cell line SW48. Samples included non-treated, AKBA-treated, and DAC-treated SW48 cells. Bisulphite converted DNA from the 3 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2012-12-01 | E-GEOD-32275 | biostudies-arrayexpress

mRNA profile of 5-aza-CR and 5-aza-CdR treated celllines

Project description:5-azacytidine and 5-aza-2'-deoxycytidine are both demethylating agents but they have shown different clinical efficiency. Since 5-azacytidine is incorporated into RNA it might have a different impact on the expression profile than 5-aza-2'-deoxycytidine. This study is designed to investigate the immediate action of the DNMTi on day 2 and the late heritable effects on day 8 after start of treatment.

2014-06-13 | E-MTAB-280 | biostudies-arrayexpress

MCF7 cells gene expression change by inducing CpG demethylation using 5-Aza-2'-deoxycytidine (Aza)

Project description:Promoter methylation is able to induce downregulation of gene expression. 5-Aza-2'-deoxycytidine(Aza), methytransferase inhibitor, induce CpG demethylation. Here, 5-Aza-2'-deoxycytidine(Aza) is treated in a human breast cancer cell, MCF7, for detection of gene expression change.

2011-08-18 | GSE31441 | GEO

Transcription profiling of three human multiple myeloma cell lines treated with 5-aza-2-deoxycytidine and/or trichostatin A

Project description:To identify epigenetically silenced genes in multiple myeloma (MM) cell lines and to determine the effects of 5-aza-2-deoxycytidine and trichostatin A on gene expression. We treated 3 multiple myeloma cell lines (MM1, NCI-H929, U266) with 5-aza-2-deoxycytidine and/or trichostatin A.

2008-02-01 | E-MEXP-1269 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data