Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [AML01 scTEM-seq]

ABSTRACT: SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [AML01 scTEM-seq]

PROVIDER: PRJNA718184 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14091400_1.fastq.gz	Fastqsanger.gz
	SRR14091400_2.fastq.gz	Fastqsanger.gz
	SRR14091401_1.fastq.gz	Fastqsanger.gz
	SRR14091401_2.fastq.gz	Fastqsanger.gz
	SRR14091402_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 192

Similar Datasets

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells

Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells

| PRJNA718180 | ENA

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [PBAT]

Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [PBAT]

| PRJNA718186 | ENA

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [RNA-seq]

Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [RNA-seq]

| PRJNA718187 | ENA

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [KG1a DAC scTEM-seq]

Project description:SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [KG1a DAC scTEM-seq]

| PRJNA718185 | ENA

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [PBAT]

Project description:Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. By targeting high-copy LINE-1 and SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of annotated loci covered in each scTEM-seq library. Parallel transcriptome analysis of the same single cell is also performed to link global DNA methylation heterogeneity with transcriptional consequences. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary cells from an AML patient. Treatment of KG1a cells with the hypomethylating agent, decitabine, induces global DNA methylation heterogeneity associated with altered expression of viral response pathways. We also compare global levels of DNA methylation to expression of transposable elements and find a predominance of negative correlations in both the KG1a and patient cells. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated KG1a cells. These observations suggest that viral mimicry processes important for epigenetic therapy and tumour immunogenicity are variably active in AML cells. By linking global DNA methylation heterogeneity with transcriptional consequences, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.

2022-04-13 | GSE171028 | GEO

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [RNA-seq]

2022-04-13 | GSE171027 | GEO

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [AML01 scTEM-seq]

2022-04-13 | GSE171026 | GEO

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [KG1a DAC scTEM-seq]

2022-04-13 | GSE171025 | GEO

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-04-13 | GSE171029 | GEO

Prediction of outcomes and response to treatments with an ultrasensitive method for assessing intratumor epigenetic heterogeneity in colorectal cancer

Project description:Primary outcome(s): The detection rates of epigenetic heterogeneity in primary tumor and plasma from colorectal cancer patients with Methylation-sensitive high resolution melt(MS-HRM).

| 2636460 | ecrin-mdr-crc

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