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Series GSE171025 Query DataSets for GSE171025
Status Public on Apr 13, 2022
Title SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [KG1a DAC scTEM-seq]
Organisms Homo sapiens; blank sample
Experiment type Methylation profiling by high throughput sequencing
Summary 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.
 
Overall design scTEM-seq (single-cell transposable element methylation sequencing)
 
Contributor(s) Hunt KV, Burnard SM, Roper EA, Bond DR, Dun M, Verrills N, Enjeti AK, Lee HJ
Citation(s) 35388081
Submission date Mar 29, 2021
Last update date Apr 14, 2022
Contact name Heather Lee
E-mail(s) Heather.lee@newcastle.edu.au
Organization name The University of Newcastle
Street address University Drive, Callaghan
City Newcastle
State/province NSW
ZIP/Postal code 2308
Country Australia
 
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL27039 Illumina MiSeq (blank sample)
Samples (96)
GSM5216545 KG1a_Alu_pool_cell_1 [i501_A1_i701_KG1a_Alu]
GSM5216546 KG1a_Alu_pool_cell_2 [i501_A2_i702_KG1a_Alu]
GSM5216547 KG1a_Alu_pool_cell_3 [i501_A3_i703_KG1a_Alu]
This SubSeries is part of SuperSeries:
GSE171029 SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells
Relations
BioProject PRJNA718185
SRA SRP312549

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE171025_RAW.tar 7.5 Mb (http)(custom) TAR (of COV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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