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Series GSE261788 Query DataSets for GSE261788
Status Public on Mar 21, 2024
Title AMAR-seq: automated multimodal sequencing of DNA methylation, chromatin accessibility, and RNA expression with single-cell resolution
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Parallel single-cell multimodal sequencing is the most intuitive and precise tool for cellular status research. In this study, we propose AMAR-seq to automate methylation, chromatin accessibility and RNA sequencing on a chip with single-cell precision. We validated the accuracy and robustness of AMAR-seq in comparison with standard single-omics methods. The high gene detection rate and genome coverage of AMAR-seq enabled us to establish a genome-wide gene expression regulatory atlas, implement single-cell copy number variation analysis, and construct a single-gene, single-base resolution gene expression, DNA methylation, and chromatin accessibility landscape. Applying AMAR-seq to investigate the process of mouse embryonic stem cell differentiation, we revealed the dynamic coupling of the epigenome and transcriptome which may contribute to the unravelling of the molecular mechanisms of early embryonic development. Collectively, these results illustrate that the employment of AMAR-seq can deeply and accurately establish single-cell multi-omics regulatory networks in a single-cell context in a cost-efficient and automated manner, which paves the way for incisive dissection of complex life procedures.
Overall design In total, 19 K562 cell line samples and 24 mESC samples were analyzed. We examined genome-wide DNA methylation, gene expression and chromatin accessibility profiles of 12 K562 single cells, two bulk K562 samples and 24 mESC single cells. We analysed DNA methylome of 3 K562 single cells by scBS-seq and transcriptome of 4 K562 single cells with smart-seq2 workflow, respectively. Mouse embryonic stem cells were grown on 6-cm culture dishes with MEF feeder cells and cultured in a complete medium supplemented with leukemia inhibitory factor (LIF) to prevent differentiation. To induce undirectional differentiation, mESCs were dissociated and replated onto 0.1% gelatin-coated dishes, and cultured without LIF in a feeder-free manner. We collected mESCs at day 0 and differentiated cells at day 3, day 6 day 9.
For library construction methods:
NOMe-seq (
scNOMe-seq (
Contributor(s) Zeng X, Yang X, Zhong Z, Zhu Z, Li J, Song J, Yang C
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Submission date Mar 18, 2024
Last update date Mar 21, 2024
Contact name Xi Zeng
Organization name Xiamen University
Street address No. 422, Siming South Road
City Xiamen
ZIP/Postal code 361005
Country China
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (83)
GSM8151951 AMAR_nucleus_1
GSM8151952 AMAR_nucleus_2
GSM8151953 AMAR_nucleus_3
BioProject PRJNA1089071

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

Supplementary file Size Download File type/resource
GSE261788_RAW.tar 6.3 Gb (http)(custom) TAR (of COV, TXT)
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Raw data are available in SRA

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