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2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [RNA-seq]

ABSTRACT: 2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [RNA-seq]

PROVIDER: PRJNA775064 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16596943_1.fastq.gz	Fastqsanger.gz
	SRR16596943_2.fastq.gz	Fastqsanger.gz
	SRR16596944_1.fastq.gz	Fastqsanger.gz
	SRR16596944_2.fastq.gz	Fastqsanger.gz

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2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [single-cell 2cChIP-seq]

Project description:We developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10–1,000 cells. Moreover, 2cChIP-seq reliably captured genomic regions with histone modification at single-cell level. Lastly, we characterized the methylome of differentiated female germline stem cells (FGSCs) with this approach. Through comparing the DNA methylation patterns of the undifferentiated and differentiated FGSCs, we observed a particular DNA methylation signature potentially involved in differentiation of mouse germline stem cells. Hence, we provided a reliable and robust epigenomic profiling approach for small cell numbers and single cells.

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2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [single-cell 2cChIP-seq]

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2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [2cMeDIP-seq]

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2cChIP-seq: an efficient and reliable method for epigenomic profiling of small cell numbers and single cells [RNA-seq]

Project description:We developed a new technique by supplementing carrier materials during ChIP procedures (thereafter referred to as 2cChIP-seq), dramatically improving immunoprecipitation efficiency and reducing sample loss. Using 2cChIP-seq, we generated high-quality epigenomic profiles of histone modifications and DNA methylation in 10-1,000 cells. Moreover, 2cChIP-seq reliably captures genomic regions with histone modification at single-cell level. We characterized the methylome of differenting female germline stem cells (FGSCs) with this this approach. Through comparing the methylome patterns of undifferentiated and differentiating FGSCs, we observed a particular DNA methylation signature potentially involved in differentiation of mouse germline stem cells. Hence, we provide a robust and universal approach for epigenomic profiling starting with extremely lower input.

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

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2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells.

Project description:Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) can profile genome-wide epigenetic marks associated with regulatory genomic elements. However, conventional ChIP-seq is challenging when examining limited numbers of cells. Here, we developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during conventional ChIP procedures (hereafter referred to as 2cChIP-seq), thus dramatically improving immunoprecipitation efficiency and reducing DNA loss of low-input ChIP-seq samples. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10-1000 cells. By introducing Tn5 transposase-assisted fragmentation, 2cChIP-seq reliably captured genomic regions with histone modification at the single-cell level in about 100 cells. Moreover, we characterized the methylome of 100 differentiated female germline stem cells (FGSCs) and observed a particular DNA methylation signature potentially involved in the differentiation of mouse germline stem cells. Hence, we provided a reliable and robust epigenomic profiling approach for small cell numbers and single cells.

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