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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]

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

PROVIDER: PRJNA694841 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13529600.fastq.gz	Fastqsanger.gz
	SRR13529700.fastq.gz	Fastqsanger.gz
	SRR13529601.fastq.gz	Fastqsanger.gz
	SRR13529602.fastq.gz	Fastqsanger.gz
	SRR13529603.fastq.gz	Fastqsanger.gz

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Project description:Establishment and subsequent validation of a aCGH protocol for WGA (whole genome amplification) products originating from single cell or low amount of starting material (i.e. microdissected FFPE tissue samples). The establishment of the protocol involved testing of three DNA labeling protocols. Two labeling protocols were designed specifically for Ampli1(TM) WGA products. Additionally random primed isothermal (Klenow-based) labeling approach was tested (MM-CM-6hlendick et al., PLoS One. 2013 Jun 25;8(6):e67031.). In addition two different types of reference samples were tested and reference based on single-cell WGA products was chosen as most suitable in the end. The validation of the protocol assessed the following aspects: (1) performance of the protocol on primary and reamplified WGA products, (2) accuracy of the protocol in term of sensitivity of the CNA detection, (3) accuracy in terms of recapitulation of complex patterns of CNAs, (4) accuracy in terms of quantitative assessment of the CNAs, (5) ability to detect genomic heterogeneity of single cells (obtained either from in vitro cultures or from clinical patient material), (6) ability to detect minimal regions of aberration within a panel of disseminated cancer cells and corresponding tumor tissues. Establishment and validation of the single-cell aCGH protocol: two condition experiment (i.e. PCR-based labeling technique 1 vs. PCR-based labeling technique 2; PCR-based labeling technique 2 vs. random-primed isothermal (Klenow) labeling approach; reference DNA from cell pool WGA product vs. reference DNA from single-cell WGA products). Validation of the protocol: comparison of the CNA profiles between single-cell WGA products and corresponding bulk DNA. Analysis of the DCC and corresponding FFPE tumor tissue samples: single-condition experiment performed on samples collected at different stages of the disease (DCCs from bone marrow) and/or from different sites (primary tumor-breast; metastasis-lymph nodes; DCCs-bone marrow). Microarray data is corresponding data depicted in the paper manuscript titled: Reliable single cell array CGH for clinical samples

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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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