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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq with ERCC spike-in) [RNA-Seq]

ABSTRACT: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq with ERCC spike-in) [RNA-Seq]

PROVIDER: PRJNA644383 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12158131.fastq.gz	Fastqsanger.gz
	SRR12158132.fastq.gz	Fastqsanger.gz
	SRR12158133.fastq.gz	Fastqsanger.gz
	SRR12158134.fastq.gz	Fastqsanger.gz
	SRR12158135.fastq.gz	Fastqsanger.gz

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq with ERCC spike-in) [RNA-Seq]

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Project description:This study aims to assess the reliability of spike-in normalization for analyzing single-cell RNA sequencing data. This is done by performing mixture experiments where two different sets of spike-in RNA (ERCC and SIRV) are added separately to a single mouse cell (416B or trophoblast stem cells (TSCs)), followed by generation of sequencing libraries using a modified version of the Smart-seq2 protocol. The aim is to measure the variance of the log-ratio of the total counts between the two spike-in sets. This will quantify how precisely the spike-in RNA was added to each well. As a control, addition was also performed with a premixed solution of both spike-ins, to quantify the variability in the log-ratios due to the experimental protocol. The same data can also be used to measure the well-to-well variability in the differences in behaviour between the two spike-in sets. The data contain four batches of libraries (block), using different batches of cells that were processed and sequenced separately. Each batch contains libraries with all three types of spike-in addition (ERCC+SIRV, SIRV+ERCC or Premixed). The 416B cells also contain a CBFB-MYH11 oncogene, which is expressed in half of the cells (Induced) and silent in the other half (Control).

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