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Identification of m6dA in genomic DNA and transcriptional patterns in human genomes by DIP-Seq and RNAseq

ABSTRACT: Identification of m6dA in genomic DNA and transcriptional patterns in human genomes by DIP-Seq and RNAseq

PROVIDER: PRJNA507429 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8257210.fastq.gz	Fastqsanger.gz
	SRR8257211.fastq.gz	Fastqsanger.gz
	SRR8257212.fastq.gz	Fastqsanger.gz
	SRR8257213.fastq.gz	Fastqsanger.gz
	SRR8257214_1.fastq.gz	Fastqsanger.gz

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Identification of m6dA in genomic DNA and transcriptional patterns in human genomes by DIP-Seq and RNAseq

Project description:We identify m6dA in human genomic DNA by DNA immunoprecipitation and subsequent Hi-Throughput Illumina sequencing (DIP-Seq). We use a dA6m specific antibody for DNA pulldown, and input as control. In addition, we performed RNA High Throughput Illumina Sequencing on biologically matched samples. This data supplements our analysis of already published data.

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Single-cell chromatin conformation capture of diploid cells by Dip-C (analyzed with the dip-c package)

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Single-cell chromatin conformation capture of mouse sensory neurons in visual and olfactory systems by Dip-C

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Single-cell chromatin conformation capture of diploid cells by Dip-C (analyzed with the hickit package)

Project description:To reconstruct the 3D genomes of single diploid human and mouse cells, we performed single-cell chromatin conformation capture by a novel method, Dip-C, on human cells. This submission is similar to our submission GSE117109, but analyzed the data with the hickit package instead of the dip-c package. The raw data for the samples in this series are identical to the related samples in GSE117109. There are links between the original and re-analyzed data on the sample pages.

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Investigation of Drosophila fruitless neurons that express Dpr/DIP cell adhesion molecules

Project description:Drosophila reproductive behaviors are directed by fruitless neurons. A reanalysis of genomic studies shows that genes encoding dpr and DIP Immunoglobulin superfamily (IgSF) members are expressed in fru P1 neurons. We find that each fru P1 and dpr/DIP (fru P1 ∩ dpr/DIP) overlapping expression pattern is similar in both sexes, but there are dimorphisms in neuronal morphology and cell number. Behavioral studies of fru P1 ∩ dpr/DIP perturbation genotypes indicates that the mushroom body functions together with the lateral protocerebral complex to direct courtship behavior. A single-cell RNA-seq analysis of fru P1 neurons shows that many DIPs have high expression in a small set of neurons, whereas the dprs are often expressed in a larger set of neurons at intermediate levels, with a myriad of dpr/DIP expression combinations. Functionally, we find that perturbations of sex hierarchy genes and of DIP-ε change the sex-specific morphologies of fru P1 ∩ DIP-α neurons.

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Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series2: 6mA DIP enrichment]

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