DOI: 10.6084/m9.figshare.25815862.v2
title: The scDART-seq data used in the <b>Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation</b>

description: The scDART-seq data used in the study "Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation" was obtained from the SMART-seq2 platform. This dataset aimed to profile the m6A epitranscriptome in 1382 HEK293T cells, consisting of 991 cells containing m6A modifications (YTH) and 391 negative control cells (YTHmut). Negative control cells were identified by their mutated YTH domain, rendering them unable to induce m6A-associated signals, thus serving to estimate background noise. Following data extraction, 510,554 candidate m6A sites were retained for further analysis.The files associated with this study include:<b>SNP File (SNP_all.rds):</b><b>Data Details:</b> Stored in RDS format, containing a GRanges object.<b>Content:</b> Each entry in the GRanges object represents a specific genomic region corresponding to an m6A modification site detected through scDART-seq.<b>seqnames:</b> Factor Rle object containing chromosome or genomic sequence names.<b>ranges:</b> IRanges object containing genomic intervals (start and end positions).<b>strand:</b> Factor Rle object indicating the strand (directionality) of the genomic region.<b>mcols:</b> DataFrame object containing optional metadata columns, such as quality scores, coverage depth, and mutation data.<b>seqinfo:</b> Seqinfo object providing information about the genomic sequences present in the GRanges object.<b>Purpose:</b> Provides detailed genomic information about identified m6A modification sites, facilitating further analysis of their distribution, characteristics, and genomic context in HEK293T cells.<b>Frequency File (frequency_all.rds):</b><b>Data Details:</b> Also stored in RDS format, consisting of a list.<b>Content:</b> Each item in the list represents a single-cell, containing counts of methylated and unmethylated reads for corresponding m6A modification sites detected in scDART-seq data.<b>Purpose:</b> Offers quantitative data on the abundance of methylated and unmethylated sequences at each m6A site across individual cells, enabling investigation of m6A modification patterns at a single-cell level.<b>Expression TPM File (expression_TPM.rds):</b><b>Data Details:</b> Stored as an RDS file, comprising a list.<b>Content:</b> Each item in the list represents a single-cell, with corresponding TPM values for gene expression.<b>Purpose:</b> Provides information on gene expression levels across individual cells, facilitating examination of potential correlations between m6A modification patterns and gene expression profiles in scDART-seq data from HEK293T cells.<b>gene Information File (gene_informations.rds):</b><b>Data Details:</b> Stored as an RDS file, comprising a data frame.<b>Content:</b> Includes information such as Gene ID, Gene Name, Reference, Strand, Start position, End position, and Coverage.<b>Purpose:</b> Offers additional details about gene expression data, aiding in the interpretation and analysis of gene expression profiles in conjunction with m6A modification patterns.<br>