CNEReg is an evolutionary Conserved Non-coding Element interpretation method by gene Regulatory network to integrate paired time-course expression and chromatin accessibility data with the available public data, including comparative genomics data and comparative transcriptomic data.
The raw data files are the original files containing reads and quality scores, as generated by the Illumina sequencing instrument. Raw Data File Format if FASTQ. All the RAW data and processed data produced in this study have been permanently deposited at the Sequence Read Archive (SRA) under project number PRJNA485657. The useres and reviewers can access the raw data with fastq files via URL: https://submit.ncbi.nlm.nih.gov/subs/sra/SUB7461604/.
The final processed data are defined as the data on which the conclusions in the related manuscript are based.
- Peak files with quantitative openness data with a format bed and txt files for ATAC-Seq data.
- The normalized gene expression profile output from Stringtie for RNA-seq data.
- The bed file of RSCNEs which consist of chromosome, start and end coordinates with the corresponding conservation score.
CNEReg model requires input as sample matched time-series RNA-seq and ATAC-seq, and RSCNEs with conservation scores from public data.
For RNA-seq, first we processed raw reads into an expression matrix with row genes and column samples.
Xiangyu Pan, Zhaoxia Ma, Xinqi Sun, Hui Li, Tingting Zhang, Zhao Chen, Nini Wang, Wing Hung Wong, Wen Wang, Yu Jiang, Yong Wang. Interpreting ruminant specific conserved non-coding elements by reconstructing developmental regulatory network. (In submission).
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