Reduced Representation Bisulfite Sequencing in Neural Stem Cells undergoing early differentiation
Description
This dataset explore the early methylation changes in Neural Stem Cells (NSCs) and after initiating differentiation at 3h and 24h. This study aims for the characterization of early dynamics at methylation level that overlap the transition-state vs the NSC-steady-state. Biological cell samples of NSC in vitro were generated at Salk Institute. Reduced Representation Bisulfite Sequencing (RRBS) was performed by the company Active Motif (North America), who processed from frozen samples to the bioinformatic analysis.
Files
Steps to reproduce
Reduced Representation Bisulfite Sequencing was performed by the Company ActiveMotif (at North America, location). Raw information of single-end 75bp sequencing reads was generated by Illumina sequencing (using NextSeq 500). First, Illumina adapter sequence is trimmed from the reads. Then, a custom script is used to trim additional bases that are added during the library creation process to facilitate sequencing. The resulting reads are then mapped to the genome using RRBSMAP using default settings (12bp seed length, max number of mismatches = 0.08 x read length); only unique alignments are kept (if a fragment maps to more than one location, it is discarded). Another custom script is then used to remove any PCR duplicates based on a randomized 6-mer barcode; if more than one fragment has the same start and end coordinates as well as the same barcode, all but one are discarded. Alignment information for the remaining reads is stored in the BAM files.