BS-RNA protocols

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BS-RNA specifications

Information


Unique identifier OMICS_13857
Name BS-RNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNA bisulfite sequencing data
Output data The annotation result of BS-RNA is exported in BED (.bed) format, including locations, sequence context types (CG/CHG/CHH, H = A, T, or C), reference sequencing depths, cytosine sequencing depths, and methylation levels of covered cytosine sites on both Watson and Crick strands.
Output format BED
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
Python, HISAT2, SAMtools, Bowtie2
Maintained Yes

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Publication for BS-RNA

BS-RNA in pipelines

 (2)
2016
PMCID: 4931328
PMID: 27356879
DOI: 10.1038/ncomms12039

[…] were digested with 4 mg ml−1 proteinase k. rna was end repaired with antarctic phosphatase and t4 polynucleotide kinase. library preparation and high-throughput sequencing were similar as for bs rna-seq., bs rna-seq reads were quality trimmed, adaptors were removed and the reads were mapped to the computationally bisulfite-converted human reference genomes (ucsc grch37/hg19) with bismark […]

2016
PMCID: 4931328
PMID: 27356879
DOI: 10.1038/ncomms12039

[…] counting with rsubread and normalization, reads from nsun3 overexpression samples were compared with reads of an unrelated protein (ensg00000182362) with edger (exacttest with dispersion 0.1)., bs rna-seq, fcab rna-seq and redbs rna-seq data were pre-processed (both quality trimming and adaptor removal) with trim galore! reads longer than 20 nt were mapped to the computationally […]


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BS-RNA in publications

 (3)
PMCID: 5416834
PMID: 28062854
DOI: 10.1093/nar/gkw1349

[…] by themselves do not change 3΄ ss selection. furthermore, these mutations appear to modify bs usage by a novel mechanism, potentially by disrupting hsh155/sf3b1 conformations that stabilize weak u2:bs rna duplexes formed on nonconsensus introns (figure , ). we show that the interaction network of hsh155 is largely unperturbed by mds mutations with the exception of prp5; however, prp5-dependent […]

PMCID: 4931328
PMID: 27356879
DOI: 10.1038/ncomms12039

[…] treatment of rna of wild-type hdfs (wt/wt), patient hdfs lacking the functional nsun3 protein (mut/mut) and mut/mut hdfs expressing a nsun3 cdna (mut/mut+nsun3). the bisulfite rna sequencing (bs rna-seq) analysis revealed that methylation in mt-trnamet (mt-tm) was decreased to background levels in nsun3 mutant cells (mut/mut), while other top mtrnas with sites enriched by miclip (; […]

PMCID: 4932649
PMID: 27329847
DOI: 10.1038/emi.2016.56

[…] or neuro-2a cells onto fresh vero and nih/3t3 cells also resulted in significant cpe (), confirming the presence of viable viral progeny in transfection supernatants. moreover, passage of ev71:bs rna transfection supernatants from vero, nih/3t3 or neuro-2a cells onto fresh vero, but not nih/3t3, cells resulted in cpe and expression of viral proteins (). these results demonstrate […]


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BS-RNA institution(s)
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
BS-RNA funding source(s)
This study was supported by grant from the National Programs for High Technology Research and Development (863 Program; 2012AA020409, 2015AA020108), the Ministry of Science and technology of the People’s Republic of China; grant from the National Science Foundation of China (No. 31271386, No. 31100915 and No. 31471248).

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