mirData: Example of IsomirDataSeq with human brain miRNA counts data
Description
This data set is the object return by IsomirDataSeqFromFiles.
It contains miRNA count data from 6 samples: 3 newborns and 3 elderly
human individuals (Somel et al, 2010).
Use colData to see the experiment design.
Source
Data is available from GEO dataset under accession number GSE18069.
Samples used are: GSM450597, GSM450598, GSM450600,
GSM450604, GSM450610 and GSM450609 . Every sample was analyzed with seqbuster tool, see
http://seqcluster.readthedocs.org/mirna_annotation.html for
more details. You can get same files running the small RNA-seq
pipeline from https://github.com/chapmanb/bcbio-nextgen. Adapter removal with the following parameters:
adrec fastq_file TCGTATGCCGTCTT 8 1 0.34 miRNAs annotation with the following parameters:
miraligner adrec_output mirbase_files hsa 1 3 3 out_prefix The data was created with isomiRs-package package: library(isomiRs) fns <- c("GSM450597.mirna", "GSM450598.mirna", "GSM450600.mirna",
"GSM450604.mirna", "GSM450610.mirna", "GSM450609.mirna") design <- data.frame(condition=c('nb', 'nb', 'nb',
'o', 'o', 'o')) mirData <- IsomirDataSeqFromFiles(fns, design)References
Mehmet Somel et al. MicroRNA, mRNA, and protein expression link
development and aging in human and macaque brain.
Genome Research,20(9):1207-1218,2010.doi:10.1101/gr.106849.110