Data package for time-series expression profiles by RNA-seq from PRJNA275011

Sources

• GEO data set: GSE65785
• Experimental data were generated by Owens et al. (2016) Original citations:
  • Owens NDL, Blitz IL, Lane MA, Patrushev I et al. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Rep 2016 Jan 26;14(3):632-647. PMID: 26774488
• Processing:
  • Sequencing reads were downloaded from SRA, at PRJNA275011
  • FASTQC was run to check for overall quality. No adapter sequence was found.
  • Reads were aligned to genome using STAR 2.7.1a, on Xenopus tropicalis genome from Ensembl, (Xtro 9.1 + ERCC-92), and abundance levels were estimated using RSEM.

Usage

Install the package, import the library and load the data set

devtools::install_github('ttdtrang/data-rnaseq-XtroDev')
data(xtro.rnaseq.gene, package='data.rnaseq.XtroDev')
dim(xtro.rnaseq.gene@assayData$exprs)

Steps to re-produce data curation

1. cd data-raw
2. Download all necessary raw data files.
3. Set the environment variable DBDIR to point to the path containing said files
4. Run the R notebook make-data-package.Rmd to assemble parts into ExpressionSet objects.