Data package for transcriptomic profiles from mouse brain regions during pregnancy and postpartum period

Sources

• Experimental data were generated by Ray et al. (2015).
  • Original citation: Ray S et al., "An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period.", G3 (Bethesda), 2015 Nov 23;6(1):221-33 (PMID: 26596646)
  • GEO data set: GSE70732
• Processing:
  • Sequencing reads were downloaded from SRA, at PRJNA289455
  • fastq files were check for adapter content, using FASTQC (no adapter sequence was found)
  • Reads were aligned on mouse genome GRCm38.p6 + 92 ERCC sequences, with Gencode m25 annotation, using STAR 2.7.1a, and then quantified by RSEM for abundance levels at gene and transcript levels.

Usage

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

devtools::install_github('ttdtrang/data-rnaseq-MmusPreg')
library(data.rnaseq.MmusPreg)
data(mpreg.rnaseq.gene)
dim(mpreg.rnaseq.gene@assayData$exprs)

The package includes 2 data sets, one for transcript-level counts/TPM and another for gene-level counts/TPM. Counts are non-integer estimate of expected_count by RSEM.

Steps to re-produce data curation

1. cd data-raw
2. Download all necessary raw data files which include

3.0M	feature_attrs.genes.tsv
7.0M	feature_attrs.transcripts.tsv
8.0K	featureCounts-summary.genes.tsv
8.0K	featureCounts-summary.transcripts.tsv
5.2M	matrix.gene.expected_count.RDS
4.2M	matrix.gene.featureCounts.RDS
5.4M	matrix.gene.tpm.RDS
17M	matrix.transcripts.expected_count.RDS
15M	matrix.transcripts.tpm.RDS
24K	PRJNA289455_metadata_cleaned.tsv
20K	starLog.final.tsv

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.

You may need to change some code chunk setting from eval=FALSE to eval=TRUE to make sure all chunks would be run. These chunks are disabled by default to avoid overwriting existing data files in the folder.