Through the smokingMouse Bioconductor data package, we offer free open access to all generated and analyzed RangedSummarizedExperiment (RSE) objects containing:
- The raw expression counts and lognorm counts of genes, exons, and exon-exon junctions, and the transcripts per million (TMP) and log-TPM of transcripts, across the 208 mouse samples from pup and adult brain, and adult blood.
- Sample-level metadata (what's contained in Maternal_Smoking_pheno.txt) and quality control metrics.
- Information of gene expression features.
The results of the DEA for smoking exposure in human postmortem prenatal and adult prefrontal cortices from Semick et al., 2020 are also accessible.
See more details of the provided datasets and how to access them in the smokingMouse web page.
The raw data from this project lives at different external directories.
The script code/01_SPEAQeasy/01_make_manifest.R creates soft links (stored in raw-data/fastq) to the original raw data.
Originally, the paths to the original data were determined by reading in: /dcl01/lieber/ajaffe/lab/Nicotine/nicotine_mouse_rnaseq/blood/preprocessed_data_RNAsp/samples.manifest and /dcl01/lieber/ajaffe/lab/Nicotine/nicotine_mouse_rnaseq/brain/preprocessed_data_RNAsp/samples.manifest, which ultimately refered to FASTQ files under /dcl01/lieber/ajaffe/lab/Nicotine/nicotine_mouse_rnaseq/FASTQ/. After data was transferred from dcl01 to dcs05, code/01_SPEAQeasy/01_make_manifest.R was re-run, referring to new paths under /dcs05/lieber/marmaypag/nicotineGonzalez2023_LIBD001.
SPEAQeasy was run after the first execution of code/01_SPEAQeasy/01_make_manifest.R and referenced files under dcl01 (which should not make a difference).