Methods Summary:
Data were processed with the RGD workflow (GitHub https://github.com/rat-genome-database/RGD_RNAseq_workflows ). 
Fastq files were downloaded from the Sequence Read Archive and transformed with the sratookit v3.1.1. 
Raw read quality metrics are generated with FastQC (Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
and FastQ-Screen (Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).  
Upon read quality review and species verification, fastq files are aligned to RefSeq genome assembly GRCr8 using 
STAR version=2.7.10b_alpha_220111 (Alexander Dobin, https://github.com/alexdobin/STAR). 
STAR alignment files are submitted to RSEM v1.3.1(Bo Li and Colin Dewey, https://github.com/deweylab/RSEM)  for expression quantification
and output as TPM and counts matrixes. 
RefSeq annotation release GCF_036323735.1 (https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/036/323/735/GCF_036323735.1_GRCr8/)
was used for gene and transcript annotation. 
Computed Sex infers the sex of a sample based on the ratio of the coverage of the X and Y chromosomes and the expression values of common 
sex specific genes. MultiQC v1.18 (Seqera, https://seqera.io/multiqc/)is used to generate a comprehensive post-processing quality report.

**Disclaimer**
Studies submitted to GEO represent a variety of experimental methods, library preparation methods, and processing softwares and algorithms. 
The HPC RGD workflow is currently limited to transcriptomic studies run on the illumina sequencing platform, with minimal
checks on quality. Therefore, the user must be aware of the following limitations to the provided data:

 The data generated by the HPC RGD workflow may not match the published data due to the variety of data processing methods 
 (software, analysis settings, read trimming, etc.) applied by the submitters to generate the data for publication. Users are encouraged to view
 the original data by navigating to the GEO accession display tool and viewing the processed data files supplied to GEO by the submitter.

 All TPM data presented for expression studies by RGD have been processed by the same pipeline, RGD does not attempt to correct for any potential
 bias or confounding factors. 

 A study may be missing values for one or many samples.  This could be a result of technical reasons such as corrupted or missing raw read files
 or low genome assembly alignment rates. Samples with less than a 50% STAR alignment rate to GRCr8 will not be processed with RSEM to 
 generate abundance estimates.

 A study may be missing values for one or many genes in the database gene expression table display, RGD does not store TPM values equal to 0.
 All genes used in the alignment process are output in the matrix files provided in the downloads directory.

 Computed sample sex may disagree with sex submitted to GEO. Sex estimates are based on x:y coverage ratio and expression of limited 
 list of sex specific genes. Coverage and expression values may be impacted for a variety of technical factors. Where there are significant 
 discrepancies at the study level, RGD curators reach out to data submitters for further clarification.