Study curation

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Each study available in RGV was manually curated to extract relevant information:

• Information relative to the associated publication (PubMed ID, authors, full publication name, abstract)
• The species investigated and the technology used
• Relevant information about investigated samples (tissues, sex, developpemental stage, ...)
• Any relevant keywords

If available, the raw data associated with the study will then be processed using a multiple-step workflow to make it compatible with the RGV visualization tools.

Sample Processing

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For each sample, seven processing steps are sequentially performed:

• 1- The raw data file (sra file) of a given sample and their associated information are downloaded from the Gene Expression Omnibus (GEO) and to the Sequence Read Archive (SRA);
• 2- The fastq file is extracted from the sra archive file;
• 3- Reads are mapped on its corresponding reference genome using the STAR tool.
• 4- Each bam file is converted into a simple tab-delimited text file (BED) in which data are standardized according to the total nuber of read counts using BEDTools;
• 5- The standardized BED file is then converted into an indexed binary format (bigWig or bw) to enable fast remote access to the data;
• 6- The pairwise alignments between genome assemblies and between species provided by UCSC made it possible to convert genome coordinates in the resulting bigWig file from a genome of a given species into a genome of another species ussing CrossMap.
• 7- Reference transcripts are quantified in the corresponding sample using the StringTie tool.