Please find attached updated gene expression data derived from the FlyAtlas2 RNAseq dataset, based on FlyBase r6.54 data files. Please note that only non-small RNAs were updated (ie, the FPKM sheet of the attached spreadsheet, not the TPM sheet) as the small RNAs have been reprocessed relatively recently.
The analysis pipeline for these figures were as follows:
-FlyAtlas2 Raw RNA samples were pseudo-aligned to all non-small RNA Drosophila melanogaster transcripts using SALMON (v1.10.1). A decoy transcriptome was created using the Drosophila chromosome sequences.
-Transcript-level abundances were summaried to the gene level using tximport (v3.18).
-Ribosomal (rRNA) transcripts, genes, and all aligned reads were removed from the datasets, to prevent biasing of FPKM values based on ribosomal content, which we found varied a great deal between samples due to batch effects.
-FPKMs were calculated using the standard calculation:
      FPKM = <up>RMg * 109 </up> / <up>RMt * L</up>
RMg: The number of reads mapped to the gene
RMt: The total number of mapped reads (excluding removed genes)
L: The length of the gene in base pairs