RNA-seq data sets of human brain and Hela cell line

Generation of HeLa cell RNA-seq data Total RNA was isolated using TRIZOL (Invitrogen) from HeLa cells grown in standard medium under standard conditions. The RNA was divided into three samples containing equal amounts of RNA. The quality of these samples was manually controlled to produce different RIN values. Specifically, the RIN value of the low-quality RNA sample was 5 and that of the two high-quality samples was 10. Next, a RiboMinus kit (Invitrogen, Carlsbad, CA, USA) was utilized to deplete ribosomal RNA in these samples. The resulting RNA was incubated at 37 ℃ and treated with 10 U μg-1 RNase R (Epicentre, Madison, WI, USA). One of the high-RIN samples and the low-RIN sample were used separately as templates for cDNA libraries following the TruSeq protocol (Illumina, San Diego, CA, USA); the other high-RIN sample was used to construct a sequencing library using the same protocol but without the fragmentation step. Fragments with a broad range of fragment size (300-800 bp) were selected for library construction. The three libraries (Low RIN/Fragmented, High RIN/Fragmented High RIN/Unfragmented) were sequenced on the Illumina HiSeq 2500 platform of the Research Facility Center at the Beijing Institutes of Life Science, CAS, with a read length of 250 bp. Generation of whole brain RNA-seq data Human, macaque, and rabbit whole brain RNA samples were purchased from Zyagen (San Diego, CA, USA). Mouse, rat and chicken whole brain tissues were obtained from the Research Facility Center at the Beijing Institutes of Life Science, CAS. RNA samples were isolated using TRIZOL (Invitrogen). For each species, three types of cDNA library were prepared. Specifically, a Ribo-/RNase R library was constructed using RNA samples that had been treated with the RiboMinus kit (Invitrogen) and then incubated at 37 ℃ with 10 U μg-1 RNase R; a Ribo-/cDNA library was constructed using RNA samples that were only treated with the RiboMinus kit; and a poly-A library was prepared according to the TruSeq v2 guide. Poly-A and Ribo- RNA samples were used as templates for cDNA libraries according to the TruSeq protocol (Illumina); Ribo-/RNase R-treated samples used the same protocol but without fragmentation. These libraries were sequenced on the Illumina HiSeq 2500 platform of the Research Facility Center at Beijing Institutes of Life Science, CAS. PolyA+ and Ribo-/RNase R libraries were sequenced with paired-end 250-bp reads, and Ribo-libraries were sequenced with paired-end 150-bp reads.