Small RNA-seq and RNA-seq data

Small RNA-seqLibraries of small RNAs were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s protocols, and then sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). Quality control and adapter trimming process were performed using Trim Galore (v0.6.4) with default parameters, and reads length between 17 and 70 were used for subsequent analyses. The sequenced reads were aligned to the human genome (GRCh38) by using Bowtie2 (v2.3.5.1). Reads that cannot be aligned to the human genome (GRCh38) were then aligned to agshRNAs. The sequences and lengths of reads aligned to agshRNA were then determined using an in-house script. Reads mapped to genome were further categorized as miRNA, tRNA, snoRNA etc. by using htseq-count (v0.11.2). Annotation file was downloaded from DASHR 2.0 (https://dashr2.lisanwanglab.org/). RNA-seqLibraries of total RNAs were constructed using MGIEasy RNA Library Preparation Kits (BGI) according to manufacturer’s protocols, and then sequenced by MGISEQ2000 (BGI) at Wuhan Institute of Virology, CAS. Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameter. All reads were mapped to the human genome (GRCh38) using Hisat2 (v2.1.0) and then annotated using htseq-count (v0.11.2). Annotation file was downloaded from NCBI. Annotated reads number were transformed into count per million reads (CPM). Statistical significance was evaluated via using unpaired t test and adjusted using Bonferroni correction. Different expression genes (DEGs) were defined by |log2FC| > 1 and P.adj < 0.05.