For bulk RNA-seq, total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490). To assess the integrity of the total RNA, samples were run on the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction. Ribosomal RNA was removed before cDNA synthesis with SuperScript II reverse transcriptase (Invitrogen) and library preparation with KAPA RNA Hyper Prep Kit (Kapa Biosystems). RNA libraries were prepared according to the manufacturers’ protocol (Kapa Biosystems). Libraries were pooled together for pair-end sequencing with NovaSeq 6000 or NextSeq 500 (High output) platform (illumina).
Pair-end sequencing reads of RNA-seq data were mapped to human genome (hg19 version) or mouse genome (mm10 version, for mouse bulk RNA-seq) with tophat software (tophat2, default parameter)81 (link), annotated repeat information was downloaded from UCSC database, repeat region quantification was done with BEDTOOLs82 (link) and normalized to cpm (count per million for each sample). Gene expression was calculated with cufflinks software83 (link). Kolmogorov–Smirnov test (KS test) was used for comparing transposon fold-change to the background. Differential expression analysis was done using DESeq284 (link).
Pair-end sequencing reads of RNA-seq data were mapped to human genome (hg19 version) or mouse genome (mm10 version, for mouse bulk RNA-seq) with tophat software (tophat2, default parameter)81 (link), annotated repeat information was downloaded from UCSC database, repeat region quantification was done with BEDTOOLs82 (link) and normalized to cpm (count per million for each sample). Gene expression was calculated with cufflinks software83 (link). Kolmogorov–Smirnov test (KS test) was used for comparing transposon fold-change to the background. Differential expression analysis was done using DESeq284 (link).
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