Rep 2: RNAseq from cells grown in MRS-T with 1% DMSO
Library construction and sequencing was performed by Novogene, (Novogene Co., Davis, CA, USA) . After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. Raw data (raw reads) of FASTQ format were first processed through fastp. The reference genome and gene model annotation files were downloaded from NCBI. Bowtie2 was used to build the index of the reference genome and to align the clean reads.  FeatureCounts was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2 R package, and the resulting p-values were adjusted using Benjamini and Hochbergs approach for controlling the false discovery rate. Genes with an adjusted p-value < 0.05 found by DESeq were assigned as differentially expressed. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with a corrected p-value less than 0.05 were considered significantly enriched by differential expressed genes. The clusterProfiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.