X ten pe150

The high‐throughput sequencing of the transcriptome was conducted by Beijing Baimaiker technology Co., Ltd. The cDNA library was sequenced on the Illumina X‐TEN PE150 (San Diego, CA, USA), thereby generating the maximum 300‐bp pair‐end reads. Raw data in fastq format were first processed through in‐house perl scripts to obtain clean data by removing the adapter, ploy‐N and low‐quality sequences (Q < 20). At the same time, Q20, Q30, GC content and the sequence duplication level of the clean data were calculated. All of the downstream analyses were based on clean data with high‐quality clean reads. The clean reads were aligned with hisat2 (http://ccb.jhu.edu/software/hisat2) with default parameters to the Ziziphus jujuba (assembly ZizJuj_1.1) [18] on National Center for Biotechnology Information. Transcripts were assembled and quantified with stringtie (http://ccb.jhu.edu/software/stringtie).

Single-cell 3’ gene expression libraries for CD45⁺ immune cells were prepared by strictly following the protocols of the Chromium Single Cell 3’v2 Library kit (10× Genomics). All resulting libraries were sequenced on the Illumina Xten PE-150 platform (ANOROAD and Novogene, Beijing, China).