24Previously, we have indicated that Hot Water Extract (HWE) from Spent Mushroom 25 Substrate (SMS) of Ganoderma lucidum enhanced immune function of normal mice, and 26 improved antioxidant activity and enhanced immune function of immunosuppression mice 27 induced by cyclophosphamide (Cy). Here we performed the high throughput RNA sequencing 28 strategy using Illumina HiSeq TM 2000 to characterize the spleen transcriptome from normal 29 (CK1), HWE-treated (CK2), Cy-treated (CY) and both high dose HWE and Cy-treated mice 30 (CH). From the RNA Sequencing, total mapped reads of map to Gene in CK1, CK2, CY and 31 CH was 54 759 942, 54 678 926, 44 728 132 and 54 006 596, respectively. And gene expression 32 was significantly different among CK1 and CK2, CY and CH. Compared with CK1, the gene 33 expression of Ugt1a6b was down-regulated in CK2 after HWE treated. In addition, compared 34 with CY, multiple tumor suppressor or tumorigenesis genes were down-regulated, such as 35 Cdkn1a, Cdkn1b, Mapk10, Vash1, and Tnc and other genes in CK2 and CH. Taken together, 36 our study highlighted the spleen transcriptome profiles of C57BL/6 mouse in response to HWE 37 from SMS of G. lucidum and Cy, and indicated that HWE can improve the immune function of 38 the mouse and accelerated the recovery of immunosuppression in Cy-treated mice. 39 Keyword: Spleen transcriptome; Ganoderma lucidum; Hot Water Extract; 40 Cyclophosphamide 41 42 43 3 44 6 109 kilograms of HWE were obtained from 100 kg of fresh SMSG. The HWE included 23.58% 110 crude protein, 17.60% ash, 4.95% amino acid, and 2.0% crude fat. The content of 111 polysaccharide in HWE was 15.79% as determined by high-performance liquid 112 chromatography using the standard provided by National Engineering Research Center of 113 JUNCAO Technology. 114