Mouse RNASeq data for "An explainable graph neural framework to identify cancer-associated intratumoral microbial communities"

These data are RNA sequencing FASTQs for mouse tumor samples. A total of 22 C57BL/6J mice were administered an antibiotic cocktail in their drinking water for five days to deplete the resident microbiome, followed by two days of regular water. This cycle was repeated three times in succession, first with a low-absorption cocktail (ertapenem (1 mg/mL; Merck and Co., Inc., Whitehouse Station, NJ, USA) Neomycin (1 mg/mL; Fagron, Inc.), and Vancomycin (1 mg/mL; Mylan Institutional LLC, Rockford, IL, USA)), then a high-absorption cocktail (ampicillin (1mg/mL; Sandoz, Inc., Austria), cefoperazone (1 mg/mL; Thermo scientific, USA), and clindamycin (1 mg/mL; Major Pharmaceuticals, Inc., NJ, USA)), followed by the low-absorption cocktail a second time. Three days before the end of the antibiotic course, 1e6 mc38 cells were injected subcutaneously in the right flank. Following the antibiotic course, mice were gavaged with 200 uL stool slurry (1g healthy donor stool in 5 mL de-gassed phosphate-buffered saline) with (n=10) or without (n=12) 1e7 CFU B. massiliensis strain FDAARGOS three days after cancer cell injection. Ten days after the start of tumor growth, mice were treated with either 5mg/kg anti-PD1 Ab (clone RMP1-14; BioXCell, USA) or isotype control (IgG) (clone 2A3, BioXCell, USA). The experiment was ended 21 days after mc38 injection. To evaluate the presence of microbes in tumors, the tumor samples were sterilely dissected upon euthanization.  RNA was purified using an AllPrep kit (QIAGEN) following the manufacturer’s instructions, with the addition of a bead-beating lysis step. Specifically, tumors were minced by scalpel and then beaten in lysis buffer with 100 mg ceramic beads at 2000 rpm for two minutes on a Powerlyzer 24 (QIAGEN). Human and mouse RNA was depleted using a KAPA RNA Hyperprep kit (Roche). Samples were sequenced 2x150nt on a NextSeq 2000 to a depth of 50M reads.