title: GSM6315158: 21dpi_Cecum_R3; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; RNA-Seq
library_construction_protocol: RNA from cecal contents and feces was extracted using the QIAGEN RNeasy PowerMicrobiome Kit following manufacturer's instructions. RNA from liquid cultures was extracted with the QIAGEN RNeasy Mini Kit following the QIAGEN supplementary protocol: purification of total RNA from bacteria. RNA libraries were prepared using the Illumina stranded total RNA prep ligation with ribo-zero plus kit. rRNA from mice was depleted prior to library construction and confirmed with Agilent Bioanalyzer Prokaryote Total RNA Pico. No experimental rRNA removal was used for the in vitro samples. RNA integrity was confirmed with Agilent Bioanalyzer Prokaryote Total RNA Pico. In vivo and in vitro libraries underwent quality control by Novogene Corporation Inc. Pulled in vivo and in vitro libraries were loaded onto separate lanes of the S4 flow cell and sequenced on an Illumina NovaSeq 6000 and were run using the PE150 strategy. Data were unequally shared, 10.11G raw data (100.4 million paired reads) for each in vivo sample and 4.5G raw data (15 million paired reads) for each in vitro sample.