title: GSM8163286: cecum, OA08, male, biol rep 1; Mus musculus; RNA-Seq
library_construction_protocol: Once we verified that the negative control was germ-free, we euthanized the mice and collected cecal tissue for total RNA extraction. Using a biopsy puncher with a diameter of 8mm we collected circular tissue pieces from the cecum of mice and preserved them in DNA/RNA Shield (Zymo Research Corporation, Irvine CA) at -80C. Total RNA was extracted using a kit (Quick-RNA MiniPrep Plus, Zymo Research Corporation). Because the tissue samples were not homogenized, tissues were treated overnight with 2X proteinase K from the kit and constant tumble-mixing until tissues were dissolved. The tissue digest was taken through the protocol provided by the manufacturer, including a step for the enzymatic degradation of DNA. To validate the extraction process, the nucleic acid concentration in the eluates was measured in a spectrophotometer. Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus