GSM3402781: B316-3-Xylan; Butyrivibrio proteoclasticus; RNA-Seq
RNA was extracted using a modified version of a liquid N2 and grinding method. Briefly, 10 g of each frozen culture sample was combined with two volumes of RNA Bacterial Protect Reagent (Qiagen). The thawed sample was centrifuged at 15,000 × g for 10 min at 4 ºC and cell pellet resuspended in 1 mL of Extraction buffer A (200 mM NaCl, 20 mM EDTA), 420 µL of 20% (w/v) SDS and 1 mL of a mixture of phenol: chloroform: isoamyl alcohol solution. The cells were disrupted by five rounds of bead-beating using a Mini-Beadbeater-96 (BioSpec) for 4 min at full speed. An equal volume of isopropanol and 0.1 volume of 3 M sodium acetate (pH 5.5) were added, gently mixed and stored at -20 ºC overnight (54). The cell pellets were ethanol precipitated, followed by DNase treatment using the Baseline-ZERO DNase (Epicentre Technologies) kit and RNA was purified using the MEGAClear kit (Thermo Fisher Scientific), based on the manufacturer's instructions. RNA yield and quality were assessed using the Bioanalyzer 2100 with a RNA 6000 Nano Assay reagent kit from Agilent (Santa Clara, CA), and stored at -85 ºC. RNA was sequenced on the Illumina HiSeq 2000 platform at the Beijing Genomics Institute, BGI (Shenzen, China). RNA libraries were prepared for sequencing using standard Illumina protocols.
GEO Accession
GSM3402781