title: Glc_2_t1
organism: Clostridium beijerinckii
description: Protocols: Total RNA was isolated from C. beijerinckii DSM 6423 for transcriptome studies. Samples were taken from duplicate 400-mL fermentations from cells in early exponential, acetogenic, and solventogenic phase. Cells were pelleted for 15 min at 3000 × g and 4 °C and stored at -80 °C until further use. Fermentations were performed at 37 °C in 400 mL working volume of CM2 medium containing (in g L-1): yeast extract, 1.00; KH2PO4, 1.00; K2HPO4, 0.61; MgSO4 × 7 H2O, 1.00; FeSO4 × 7 H2O, 0.0066; para-aminobenzoic acid, 0.10; and ammonium acetate, 2.90 and with either 40.0 glucose or rhamnose. RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) and the PureLink RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer's protocol. In short, the cell pellet was thawed on ice and resuspended in 5 mL TRIzol reagent for cell lysis. Next, 1 mL chloroform was added and after centrifugation for 15 min at 13,000 × g, the upper aqueous phase was mixed with an equal volume of 70 % ethanol. The solution was loaded on a spin cartridge, washed once and treated with 30 U DNase I. After two additional washing steps, the RNA was eluted in RNase-free water. Quality and quantity of the isolated RNA was checked by gel electrophoresis and NanoDrop, respectively. Afterwards, the samples were stored at -80 °C before being sent for sequencing. Library construction and sequencing was performed by Novogene Co. Ltd. Messenger-RNA was depleted with the Ribo-Zero Magnetic Kit and a 250-300 bp insert cDNA library was constructed.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2019-01-14T17:03:32Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-12-14T14:48:44Z
attributes.tag: External Id
attributes.value: SAMEA5176454
attributes.tag: INSDC center name
attributes.value: Wageningen Food and Biobased research
attributes.tag: INSDC first public
attributes.value: 2019-01-14T17:03:32Z
attributes.tag: INSDC last update
attributes.value: 2018-12-14T14:48:44Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7487:Glc_2_t1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: replicate
attributes.value: 2
attributes.tag: sample name
attributes.value: E-MTAB-7487:Glc_2_t1
attributes.tag: scientific_name
attributes.value: Clostridium beijerinckii