| Sample |
Details |
Platform |
Type |
Download (ENA) |
| rRNAstat |
Gluconobacter oxydans 621H was cultivated in mannitol medium containing 220 mM (4% w/v) mannitol, 5 g L-1 yeast extract, 1 g L-1 KH2PO4, 1 g L-1 (NH4)2SO4, 2.5 g L-1 MgSO4 x 7 H2O, and 50 µg mL-1 cefoxitin as antibiotic and harvested at an OD600 of 3. Cells were broken in a French press (SLM Aminco) at 15,000 psi (3 passages) using 10 mL of cell suspension. Ribosomes were purified based on the use of a strong anion exchange monolithic column with an ÄKTA pure FPLC system equipped with fraction collector F9-C to two CIM® QA-0.34 mL monolithic disks. RNA purified from ribosomes was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina) according to manufacturer´s instructions, yet without the fragmentation step. The library was quantified via qPCR with the KAPA Library Quantification Kit (Peqlab) and sequenced on a MiSeq desktop sequencer (Illumina), generating paired-end reads with a read length of 75 bp. |
Illumina MiSeq |
2x75bp paired-end TruSeq stranded mRNA |
ERR2809932 |
| rRNAexp |
Gluconobacter oxydans 621H was cultivated in mannitol medium containing 220 mM (4% w/v) mannitol, 5 g L-1 yeast extract, 1 g L-1 KH2PO4, 1 g L-1 (NH4)2SO4, 2.5 g L-1 MgSO4 x 7 H2O, and 50 µg mL-1 cefoxitin as antibiotic and harvested at an OD600 of 1.4. Cells were broken in a French press (SLM Aminco) at 15,000 psi (3 passages) using 10 mL of cell suspension. Ribosomes were purified based on the use of a strong anion exchange monolithic column with an ÄKTA pure FPLC system equipped with fraction collector F9-C to two CIM® QA-0.34 mL monolithic disks. RNA purified from ribosomes was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina) according to manufacturer´s instructions, yet without the fragmentation step. The library was quantified via qPCR with the KAPA Library Quantification Kit (Peqlab) and sequenced on a MiSeq desktop sequencer (Illumina), generating paired-end reads with a read length of 75 bp. |
Illumina MiSeq |
2x75bp paired-end TruSeq stranded mRNA |
ERR2809931 |
| Mannitol-exp |
Mannitol-exp: Gluconobacter oxydans 621H was cultivated in mannitol medium with 220 mM (4% w/v) mannitol, 5 g L-1 yeast extract, 1 g L-1 KH2PO4, 1 g L-1 (NH4)2SO4, 2.5 g L-1 MgSO4 x 7 H2O, and 50 µg mL-1 cefoxitin as antibiotic and harvested at an OD600 of 1.4. RNA was isolated and rRNA was depleted with the Ribo-Zero magnetic kit for Gram-negative bacteria (Illumina). For library preparation, the TruSeq stranded mRNA sample preparation kit from Illumina was used according to manufacturer´s instructions with the exception that 5 µl of rRNA-depleted RNA was mixed with 13 µl of Fragment, Prime, Finish Mix and incubated at 94 °C for 4 min for fragmentation and priming. The library was quantified via qPCR with the KAPA Library Quantification Kit (Peqlab) and sequenced on a MiSeq desktop sequencer (Illumina), generating paired-end reads with a read length of 75 bp. |
Illumina MiSeq |
2x75bp paired-end TruSeq stranded mRNA |
ERR2232412 |
