title: Illumina MiSeq sequencing; RNA-Seq of sorted and unsorted prophage-induced subpopulations in Corynebacterium glutamicum
design: RNA-Seq of sorted and unsorted prophage-induced subpopulations in Corynebacterium glutamicum
library_construction_protocol: Strain ATCC 13032, harvesting cells after cultivation and/or sorting using a FACS device.  First the cells were grown in BHI complex media for 5 to 6 hours. After this, the cells that were starved to iron by cultivating them under low iron conditions (1 µM) over night. In the next day the cells were used to inoculate a new culture under normal iron conditions (36 µM). In the iron shift experiments a plasmid based reporter was used. This reporter system consists of the venus gene cloned under the control of a promoter of the SOS-response gene divS. For large volumes:  RNeasy Kit (Qiagen, Hilden, Germany), cell disruption was performed with glass beads  For small volumes (sorted samples): NucleoZol (Machery-Nagel, Düren, Germany) was used, cell disruption was performed with lysozyme + mutanlysin large sample volumes: rRNA depletion was done using Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) (Epicentre/illumina, Munich, Germany)  small volumes: a "Protocol for Removal of rRNA from Small Amounts of Total RNA” from Clontech used  All libraries were generated using: TruSeq Stranded emRNA Library Prep Kit (Illumina, Munich, Germany)
attributes.tag: Experimental Factor: stimulus
attributes.value: iron shift
attributes.tag: Experimental Factor: compound
attributes.value: none
attributes.tag: Experimental Factor: phenotype
attributes.value: negative
attributes.tag: Experimental Factor: protocol
attributes.value: 10^6 cells, RNAprotect