organism: Sinorhizobium meliloti 1021
description: Protocols: Rm1021 cells (OD600 = 0.5) were challenged in 10 mL TY medium with 25 μg/mL of DgDef1 delta SP delta CTPP in 50 mL conical tubes at 30ºC, 150 rpm for 1h. The negative control was challenged with acetonitrile:water (1:3). Assays were performed in triplicates. Cells were centrifuged at 10.000 rpm for 5 min and supernatant was removed. Cell pellets were used for RNA isolation. For RNA isolation, cells pellets were resuspended in 1 mL of QIAzol lysis reagent and homogenized in a FastPrep® sample preparation system (3 x 6.500 rpm, 20 sec, 15 sec break) using Lysing Matrix B containing 0.1 mm silica beads (MP biomedicals, cat. no. 6911). Suspensions were then i) incubated 5 min at 15-25 ºC and 140 μl of chloroform was added; ii) shaken vigorously for 15 sec and incubated for 3 min at 15-25 ºC, centrifuged (12.000 rpm, 15 min, 4ºC) to collect the upper aqueous phase, which was subsequently mixed with 1.5 volumes of absolute ethanol. The protocol proceeded with the miRNeasy Mini Kit (Qiagen, cat. no. 217004) according to the manufacturer's instructions with an on-column DNase digestion.Since only a single library was prepared for each condition (i.e., treated and untreated), attention was paid to include RNA representing the four independent biological replicates in order to minimize the possibility of results biased by sample choice. Pooled samples used for RNAseq contained equal amounts of RNA from each biological replicate. rRNA depletion was conducted with the Illumina Ribo-Zero rRNA removal Kit (Bacteria). The cDNA library was prepared using the NEB Ultra directional Kit
identifiers.namespace: BioSample
identifiers.id: SAMEA11299073
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2022-11-16
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2022-11-16
attributes.tag: External Id
attributes.value: SAMEA11299073
attributes.tag: INSDC center alias
attributes.value: Center for Synthetic Microbiology Philipps-Universitat Marburg
attributes.tag: INSDC center name
attributes.value: Center for Synthetic Microbiology Philipps-Universitat Marburg
attributes.tag: INSDC first public
attributes.value: 2022-11-16T00:13:37Z
attributes.tag: INSDC last update
attributes.value: 2022-11-16T00:13:37Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-11181:S. meliloti untreated control
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: developmental stage
attributes.value: vegetative growth
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: organism part
attributes.value: whole organism
attributes.tag: sample name
attributes.value: E-MTAB-11181:S. meliloti untreated control