|
| Status |
Public on Aug 11, 2022 |
| Title |
d73_minus_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CL14
|
| Organism |
Variovorax paradoxus |
| Characteristics |
bacteria: d73
iaa: No
rep: Rep1
treatment: d73_minus
strain: CL14
|
| Treatment protocol |
Cultures were supplemented with 15mM succinate and 0.5% (v/v) ethanol alone or containing IAA. IAA was at a final concentration of 0.1 mg/mL in the medium to which it was added. Cultures were prepared at a starting OD600 of 0.02 and incubated at 28°C, shaking at 250rpm.
|
| Growth protocol |
V. paradoxus CL14 was grown in 5mL cultures of M9 minimal medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from all samples were harvested for RNA-Seq at 18 hours to ensure IAA was still present in the cultures of strains that degraded IAA most rapidly. Cells were pelleted by centrifuging the culture at 4,200 x g for 15 min and removing the supernatant. Cell pellets were frozen at -80°C prior to RNA extraction. To extract RNA, cells 27 were lysed in TRIzol Reagent (Invitrogen) according to the manufacturer instructions for lysis and phase separation.
After these steps RNA was purified from the aqueous phase using the RNeasy Mini kit (Qiagen) including the optional on-column DNase Digestion with RNase-Free DNase Set (Qiagen). Total RNA was quantified using the Qubit 2.0 fluorometer (Invitrogen) and RNA-seq libraries were prepared using the Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete kit (Tecan) according to the manufacturer instructions. The resulting libraries were pooled and sequenced on the Illumina HiSeq4000 to generate 50 bp single-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
d73_minus_Rep1
|
| Data processing |
Briefly, the raw reads were mapped to the Variovorax paradoxus CL14 genome (fasta file available on: https://github.com/isaisg/variovoraxRGI/blob/master/rawdata/2643221508.fna) using bowtie2 with the ‘very sensitive’ flag. Hits to each individual coding sequence were counted and annotated using the function featureCounts from the R package Rsubread , inputting the Variovorax paradoxus CL14 gff file (available on: https://github.com/isaisg/variovoraxRGI/blob/master/rawdata/2643221508.gff) and using the default parameters with the flag allowMultiOverlap = FALSE.
|
| |
|
| Submission date |
Aug 10, 2022 |
| Last update date |
Aug 11, 2022 |
| Contact name |
Isai Salas Gonzalez |
| E-mail(s) |
[email protected]
|
| Phone |
919-537-3890
|
| Organization name |
The University of North Carolina at Chapel Hill
|
| Street address |
250 Bell Tower Drive, Room 4244
|
| City |
Chapel Hill |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL32559 |
| Series (1) |
| GSE210968 |
Structure, function and microbial ecology of diverse MarR bacterial regulators of auxin catabolism |
|
| Relations |
| BioSample |
SAMN30244238 |
| SRA |
SRX17025371 |
