|
| Status |
Public on Jun 01, 2018 |
| Title |
Succinate_3 |
| Sample type |
SRA |
| |
|
| Source name |
Rhodococcus EP4 culture
|
| Organism |
Rhodococcus rhodochrous |
| Characteristics |
growth-phase: mid-log
compound: succinate
media: M9-Goodies
|
| Treatment protocol |
1.0 mM each compound as carbon source
|
| Growth protocol |
Rhodococcus EP4 for RNA extraction grown at 30°C grown to mid-log phase on M9-Goodies with 1.0 mM of each compound in 50ml Erlenmeyer flasks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol RNA extraction
Ribosomal RNA depletion with Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) + TruSeq LT (Illumina) library preparation
1 lane (1/9 samples per lane) HiSeq4000 100bp-PE sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Rhodococcus EP4 Succinate 3
|
| Data processing |
Filtered to Q30 using Trimmomatic 0.3.6
Mapped to transcriptome with bowtie2
Quantified with Salmon
Normalized counts with deseq2
Genome_build: https://www.ncbi.nlm.nih.gov/genome/11941?genome_assembly_id=367165
Supplementary_files_format_and_content: Normalized deseq2 counts (.csv)
|
| |
|
| Submission date |
Mar 22, 2018 |
| Last update date |
Jun 01, 2018 |
| Contact name |
David Levy-Booth |
| E-mail(s) |
[email protected]
|
| Organization name |
University of British Columbia
|
| Department |
Microbiology and Immunology
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24760 |
| Series (1) |
| GSE112193 |
Rhodococcus EP4 Aromatic Transcriptomics |
|
| Relations |
| BioSample |
SAMN08771265 |
| SRA |
SRX3830333 |
