|
| Status |
Public on Aug 03, 2021 |
| Title |
2.4.1 d0827 exp_3 |
| Sample type |
SRA |
| |
|
| Source name |
d0827 exp
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
strain: 2.4.1 d0827
genotype: StsR deletion
|
| Treatment protocol |
Cells were harvested during indicated growth phases (exponential, 72h, 72h outgrowth, 144h, 144h outgrowth).
|
| Growth protocol |
All cultures were grown in malate minimal medium under microaerobic conditions (25 μM dissolved oxygen) at 32°C and 140 rpm in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the hot phenol method and remaining DNA was removed by a DNaseI treatment (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline subcommand align with the integrated mapper segemehl
READemption was used for gene quantification with parameters gene_quanti
READemption with DESeq2 was used to perform the differential gene expression analysis, subcommand deseq
Genome_build: GCF_000012905.2 ASM1290v2
Supplementary_files_format_and_content: xlsx contain raw counts and DESeq2 analysis
Supplementary_files_format_and_content: wig files contain merged total read coverage
|
| |
|
| Submission date |
Jun 02, 2021 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Gabriele Klug |
| E-mail(s) |
Gabriele.Klug@mikro.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig University Gießen
|
| Department |
Molecular- and Microbiology
|
| Street address |
Heinrich-Buff-Ring 26-32
|
| City |
Gießen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL28141 |
| Series (1) |
| GSE175997 |
Transcriptome analysis of total RNA from Rhodobacter sphaeroides 2.4.1 wildtype and StsR (RSs0827) deletion strain during different growth phases |
|
| Relations |
| BioSample |
SAMN19513404 |
| SRA |
SRX11049138 |
