|
| Status |
Public on Feb 01, 2024 |
| Title |
AP64, 4 hours after the shift to light, dark control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
AP64
|
| Organism |
Gemmatimonas phototrophica |
| Characteristics |
tissue: AP64
cell type: 4 hours after the shift to light, dark control
genotype: WT
|
| Treatment protocol |
After reaching approx. OD600 = 0.2 cultures were illuminated with photon flux density of 100 µmol photons m-2 s-1 for 2, 4, and 8 hours
|
| Growth protocol |
G. phototrophica AP64T (= DSM 29774) was grown in an optimized liquid medium described earlier (Shivaramu et al., 2023) at 25°C. At the beginning of the experiment, the inoculum (approx. OD600 = 0.2) was diluted in 100 mL of a fresh medium to approx. OD600 = 0.03. Cultures were grown aerobically at dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells from triplicate cultures were harvested by centrifugation, resuspended in 1 mL PGTX extraction solution (Pinto et al., 2009) and immediately frozen in liquid nitrogen. RNA was extracted as described earlier (Kopejtka et al., 2020).
Libraries were generated according to the protocol of Shishkin et al. (2015) including rRNA removal with the RiboZero Kit (Illumina, USA) and sequenced on a NovaSeq 6000 (Illumina, USA) in paired-end mode with 100 cycles in total.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
22_AP64_Post4h_DA
|
| Data processing |
Raw reads were processed, and differential gene expression was assessed as described before (Kopejtka et al., 2020).
Quality filtered reads were mapped to the G. phototrophica AP64T genome (GenBank accession number GCF_000695095.2) using bowtie2.
Normalization and identification of significantly differentially regulated genes (FDR < 0.01) was performed with edgeR.
Assembly: GCF_000695095.2
Supplementary files format and content: text file includes counts for each sample
|
| |
|
| Submission date |
Jan 16, 2024 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Karel Vaclav Kopejtka |
| E-mail(s) |
kopejk00@alga.cz
|
| Phone |
+420777623254
|
| Organization name |
Institute of Microbiology Czech Acad. Sci.
|
| Department |
Centre Algatech
|
| Lab |
Laboratory of Anoxygenic Phototrophs
|
| Street address |
Novohradska
|
| City |
Trebon |
| ZIP/Postal code |
37981 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL32851 |
| Series (1) |
| GSE253351 |
Transcriptional response of Gemmatimonas phototrophica to changing light regimes [AP64_LowLight] |
|
| Relations |
| BioSample |
SAMN39459290 |
| SRA |
SRX23231235 |
