|
| Status |
Public on Jan 26, 2024 |
| Title |
CoIP_6037FLAG_exponential |
| Sample type |
SRA |
| |
|
| Source name |
Immunoprecipitated RNA from Rhodobacter sphaeroides expressing CcaF1-3xFLAG grown under phototrophic conditions to mid exponential growth phase
|
| Organism |
Cereibacter sphaeroides |
| Characteristics |
genotype: expressing CcaF1-3xFLAG
treatment: grown under phototrophic conditions to mid exponential growth phase
|
| Treatment protocol |
Cells were harvested either during exponential growth phase of after 48h of growth.
|
| Growth protocol |
Cells were grown anaerobically, illuminated with 80 W*m^2 white light in malate minimal medium (phototrophic conditions).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA and immunoprecipated RNA were isolated as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146)
RNA was processed as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146); NEBnext Multiplex Small RNA Library Prep Set
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All reads were trimmed for adaptor sequences using trim-galore (version 0.6.3), low-quality reads have been rejected in the same data processing step. Options were set to -q 10 --length 15 -j 8
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 (version 0.4.3) subcommand align with the integrated mapper segemehl (version 0.2.0)
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: wiggle format
|
| |
|
| Submission date |
Apr 19, 2023 |
| Last update date |
Jan 26, 2024 |
| Contact name |
Gabriele Klug |
| E-mail(s) |
[email protected]
|
| 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 |
GPL33350 |
| Series (1) |
| GSE230031 |
RIPSeq analysis (CoIP) of CcaF1 from R. sphaeroides 2.4.1 under phototrophic growth conditions |
|
| Relations |
| BioSample |
SAMN34247395 |
| SRA |
SRX20007057 |
