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| Status |
Public on Dec 28, 2022 |
| Title |
rne_phototroph_Rep_2 |
| Sample type |
SRA |
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| Source name |
bacterial cells
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| Organism |
Cereibacter sphaeroides |
| Characteristics |
growth condition: phototrophic
genotype: RNase E mutant
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| Treatment protocol |
Cells were harvested during exponential growth phase.
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| Growth protocol |
Cells were grown in malate minimal medium, either in presence of high oxygen concentration of 180 µM dissolved oxygen (aerobic cultures), low oxygen concentration of 25 µM dissolved oxygen (microaerobic cultures) or without oxygen but illuminated with 60 W*m-2 white light (phototrophic cultures).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Rhodobacter sphaeroides rne-ts mutant grown under phototrophic conditions, rep 2
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| Data processing |
Alignment of FASTQ files against the Rhodobacter sphaeroides 2.4.1 genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) was performed using READemption v.1.0.5.
Read counts per gene were calculated using the summarizedOverlaps function.
DESeq2 v.1.32 was used for the normalisation of the reads and the identification of transcriptional changes.
Additionally, bona fide RNase E cleavage sites or 5’ends enriched in the mutant were identified.
Assembly: Rhodobacter sphaeroides 2.4.1
Supplementary files format and content: Comma separated files include raw read counts per gene for each sample.
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| Submission date |
Apr 18, 2022 |
| Last update date |
Dec 28, 2022 |
| Contact name |
Tobias Friedrich |
| E-mail(s) |
tobias.friedrich@pennmedicine.upenn.edu
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| Organization name |
University of Pennsylvania
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| Street address |
421 Curie Boulevard
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| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL32157 |
| Series (1) |
| GSE200990 |
Transcriptome analysis and 5‘-end mapping of total RNA from Rhodobacter sphaeroides wild type and RNase E (rne) mutant strain, grown under aerobic, microaerobic or phototrophic conditions |
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| Relations |
| BioSample |
SAMN27622487 |
| SRA |
SRX15245614 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6048083_rne_phototroph_2.csv.gz |
16.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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