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| Status |
Public on Feb 19, 2024 |
| Title |
rnc_GDSR_aerob_3 |
| Sample type |
SRA |
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| Source name |
rnc_GD48,49SR (rnc-)
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| Organism |
Cereibacter sphaeroides |
| Characteristics |
cell line: rnc_GD48,49SR (rnc-)
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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, Nucelic 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 NovaSeq 6000 |
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| Description |
Rhodobacter sphaeroides rnc mutant grown under aerobic conditions, rep 3
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| Data processing |
Alignment of FASTQ files against the Cereibacter 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 the READemption v.1.0.5.
Read counts per gene were calculated using the summarizedOverlaps.
DESeq2 v.1.32 was used for the normalization of the reads and the identification of transcriptional changes.
Additionally, bona fide RNase III cleavage sites were identified.
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: wiggle format containing the total read coverage merged from the biological triplicates
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| Submission date |
Jul 07, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Gabriele Klug |
| E-mail(s) |
[email protected]
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| Organization name |
Justus-Liebig University Gießen
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| Department |
Molecular- and Microbiology
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| Street address |
Heinrich-Buff-Ring 26-32
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| City |
Gießen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
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| Platform ID |
GPL33350 |
| Series (1) |
| GSE236804 |
Transcriptome analysis of the Rhodobacter sphaeroides RNase III mutant (inactivated enzyme) by total RNA sequencing |
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| Relations |
| BioSample |
SAMN36367229 |
| SRA |
SRX20943685 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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