|
| Status |
Public on Sep 13, 2024 |
| Title |
rne_phototrophic_72h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
rne(ts) strain (substitution of native rne gene with thermosensitive rne gene from E. coli)
|
| Organism |
Cereibacter sphaeroides 2.4.1 |
| Characteristics |
cell line: rne(ts) strain (substitution of native rne gene with thermosensitive rne gene from E. coli)
treatment: phototrophic growth to late stationary phase
|
| Treatment protocol |
Cells were grown under microaerobic or phototrophic conditions and harvested during exponential or late stationary growth phase.
|
| Growth protocol |
Independent biological triplicates of each strain were grown in malate minimal medium under microaerobic (~25 µM dissolved oxygen) or phototrophic (anaerobic and illuminated with 60 W per square meter) growth conditions to exponential or late stationary growth phase (72 hours).
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Biologoical replicate 2
|
| Data processing |
The software Curare v0.6 Blumenkamp et al., 2024) was used for the differential gene expression analysis. The raw sequencing data was adapter trimmed and quality filtered (phred score < 20 filtered out) with fastp v0.23.4 (Chen et al., 2018 ). Afterward, the reads were aligned to the reference genome of R. sphaeroides (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2 and NC_009008.1) using bowtie2 v2.5.2 (Langmead and Salzberg) and saved as binary alignment maps (BAM) with Samtools v1.18 (Danecek et al., 2021 ).
The differential gene expression analysis used subreads featureCounts v2.0.6 (Yang et al., 2014) for counting and DESeq2 v1.40.2 (Love et al., 2014) for the statistical analyses. Counting was done in featureCounts with "-s 1 -M --fraction" options on the "gene" level, and the NCBI GFF file for assembly GCF_000012905.2 was used as an annotation.
The alignments were summarized as bedgraph files using deeptools' v3.5.4 bamCoverage function [Ramirez et al., 2016). The coverage data (bedgraph files) was normalized by dividing each data point/base position by the total read number in each sample. For the screenshots, the replicates of each condition were averaged by the arithmetic mean.
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: count tabl/gene expression matrixe created with featureCounts in tab-separated format
|
| |
|
| Submission date |
Jul 10, 2024 |
| Last update date |
Sep 13, 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 |
GPL34692 |
| Series (1) |
| GSE271933 |
Transcriptome analysis by total RNA sequencing of Cereibacter sphaeroides RNase E, RNase III or StsR mutant strains grown to stationary phase |
|
| Relations |
| BioSample |
SAMN42396813 |
| SRA |
SRX25267402 |
