|
| Status |
Public on May 03, 2023 |
| Title |
So ce836, Day 21, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Sorangium sp. |
| Characteristics |
strain: So ce836
cell type: bacterial cell
time: Day 21
|
| Growth protocol |
Pre-cultures of Sorangium sp. So ce836 were grown in CYH-medium for 4 days at 28°C with shaking at 160 rpm. Subsequently, 90 mL H-medium were inoculated with 10 mL of pre-culture, with five replicates for each growth period (0, 4, 7, 11, 14, and 21 days). Culture flasks were incubated at 28°C with shaking until the corresponding growth time was reached.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy Mini kit (Qiagen). After removal of residual DNA with DNase Turbo (Ambion), RNA was precipiated with three volumes of 100% ethanol at -20°C and redissolved in RNase-free water. Ribosomal RNA was depleted by applying the Ribo-off kit (Absource).
RNA libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
DESeq2_normalized_counts_So_ce836.txt
|
| Data processing |
Reads were preprocessed with fastp (version 0.20.1)
Trimmed reads were mapped to the reference genome (GenBank accession: CP102233) with an in-house script using BWA-MEM (version 0.7.12) and SAMtools (version 0.1.19)
Reads mapping to genes were counted with HTSeq-count with mode union and stranded reverse (version 0.13.5)
Read counts were normalized and filtered with DESeq2 (version 1.32.0)
Assembly: GenBank accession: CP102233
Supplementary files format and content: tab-delimited files (.tsv) include raw read counts per gene for each sample
Supplementary files format and content: tab-delimited text file (.txt) includes read counts per gene (rows) and per sample (columns) after DESeq2 normalization
|
| |
|
| Submission date |
Nov 07, 2022 |
| Last update date |
May 03, 2023 |
| Contact name |
Janina Leinberger |
| E-mail(s) |
janina.leinberger@gmx.de
|
| Organization name |
University of Oldenburg
|
| Department |
Institute for Chemistry and Biology of the Marine Environment
|
| Street address |
Ammerländer Heerstraße 114-118
|
| City |
Oldenburg |
| ZIP/Postal code |
26129 |
| Country |
Germany |
| |
|
| Platform ID |
GPL32843 |
| Series (1) |
| GSE217497 |
Surges in biosynthetic gene cluster transcription are accompanied by bursts in natural compound production in the myxobacterium Sorangium sp. So ce836 |
|
| Relations |
| SRA |
SRX18200687 |
| BioSample |
SAMN31648030 |
