|
| Status |
Public on Dec 06, 2022 |
| Title |
T7_minus_P1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Nodularia spumigena CCY9414 |
| Characteristics |
strain: CCY9414
cell type: bacterial cells
treatment: phosphate starvation (P-deplete)
time: day7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell cultures were preserved with a 5% phenol(v/v in ethanol) stop solution for 20 min prior to cell harvesting via centrifugation. Cell pellets were suspended in 1 ml TRIzol reagent, followed by bead-beating, incubation at 65°C for 10 min, and RNA extraction according to Steunou et al. (2006). RNA extracts were DNase I digested for 30 min and purified with phenol/chloroform followed by sodium acetate precipitation.
mRNA non-stranded library preparation with rRNA depletion performed by LGC, Biosearch Technologies, Berlin, Germany
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
culture sample of Nodularia spumigena CCY9414 cultivated in limiting conditions of phosphate and collected after 7 days (biol rep 1)
|
| Data processing |
Removal of adapters performed by the sequencing company. Those files are provided as raw data. Quality trimming was performed with BBduk.
Mapping against reference genome with bwa-mem. Removal of rRNA reads. Mapped reads were further filtered to remove secondary and supplementary alignments, as well as alignments shorter than 50 bp and those with less than 95% sequence identity across the whole read to the reference.
Mapped reads per gene were counted with featureCounts.
Differential gene expression was assessed with DESeq2 based on the count table.
Further details on data processing are available on: https://git.io-warnemuende.de/bio_inf/IOWseq000008_Cyanobloom_RNAseq_Nodularia
Assembly: GCF_000340565.2_ASM34056v3
Supplementary files format and content: tab-delimited read count matrix; column names correspond to the sample title specified in the SAMPLES section; row names refer to the locus tag as in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/340/565/GCF_000340565.2_ASM34056v3/GCF_000340565.2_ASM34056v3_genomic.gff.gz
|
| |
|
| Submission date |
Sep 14, 2022 |
| Last update date |
Dec 06, 2022 |
| Contact name |
Christiane Hassenrück |
| E-mail(s) |
christiane.hassenrueck@io-warnemuende.de
|
| Organization name |
Leibniz Institute for Baltic Sea Research Warnemünde (IOW)
|
| Department |
Biological Oceanography
|
| Street address |
Seestraße 15
|
| City |
Rostock-Warnemünde |
| ZIP/Postal code |
18119 |
| Country |
Germany |
| |
|
| Platform ID |
GPL32673 |
| Series (1) |
| GSE213384 |
Acclimation of Nodularia spumigena CCY9914 to inorganic phosphate limitation |
|
| Relations |
| BioSample |
SAMN30860337 |
| SRA |
SRX17584676 |
