|
| Status |
Public on Jul 27, 2022 |
| Title |
Free-living cells with L. digitata rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Marine flavobacteria
|
| Organism |
Zobellia galactanivorans |
| Characteristics |
strain: DsijT
carbon source: Laminaria digitata
cell type: free-living
|
| Treatment protocol |
During the exponential phase, 10 ml of culture medium and algal pieces (when applicable) were retrieved on ice. 0.5 volume of killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3) was added to the liquid samples and cell pellets were frozen in liquid nitrogen. Algal pieces were washed twice in killing buffer:H2O (1:1) and frozen in liquid nitrogen. Samples were stored at -80 °C before further RNA extraction.
|
| Growth protocol |
Z. galactanivorans was grown with the respective carbon source (either 10 algal pieces or 4 g/l of purified sugars) at 20 °C under agitation in 50 ml of marine minimum medium supplement with antibiotics to which the strain is resistant. Initial OD = 0.05.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Free-living bacterial cells were lysed by adding 400 μl of lysis buffer (4 M guanidine thiocyanate, 25 mM sodium acetate pH 5.2, 5 g.l-1 N-laurylsarcosinate) and 500 μl of phenol and incubated 5 min at 65 °C. RNA was extracted using phenol-chloroform. Extracts were treated 1 h at 37 °C with 2 units of Turbo DNAse and purified on mini-columns NucleoSpin RNA Clean-up following the manufacturer's instructions. RNA was eluted in 50 μl of nuclease-free water. RNA from algae-attached bacteria was extracted as follows. Two algal pieces were immersed in killing buffer, vortexed and placed 7 min in an ultrasonic bath to detach bacteria from the algal surface. Algae were removed and cell pellets resuspended in lysis buffer. RNA extraction and DNAse treatment were performed as described above for the free-living bacteria. DNAse were inactivated using DNAse inactivation reagent following the manufacturer instructions.
Librairies were performed by the Plateforme de Séquençage I2BC (UMR9198, CNRS, Gif-sur-Yvette) on a NextSeq instrument (Illumina) using the NextSeq 500/550 High Output Kit v2 (75 cycles) which included a Ribo-Zero ribosomal RNA depletion step.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
FL_Ldig2
norm_gene_count_matrix_CarbonSource.txt
|
| Data processing |
Quality filtering using Trimmomatic v0.38.0 on https://galaxy.sb-roscoff.fr
Transcript quantification using Salmon v0.8.2 on https://galaxy.sb-roscoff.fr
Read count noralization and downstream processing analyses were performed using the DESeq2 v1.26.0 package in R v3.6.2.
Genome_build: NC_015844.1
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every genes and every samples from free-living cells. Used for comparison between the different carbon sources.
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every genes in samples from microcosms with L. digitata and F. serratus (free-living and algae-attached cells). Used for comparison between free-living and algae-attached cells.
|
| |
|
| Submission date |
Nov 22, 2021 |
| Last update date |
Jul 27, 2022 |
| Contact name |
Francois Thomas |
| E-mail(s) |
[email protected]
|
| Organization name |
Station Biologique de Roscoff
|
| Department |
UMR8227, CNRS-UPMC
|
| Lab |
Marine Glycobiology group
|
| Street address |
Place George Teissier
|
| City |
Roscoff |
| ZIP/Postal code |
29680 |
| Country |
France |
| |
|
| Platform ID |
GPL30989 |
| Series (1) |
| GSE189322 |
Unraveling the metabolic mechanisms of pioneer bacteria during the utilization of fresh macroalgae |
|
| Relations |
| BioSample |
SAMN23384255 |
| SRA |
SRX13191395 |
