|
| Status |
Public on Apr 09, 2024 |
| Title |
StC in N-fix+NH3Cl2 biol5 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Carbonactinospora thermoautotrophica |
| Characteristics |
strain: StC
cell type: bacterial cell
treatment: carbon gasses; organic nitrogen NH4Cl3
|
| Treatment protocol |
The cells of StC were grown for four days at 60 °C
|
| Growth protocol |
The cells of StC were grown under three different conditions: i) autotrophically in a N-FIX solid culture medium with a gas atmosphere (CO/CO2/N2/O2); ii) heterotrophically in R2A culture medium (glucose and peptone as carbon and nitrogen source respectively) solidified with Noble Ágar (Sigma-Aldrich); II)N-FIX solid culture medium with a gas atmosphere (CO/CO2) Aand NH4Cl2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from the same sample using NucleoSpin TriPrep kit (Macherey-Nagel). 100 ug of a total RNA was used for Total RNA for the construction the sequencing libraries
RNA libraries for RNA-seq were prepered using using the KAPA mRNA HyperPrep Kits (Roche) by following the manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
sample15
|
| Data processing |
The library cleaning step was performed using Trimmomatic Ver. 0.39, where possible adapters and low-quality bases were removed from the raw data files.
Reads from each library were mapped against the C. thermoautotrophica StC genome using Bowtie2 Ver. 2.3.4.3 (Li et al., 2023). Mapping text files (SAM) were converted to binary format (BAM) using Samtools Ver. 0.1.20 (Li et al., 2009), and then used to count mapped reads by genes. HTSeq Ver. 2.0.3 (Siddique et al., 2021) was used to perform the step of counting of mapped reads over the genome, and the expression values were normalized to TPM (Transcript Per Million).
Supplementary files format and content: text format of raw counts
|
| |
|
| Submission date |
Apr 03, 2024 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Luis Willian Pacheco Arge |
| Organization name |
UFRJ
|
| Department |
Genetica
|
| Lab |
LGMBV
|
| Street address |
Av. Carlos Chagas Filho, 373
|
| City |
Rio de Janeiro |
| State/province |
Rio de Janeiro |
| ZIP/Postal code |
21941-590 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL34357 |
| Series (1) |
| GSE263135 |
Co-existence of CBB cycle and rTCA carbon fixation pathway in thermophilic Actinomycetota Carbonactinospora thermoautotrophica StC and correlation with the CO2-concentrating microcompartment |
|
| Relations |
| BioSample |
SAMN40741634 |
| SRA |
SRX24146188 |
