NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8186531 Query DataSets for GSM8186531
Status Public on Apr 09, 2024
Title StC in N-fix biol3
Sample type SRA
 
Source name bacterial cell
Organism Carbonactinospora thermoautotrophica
Characteristics strain: StC
cell type: bacterial cell
treatment: Autotrophic condition
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 sample3
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 SAMN40741645
SRA SRX24146177

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap