|
| Status |
Public on Nov 23, 2020 |
| Title |
anaerobically grown cells rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Acidithiobacillus ferrooxidans |
| Characteristics |
strain: CCM 4253
growth: anaerobic
electron donor: hydrogen
electron acceptor: ferric iron
|
| Treatment protocol |
–
|
| Growth protocol |
Acidithiobacillus ferrooxidans strain CCM 4253 was grown aerobically (electron acceptor O2) and anaerobically (electron acceptor Fe3+) in the atmosphere enriched by H2 (electron donor) and CO2 (carbon source) in sealed jars at 30 °C and agitated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted with a TRI reagent (Sigma-Aldrich) and was treated with a TURBO DNA-free kit (Ambion) to remove the contaminating DNA.
The cDNA libraries were constructed using the ScriptSeq™ Complete Kits (Bacteria) (Illumina), including Ribo-ZeroTM technology for ribosomal RNA removing and ScriptSeq v2 RNA-Seq Library Preparation Kit.
Sequencing was performed on the Illumina MiSeq platform with MiSeq Reagent Kit v2 (500-cycles), which generated 250-bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
AFE5
|
| Data processing |
Quality control of reads was performed using R package ShortRead.
Subsequently, reads were aligned to the genome sequence of the At. ferrooxidans CCM 4253 (GCA_003233765.1) using the software BBmap.
R package DeSeq2 was used for differential analysis of count data. Transcripts with a |log2 fold change| > 1 and q < 0.05 (FDR-adjusted P-values) were considered as significantly change.
Genome_build: GCA_003233765.1
Supplementary_files_format_and_content: Tab-delimited text file includes gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for every gene and every sample
|
| |
|
| Submission date |
Jul 21, 2020 |
| Last update date |
Nov 23, 2020 |
| Contact name |
Jiri Kucera |
| E-mail(s) |
jiri.kucera@sci.muni.cz
|
| Organization name |
Masaryk University
|
| Department |
Department of Biochemistry
|
| Street address |
Kamenice 753/5
|
| City |
Brno |
| ZIP/Postal code |
625 00 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL28899 |
| Series (1) |
| GSE154815 |
Transcriptome profiling of hydrogen-oxidizing Acidithiobacillus ferrooxidans |
|
| Relations |
| BioSample |
SAMN15590243 |
| SRA |
SRX8783923 |
