|
| Status |
Public on Apr 26, 2022 |
| Title |
W_S_Fe |
| Sample type |
SRA |
| |
|
| Source name |
Wild type strain grown on switched energy source from S0 to Fe(II)
|
| Organism |
Acidithiobacillus ferrooxidans ATCC 23270 |
| Characteristics |
genotype: wildtype
|
| Growth protocol |
The cells of A. ferrooxidans ATCC 23270 wild type and the Δcyc2 mutant were prepared in two ways. One was unvaried Fe(II) energy substrate by using the inoculum cultivated from 9K-Fe(II) medium and the other was altered Fe(II) energy substrate by employing the inoculum cultured from 9K-S0 medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested after the ferric precipitates produced or sulfur powder remained was intercepted by qualitative filter papers. Total RNA was then extracted with TRIzolTM reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
W_S_Fe
|
| Data processing |
RTA 2.7.3 was used for basecalling and bcl2fastq2-v2.16 was used for file conversion
Remove reads with adaptors, remove reads in which unknown bases are more than 10%, remove low-quality reads (the percentage of low quality bases is over 20% in a read), then map to A. ferrooxidans ATCC 23270 reference genome using SOAPaligner/SOAP2.
Expression levels of genes were determined based on the value of RPKM, which is the abbreviation of reads per kilobase per million mapped reads.
Genome_build: A. ferrooxidans ATCC 23270
Supplementary_files_format_and_content: txt files include RPKM values for all genes that have a difference express
|
| |
|
| Submission date |
Jan 02, 2019 |
| Last update date |
Apr 26, 2022 |
| Contact name |
Xiangmei Liu |
| Organization name |
Shandong University
|
| Department |
State Key laboratory of Microbial Technology
|
| Street address |
72 Binhai Road
|
| City |
Qingdao |
| State/province |
Shandong Province |
| ZIP/Postal code |
266237 |
| Country |
China |
| |
|
| Platform ID |
GPL25999 |
| Series (1) |
| GSE124570 |
Genome-wide transcriptome profiling of Acidithiobacillus ferrooxidans ATCC 23270 in response to the cyc2 knockout |
|
| Relations |
| BioSample |
SAMN10685779 |
| SRA |
SRX5194587 |
