|
| Status |
Public on Jun 26, 2022 |
| Title |
Wild-type, stationary phase, biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Prokaryotic cell
|
| Organism |
Clostridium sp. AWRP |
| Characteristics |
cell type: Prokaryotic cell
strain: AWRP
genotype: WT
growth phase: stationary phase
|
| Treatment protocol |
The harvested culture was stabilized by mixing with 2 volumes of RNAProtect Bacteria reagent (Qiagen) and incubating at room temperature for 20 min
The stabilized cells were harvested and resuspended in 100 μL of the lysozyme solution (15 mg/mL in 30 mM Tris Cl and 1 mM EDTA) and 10 μL of the proteinase K solution (Qiagen)
|
| Growth protocol |
The wild-type AWRP and acetated adapted strain were cultivated in a bioreactor containing basal medium with the gas substrate (20% CO2 and 80% H2)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted manually using RiboEX solution (GeneAll, Republic of Korea).
RNA libraries for RNA-seq were prepared using Truseq RNA sample prep (Illumina) according to manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw reads were assembled and aligned with the reference AWRP genome by using TopHat2 v2.0.13
The differential expression was analyzed by using the Cuffdiff v2.2.0
Assembly: ASM400639v2
Supplementary files format and content: mean values of FPKM obtained from two biological replicates
|
| |
|
| Submission date |
Jun 23, 2022 |
| Last update date |
Jun 26, 2022 |
| Contact name |
Soo Jae Kwon |
| E-mail(s) |
skwon@kiost.ac.kr
|
| Phone |
01077076084
|
| Organization name |
KIOST
|
| Street address |
KIOST, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City, KOREA
|
| City |
Busan |
| ZIP/Postal code |
49111 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL32381 |
| Series (1) |
| GSE206757 |
Effect of long-term adaptation of an acetogenic bacterium Clostridium sp. AWRP under acetate stress |
|
| Relations |
| BioSample |
SAMN29261714 |
| SRA |
SRX15837283 |
