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Status |
Public on Jun 26, 2022 |
Title |
46T-a, exponential phase, biol rep 2 |
Sample type |
SRA |
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Source name |
Prokaryotic cell
|
Organism |
Clostridium sp. AWRP |
Characteristics |
cell type: Prokaryotic cell strain: 46T-a genotype: Acetate-adapted strain growth phase: exponential 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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
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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
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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 |
SAMN29261711 |
SRA |
SRX15837286 |