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Sample GSM6261898 Query DataSets for GSM6261898
Status Public on Jun 26, 2022
Title 46T-a, exponential phase, biol rep 2
Sample type SRA
 
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.
 
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 SAMN29261711
SRA SRX15837286

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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