|
| Status |
Public on Jan 06, 2013 |
| Title |
HA+H2O2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Corynebacterium glutamicum ATCC 13032 |
| Characteristics |
genotype/variation: 10 mM H2O2 adapted (HA)
condition: MCGC+10 mM H2O2
strain: ATCC 13032
|
| Treatment protocol |
The wild-type strain grown (OD600=3.0) under no stress condition and HA strain grown (OD600=3.0) under 10 mM H2O2 condition in MCGC minimal medium were harvested for RNA isolation.
|
| Growth protocol |
Cells were grown in a 500 ml baffled flask containing 50 ml MCGC minimal medium. Actively growing cells (OD600nm = 3) were harvested by centrifugation, and the pellets were used for RNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested from C. glutamicum cells using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and NucleoSpin® (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions with the following modifications. Cells were harvested by centrifugation, resuspended in TRIzol® reagent, and transferred to a vial containing Lysing Matrix B® (MP Biomedicals, Solon, OH, USA) for lysis. The suspension was centrifuged, and the supernatant was applied to a NucleoSpin® RNA II kit for purification.
Library construction protocol: First and second strand cDNA synthesis was carried out using the Ovation® Prokaryotic RNA-Seq System (NuGEN Technologies Inc., San Carlos, CA, USA), and NuGEN’s Encore NGS Library System was applied to construct the cDNA library for the Illumina Genome Analyzer II platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Xpression (https://depts.washington.edu/cshlab/html/rnaseq.html) was used for RNA-Seq data processing.
Xpression was used for filtering and trimming reads.
Reference files for the genome sequence being queried, Corynebacterium glutamicum ATCC13032 genome (BX927147.1) were uploaded.
Raw sequencing reads (FASTQ) were processed by Xpression and only the uniquely mapped reads were subjected to further analysis.
The number of reads overlapping each gene was recorded and normalized based on reads per kilobase per million (RPKM) uniquely mapped reads.
genome build: BX927147.1
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Sep 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Joo-Young Lee |
| E-mail(s) |
joo02@catholic.ac.kr
|
| Phone |
+82-2-2164-4964
|
| Fax |
+82-2-2164-4965
|
| Organization name |
The Catholic University of Korea
|
| Department |
Department of Biotechnology
|
| Lab |
Molecular Microbiology & Metabolic Engineering
|
| Street address |
43-1 Yokgok2-dong
|
| City |
Bucheon |
| State/province |
Gyonggi |
| ZIP/Postal code |
420-743 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16168 |
| Series (1) |
| GSE41232 |
Adaptive evolution of Corynebacterium glutamicum resistant to oxidative stress and its global gene expression profiling |
|
| Relations |
| SRA |
SRX193574 |
| BioSample |
SAMN01761008 |
