|
| Status |
Public on Dec 22, 2016 |
| Title |
Aerobic, fumarate, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mid-exponential growth phase
|
| Organism |
Actinobacillus succinogenes 130Z |
| Characteristics |
oxygen: Aerobic
substrate: Fumarate with glycerol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TruSeq RNA Sample Preparation Kit (Illumina) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
AsuRPKM.csv
|
| Data processing |
Low quality (Q<30) reads were trimmed at the 5' and 3' ends using the ShortRead package.
Quality controlled read data were aligned on the reference genome sequence using Bowtie2.
DESeq and edgeR package in the Bioconductor/R packages were used for making RPKM values.
Genome_build: Actinobacillus succinogenes strain 130Z (NCBI RefSeq ID: NC_009655.1)
Supplementary_files_format_and_content: CSV file of normalized RPKM value from edgeR for every samples
|
| |
|
| Submission date |
Dec 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
kucsbl submitter |
| E-mail(s) |
[email protected]
|
| Organization name |
Korea University
|
| Department |
Department of Biotechnology
|
| Lab |
Computational and Synthetic Biology Laboratory
|
| Street address |
Anamdong 5-ga, Seongbuk-gu
|
| City |
Seoul |
| State/province |
Seoul |
| ZIP/Postal code |
KS013 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL22828 |
| Series (1) |
| GSE92722 |
Transcriptome of aerobically/anaerobically grown Actinobacillus succinogenes strain 130Z on fumarate/glucose |
|
| Relations |
| BioSample |
SAMN06173550 |
| SRA |
SRX2439480 |
