|
| Status |
Public on Apr 25, 2020 |
| Title |
Elm_HC_es_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cultivated cell colony
|
| Organism |
Eubacterium limosum |
| Characteristics |
substrate: H2/CO2
growth phase: early-stationary phase
strain: KIST612
|
| Growth protocol |
E. limosum KIST612 was cultivated separately supplemented with 20 mM glucose or 101 kPa of gaseous CO or H2/CO2 (80:20, v/v) as a substrate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from E. limosum KIST612 at the mid-log and early-stationary phases. The RNAprotect Bacterial Reagent and an RNeasy Mini Kit (Qiagen, Germany) were used for RNA isolation and a Ribo-zero rRNA Removal Kit (Epicentre, USA) was used for ribosomal RNA removal.
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 |
HCes1
|
| Data processing |
Read data were aligned on the reference genome sequence.
DESeq and edgeR package in the Bioconductor/R packages were used for making RPKM values.
Base-calling by the MiSeq platform
Alignment by Bowtie software
Using R packages for DEG analysis
Genome_build: Eubacterium limosum KIST612 (GenBank ID: GCA_000152245.2)
Supplementary_files_format_and_content: TSV file of normalized RPKM value from edgeR for every samples.
|
| |
|
| Submission date |
Apr 24, 2020 |
| Last update date |
Apr 26, 2020 |
| Contact name |
kucsbl submitter |
| E-mail(s) |
kucsbl.group@gmail.com
|
| 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 |
GPL23275 |
| Series (1) |
| GSE149269 |
RNA-seq analysis of Eubacterium limosum KIST612 across different carbon/energy/electron sources and growth phases. |
|
| Relations |
| BioSample |
SAMN14688106 |
| SRA |
SRX8170771 |
