|
| Status |
Public on May 01, 2020 |
| Title |
Diel Cycle (Day 6) |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture of strain IMCC1322
|
| Organism |
Candidatus Puniceispirillum marinum IMCC1322 |
| Characteristics |
strain: IMCC1322
culture condition: Diel Cycle/R2A medium
cell stage: Stationary
|
| Treatment protocol |
[1] Dark culture [2] Light culture : 260 μJ/cm2 Green Light [3] Incubator for Diel cycle: 260 μJ/cm2 Green Light for 14hr and Dark for 10hr.
|
| Growth protocol |
Modified R2A broth prepared in sea water was used for culture medium. Strain IMCC1322 was inoculated in spinner flasks (~1000 ml) and was treated as dark, light, and diel under green LED.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lysates were obtained by direct addition of 2.5 ml Trizol Reagent (Invitrogen) on to the pellets from 300 ml cultures. After adding 0.5 ml BCP phase separation reagent (MRC) upper aqueous total RNA fractions were centrifuged in MaxTract Low Density tubes (Qiagen). RNA solution, RLT buffer, and ethanol (2:7:5) were mixed for Qiagen RNeasy Maxi Kit protocol. Purified and concentrated RNAs were quality-checked on a Bioanalyzer and total RNAs in 10-μg aliquots were purified using MICROBExpress⢠Bacterial mRNA Enrichment Kit (Ambion). For each mRNA from 20 μg of RNA was purified once again on a MICROBExpress⢠kit (Ambion) and was quality-checked as above-mentioned. MessageAmp⢠II-Bacteria RNA Amplification Kit (Ambion) was exploited to amplify mRNA into cRNA. Libraries were prepared according to proprietary reagents from Illumina's and instructions therein. The purified DNA was captured on an Illumina flow cell for cluster generation. Six libraries were sequenced on the Genome Analyzer following the manufacturer's protocols using 36 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the IMCC1322 genome (GenBank Acc. No. CP001751) using Burrows-Wheeler Aligner (BWA) (K-mer=32, mismatch=2); All reads mapping with two or fewer mismatches were retained.
Arithmetic: Filtered and aligned reads were counted using BEDTools (version 2.9) and summarized in BAM file formats.
|
| |
|
| Submission date |
May 20, 2011 |
| Last update date |
May 01, 2020 |
| Contact name |
Hyun-Myung Oh |
| E-mail(s) |
[email protected]
|
| Phone |
+82-51-629-6869
|
| Organization name |
Pukyong National University
|
| Department |
Marine Bio-Cnvergence Science
|
| Lab |
Marine Genomics & Biotechnology Lab
|
| Street address |
Yongdang Campus, Sinseonro 365 Namgu
|
| City |
Busan |
| State/province |
South Korea |
| ZIP/Postal code |
608-739 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13628 |
| Series (1) |
| GSE29423 |
Transcriptome analysis of light-utilizing Strain IMCC1322, a member of SAR116 group bacteria |
|
| Relations |
| SRA |
SRX063956 |
| BioSample |
SAMN00619187 |
