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| Status |
Public on Jul 11, 2017 |
| Title |
1001957_OCT_Contact3 |
| Sample type |
SRA |
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| Source name |
Small Octopus
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| Organism |
Vibrio vulnificus |
| Characteristics |
strain: FORC_036
treatment: Contact
time: 1 h
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| Treatment protocol |
We artificially contact the FORC_036 strain to small octopus, and contact to small octopus for 1 h, and 4 h. Non-contact strain to crab in VFGM medium also prepared as negative control.
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| Growth protocol |
FORC_036 was grown to mid-log phase (A600 of 0.8) in VFMG (Vibrio fisheri minimal medium containing glycerol) medium
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer's procedure. The DNA contaminations were removed by TURBO DNase (AMbion, Austin, TX), and then extracted RNAs were cleaned up using RNeasy MinElute Cleanup kit (Qiagen). The extracted RNA was verified by Agilent 2100 Bioanalyzer with Agilent RNA 6000 Nano reagens (Agilent Technologies, Waldbronn, Germany).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 2 (1-2)
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| Data processing |
The Ribo-Zero rRNA removal kit (Epicentre, USA) was used for ribosomal RNA depletion according to manufacturer instructions.
Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA sample prep kit (Illumina, USA) following the manufacturer’s protocol.
The quality of cDNA libraries was determined by Agilent 2100 Bioanalyzer (Agilent Technologies). Strand-specific paired-ended 100 nucleotide reads from each cDNA library were obtained using HiSeq2500 (Illumina).
For biological replication, two libraries were separately constructed and sequenced from RNAs isolated from two independent filtered culture supernatants of FORC_036.
The reads obtained from RNA-sequencing were mapped to the FORC_036 reference genome using CLC Genomics Workbench ver. 7.5.1 (CLC bio, Aarhus, Denmark). The GenBank (http://www.ncbi.nlm.nih.gov) accession numbers of the reference genome are CP015512 (Chromosome I), CP015513 (Chromosome II), and CP015514 (Plasmid)
Genome_build: ASM211720v1 [CP015512 (Chromosome I), CP015513 (Chromosome II), and CP015514 (Plasmid)]
Supplementary_files_format_and_content: Count calculation by Cuffquant and Cuffdiff
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| Submission date |
Jul 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Han Young Chung |
| E-mail(s) |
robin302@naver.com
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| Phone |
82-2-880-4864
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| Organization name |
Seoul National University
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| Street address |
1 Gwanak-ro, Gwanak-gu, Seoul 151-742
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| City |
Seoul |
| ZIP/Postal code |
151-742 |
| Country |
South Korea |
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| Platform ID |
GPL23679 |
| Series (1) |
| GSE101055 |
Transcriptome analysis of virulence factors in Vibrio vulnificus FORC_036, isolated from a surf clam |
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| Relations |
| BioSample |
SAMN07338865 |
| SRA |
SRX2993290 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2698735_1-2.count.txt.gz |
25.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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