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| Status |
Public on Mar 03, 2015 |
| Title |
Pelagibacter_T11_Rep_3 |
| Sample type |
SRA |
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| Source name |
Heterotrophic marine bacteria
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| Organism |
Candidatus Pelagibacter ubique HTCC1062 |
| Characteristics |
strain: HTCC1062
growth phase: slow growth
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| Growth protocol |
Batch culture, 19°C, aerated in darkness
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial biomass was collected by vacuum filtration using 0.2 µm-pore-size Durapore filters. The filters were stored at -80°C in RLT buffer until DNA and RNA were extracted using the AllPrep DNA/RNA (Qiagen) kit following the manufacturer's instructions.
RNA libraries were prepared for sequencing using Ribo-Zero rRNA Removal Kit (Bacteria) and TruSeq RNA Sample Prep Kit following Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Candidatus Pelagibacter ubique (HTCC1062)
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| Data processing |
HiSeq Control Software
Rockhopper software (http://cs.wellesley.edu/~btjaden/Rockhopper/)
Genome_build: Candidatus Pelagibacter ubique HTCC1062, complete genome (NC_007205.1), Polaribacter sp. MED152, complete genome (CP004349.1), Ruegeria pomeroyi DSS-3, complete genome (NC_003911.12), Ruegeria pomeroyi DSS-3 megaplasmid (NC_006569.1), marine gamma proteobacterium HTCC2207 scaffolds (NZ_CH672400,NZ_CH672399,NZ_CH672398,NZ_CH672397,NZ_CH672396)
Supplementary_files_format_and_content: Excel file containing Rockhopper output
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| Submission date |
Mar 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Cottrell |
| E-mail(s) |
[email protected]
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| Phone |
302 645 4383
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| Organization name |
University of Delaware
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| Street address |
700 Pilottown Rd
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| City |
Lewes |
| ZIP/Postal code |
19958 |
| Country |
USA |
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| Platform ID |
GPL19838 |
| Series (1) |
| GSE66443 |
Transcriptional control in Candidatus Pelagibacter ubique and other marine bacterial taxa |
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| Relations |
| BioSample |
SAMN03382909 |
| SRA |
SRX895283 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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