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OAS accession Detail for 0291923
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| accessions_id: | 0291923 | archive |
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| Title: | NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ) from 2018-06-20 to 2018-06-23 (NCEI Accession 0291923) |
| Abstract: | This dataset contains biological, optical, physical, and survey - biological data collectedat Bergen, Norway from 2018-06-20 to 2018-06-23. These data include irradiance, species, and water temperature. The instruments used to collect these data include Automated DNA Sequencer. These data were collected by Kristen E. Whalen of Haverford College and Elizabeth Harvey of Skidaway Institute of Oceanography as part of the "Collaborative Research: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics (HHQSignals)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2020-07-31. The following is the text of the dataset description provided by BCO-DMO: Transcriptomic response of Emiliania huxleyi to HHQ Dataset Description: Sequences from this study are available at the NCBI GEO under accession series GSE131846 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE131846 |
| Date received: | 20200731 |
| Start date: | 20180620 |
| End date: | 20180623 |
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| Observation types: | biological, optical, physical, survey - biological |
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| Datatypes: | irradiance, SPECIES IDENTIFICATION, WATER TEMPERATURE |
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| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
| Collecting institutions: | Haverford College, Skidaway Institute of Oceanography |
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| Supplementary information: | Acquisition Description: Batch 2 L cultures of axenic Emiliania huxleyi strain CCMP2090 were grown in natural seawater-based f/2-Si medium (Guillard 1975) in sterile acid-washed polycarbonate bottles. Cultures were maintained on a 14:10 light (80 +/- 5 µmol photons m⁻² s⁻¹):dark cycle at 17.5 - 17.8 ᵒC. After 48 hr of growth, quadruplicate 2 L cultures were exposed to either 1 ng/ml, 10 ng/ml, or 100 ng/ml concentrations of 2-heptyl-4-quinolone (HHQ). Quadruplicate bottles were also exposed to dimethyl sulfoxide (DMSO) to serve as a vehicle control (final concentration 0.002% DMSO in all bottles). Cell biomass was collected 24 hr and 72 hr after treatment via centrifugation (9,000 RPM for 8 min at 4 ᵒC) of 400 ml of culture and total RNA extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommendations using 350 µl RLT plus buffer per sample and the optional centrifugation (14,000 RPM for 1 min) step to ensure membranes were dry prior to elution with 30 µl RNase free water. Eluent was reapplied to the membrane, and incubated for 8 min at room temperature before repeating the elution step to increase yield. Strand-specific RNAseq library construction was performed using the KAPA Stranded mRNA-Seq library preparation kit with KAPA mRNA capture beads (Kapa Biosystems) and sequenced on the NextSeq platform (Illumina) to generate 75 bp paired-end reads. |
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| Metadata version: | 1 |
| Keydate: | 2024-04-27 17:06:45+00 |
| Editdate: | 2024-04-27 17:07:05+00 |