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13 results for “Emiliania huxleyi”
The Emiliania huxleyi stoichiometry database
<p>The <em>Emiliania huxleyi</em> stoichiometry database contains data for the growth rate, cellular elemental content (particulate inorganic carbon - PIC, organic carbon - C, nitrogen - N and phosphorous - P) and C:N:P stoichiometry (PIC:C, C:N, N:P, C:P) compiled through a meta-analysis of literature reporting the results of laboratory experiments (cultures) on the coccolithophore species <em>Emiliania huxleyi</em>, an important calcifying marine phytoplankton.</p> <p>The database also reports selected additional parameters including cell size and/or volume, and chlorophyll<em> a </em>as well as additional meta-data associated with the original data source including strain details and culture experimental conditions. A description of the parameters contained in the database can be found in the file "The Emiliania huxleyi stoichiometry database data description".</p> <p>Please cite this dataset as:</p> <p>Sheward et al. (2023) The <em>Emiliania huxleyi</em> stoichiometry database. doi:10.5281/zenodo.7594880</p>
Scanning electron microscopy datasets -- Emiliania huxleyi strains from naturally high and low CO2 waters responding to high and low CO2 in the lab
<p>Study question: How do Emiliania huxleyi strains isolated from naturally high CO2 waters or low CO2 waters respond to exposure to high and low CO2 levels?</p> <p> </p> <p>Associated article:<br> Peter von Dassow, Francisco Díaz-Rosas, El Mahdi Bendif, Juan-Diego Gaitán-Espitia, Daniella Mella-Flores, Sebastian Rokitta, Uwe John, and Rodrigo Torres. 2018. Over-calcified forms of the coccolithophore <em>Emiliania huxleyi </em>in high-CO2 waters are not preadapted to ocean acidification. Biogeosciences. <a href="https://doi.org/10.5194/bg-15-1-2018">https://doi.org/10.5194/bg-15-1-2018</a></p> <p> </p> <p>Technical notes:</p> <p>Three electron microscopes were used:</p> <ol> <li>TM3000 (Hitachi High-Technologies, Tokyo, Japan) in the Unidad de Microscopía Avanzada of the Facultad de Ciencias Biológicas, Pontificia Univesidad Católica de Chile. The Hitachi microscope is not of high quality, and, when available, other electron microscopes were used.</li> <li>Quanta 250 (FEI, Hillsboro, Oregon, USA) in the Facultad de Geología, Universidad de Chile</li> <li>Quanta FEG 250 (FEI, Hillsboro, Oregon, USA) in the laboratory CIEN-UC, Facultad de Física, Pontificia Universidad Católica de Chile.</li> </ol> <p> </p> <p>Data set 1: Data-sharing-SEM_Calfuco-CO2 experiment.zip</p> <p>Scanning electron microscopy images of E. huxleyi strains after bubbling with 1200 µatm CO2 and 400 µatm CO2 air/CO2 mixes.</p> <p> </p> <p>Data set 2: Field-SEM-2011-2013.zip</p> <p>Scanning electron microscope images of filters of plankton samples taken during field campaigns. See article for methodology. For the samples from ElQuisco_2012 and JuanFernandez_2011, note that the last two digits in the sample name refer to the depth from which the sample was obtained (ej., “FQ.01.01.05D” is from 5 m and “FQ.01.01.15D” is from 15 m). Tables are provided to associate counts and taxonomic identifications to environmental variables from the samples for which data was used in statistical analysis. Note also that images do not correspond to all counts reported, as sometimes counts were made without capturing images due to time pressure for microscope use. </p>
Supplemental data for the publication: "The Role of Vitamin D in Emiliania huxleyi: A Microalgal Perspective on UV-B Exposure"
<p>The following table contains raw transcriptomic data of Emiliania huxleyi CCMP3266 grown under continuous UV radiation or control conditions for 7, 10, and 13 days, obtained using the MARS-seq protocol (Keren-Shaul H. et al. 2013)</p> <p>Column A - Gene ID (Sperfeld M. et al. 2023)<br> Column B - NCBI accession number<br> Columns C - T: raw read counts<br> Columns U - AL: normalized read counts<br> Columns AM - BD: rlog transform read counts<br> Columns BE - FB: Every 6 columns represent differential expression data between two treatments (time point or UV/nonUV)<br> Columns FC - FK: Functional annotations automatically generated, as previously described (Sperfeld M. et al. 2023)</p>
Supplemental data for the publication: "The Role of Vitamin D in Emiliania huxleyi: A Microalgal Perspective on UV-B Exposure"
<p>The following table contains raw transcriptomic data of Emiliania huxleyi CCMP3266 grown under continuous UV radiation or control conditions for 7, 10, and 13 days, obtained using the MARS-seq protocol (Keren-Shaul H. et al. 2013)</p> <p>Column A: E. huxleyi CCMP3266 gene locus IDs<br> Column B: E. huxleyi CCMP3266 representative gene transcripts<br> Columns C: Best matching transcripts in E. huxleyi CCMP1516<br> Columns D - U: Raw read counts<br> Columns V - AM: DESew2 normalized read counts<br> Columns AN - BE: rlog transformed read counts.<br> Columns BF - FC: Each block of 6 columns represents the results of the differential gene expression analysis between two treatments (time point or UV/nonUV).<br> Columns FD - FJ: Functional annotations </p>
Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi
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Scanning electron microscopy image dataset -- Abundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonian fjords and channels
<p>Data set 1: E.huxleyi_morphotypes_Patagonia.zip</p> <p>Scanning electron microscopy images of <em>Emiliania huxleyi</em> cells found inhabit the southern Patagonia fjords during the late-spring 2015 and early-spring 2017.</p> <p> </p> <p>Data set 2: E.huxleyi_abundances_Patagonia.zip</p> <p>Scanning electron microscope images of filters of plankton samples taken in 2015 and 2017 throughout southern Patagonia fjords.</p> <p>The "m" in sample name refer to the depth from which the sample was obtained. </p> <p>Tables are provided to associate <em>Emiliania huxleyi</em> morphotypes' counts and taxonomic identifications to environmental variables from the samples for which data was used in statistical analysis.</p>
Growth and morphological measurements of the coccolithophore Emiliania huxleyi under three salinity conditions
<p>Three datasets presenting results from laboratory culture experiments with the coccolithophore <em>Emiliania huxleyi</em> (Norwegian coastal strain PLYB11 and Mediterranean Sea strain RCC1232) grown for a duration of 156 h under salinity 25 (hyposaline/low salinity), salinity 35 (control) and salinity 45 (hypersaline/high salinity) conditions.<br><br>Cell concentrations and cell size (mean and standard deviation of triplicate counts) were measured using a CASY automated cell counter. Morphometric measurements of coccolith length, coccosphere size and number of coccoliths per cell were measured on scanning electron microscopy images. </p> <p>Supplementary Fig. S1 shows scanning electron microscopy (SEM) images of E. huxleyi coccosphere from strains PLYB11 and RCC1232 under salinity 25, 35, 45 conditions during the early (first 48 h), middle (76-100 h), and end (last 48 h) of each 156-h experiment. A full caption is included within the image file.</p> <p><br><br>These datasets are associated with the following manuscript:</p> <p>Sheward, R. M., Gebühr, C., Bollmann, J. and Herrle, J. O. Short-term response of <em>Emiliania huxleyi</em> growth and morphology to abrupt salinity stress. EGUsphere (preprint), https://doi.org/10.5194/egusphere-2024-349.</p> <p> </p> <p>Correspondence to: Rosie M. Sheward (sheward@em.uni-frankfurt.de)</p>
Scanning electron microscopy datasets -- Emiliania huxleyi strains from naturally high and low CO2 waters responding to high and low CO2 in the lab
<p>Study question: How do Emiliania huxleyi strains isolated from naturally high CO2 waters or low CO2 waters respond to exposure to high and low CO2 levels?</p> <p> </p> <p>Associated article:<br> Peter von Dassow, Francisco Díaz-Rosas, El Mahdi Bendif, Juan-Diego Gaitán-Espitia, Daniella Mella-Flores, Sebastian Rokitta, Uwe John, and Rodrigo Torres. 2018. Over-calcified forms of the coccolithophore <em>Emiliania huxleyi </em>in high-CO2 waters are not preadapted to ocean acidification. Biogeosciences. <a href="https://doi.org/10.5194/bg-15-1-2018">https://doi.org/10.5194/bg-15-1-2018</a></p> <p> </p> <p>Technical notes:</p> <p>Three electron microscopes were used:</p> <ol> <li>TM3000 (Hitachi High-Technologies, Tokyo, Japan) in the Unidad de Microscopía Avanzada of the Facultad de Ciencias Biológicas, Pontificia Univesidad Católica de Chile. The Hitachi microscope is not of high quality, and, when available, other electron microscopes were used.</li> <li>Quanta 250 (FEI, Hillsboro, Oregon, USA) in the Facultad de Geología, Universidad de Chile</li> <li>Quanta FEG 250 (FEI, Hillsboro, Oregon, USA) in the laboratory CIEN-UC, Facultad de Física, Pontificia Universidad Católica de Chile.</li> </ol> <p> </p> <p>Data set 1: Data-sharing-SEM_Calfuco-CO2 experiment.zip</p> <p>Scanning electron microscopy images of E. huxleyi strains after bubbling with 1200 µatm CO2 and 400 µatm CO2 air/CO2 mixes.</p> <p> </p> <p>Data set 2: Field-SEM-2011-2013.zip</p> <p>Scanning electron microscope images of filters of plankton samples taken during field campaigns. See article for methodology. For the samples from ElQuisco_2012 and JuanFernandez_2011, note that the last two digits in the sample name refer to the depth from which the sample was obtained (ej., “FQ.01.01.05D” is from 5 m and “FQ.01.01.15D” is from 15 m). Tables are provided to associate counts and taxonomic identifications to environmental variables from the samples for which data was used in statistical analysis. Note also that images do not correspond to all counts reported, as sometimes counts were made without capturing images due to time pressure for microscope use. </p> <p> </p>
Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms.
GEO Series GSE24341. Emiliania huxleyi virus 163; Emiliania huxleyi; Emiliania huxleyi virus 86; marine metagenome. 85 samples. Type: Expression profiling by array.
The Role of Vitamin D in Emiliania huxleyi: A Microalgal Perspective on UV-B Exposure
GEO Series GSE243677. Emiliania huxleyi. 18 samples. Type: Expression profiling by high throughput sequencing.
Emiliania huxleyi (UNC1419) reference transcriptome
<p>Reference transcriptome and associated annotations for <em>Emiliania huxleyi </em>(UNC1419). </p> <p>A culture was grown into late exponential phase for filtration. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol except for an initial bead beating step and two instead of one chloroform steps to separate proteins and DNA. RNA libraries were created with the KAPA Stranded mRNA-Seq kit for Illumina platforms. The library was sequenced on an Illumina MiSeq (300 bp, paired-end reads) and an Illumina HiSeq 2500 with one lane in high output mode (100 bp, paired-end reads) and another lane in rapid run mode (150 bp, paired-end reads).</p> <p>Raw reads were trimmed for quality with Trimmomatic v0.36 then assembled <em>de novo </em>with Trinity v2.5.1 with the default parameters for paired-reads and a minimum contig length of 90 bp. Contigs were clustered based on 99% similarity using CD-HIT-EST v4.7 and then protein sequences were predicted with GeneMark S-T. Protein sequences were annotated by best-homology (lowest E-value) with the KEGG (Release 86.0), UniProt (Release 2018_03), and PhyloDB (v1.076) databases via BLASTP v2.7.1 (E-value ≤ 10<sup>-5</sup>) and with Pfam 31.0 via HMMER v3.1b2 (Dataset S2). KEGG Ortholog (KO) annotations were assigned from the top hit with a KO annotation from the top 10 hits (<a href="https://github.com/ctberthiaume/keggannot">https://github.com/ctberthiaume/keggannot</a>).</p> <p>Provided here are predicted proteins as nucleotides and peptides. Raw reads are deposited in SRA (SRP234650).</p>
LongSAGE transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi
GEO Series GSE8376. Emiliania huxleyi CCMP1516. 3 samples. Type: Expression profiling by SAGE.
Transcriptional response of Emiliania huxleyi CCMP2090 exposed to the bacterial signaling molecule 2-heptyl-4-quinolone
GEO Series GSE131846. Emiliania huxleyi CCMP1516. 36 samples. Type: Expression profiling by high throughput sequencing.
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