<div><p>Six clones of high light II Prochlorococcus VOL4, a streptomycin-resistant derivative of strain MIT9312 were isolated by dilution to extinction in Pro99 media pretreated with the helper bacterium Alteromonas sp. strain EZ55. Prochlorococcus clones were made axenic by addition of streptomycin. For co-culture experiments, Alteromonas bacteria were introduced to Prochlorococcus cultures prior to growth experiments. Alteromonas was diluted onto YTSS agar plates and each Prochlorococcus culture was inoculated with a single separate colony. Alteromonas stock cultures were grown in YTSS liquid medium and cryopreserved in 20% glycerol at -80 C.</p>
<p>Each of the six Prochlorococcus clones was grown in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.</p>
<p>The mRNA libraries were prepared for Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).</p>
<p>RNA extractions were performed with the RNeasy Mini Kit.</p></div>
Clones of Prochlorococcus MIT9312 and link to BioProject
<div><p>This dataset includes a link to Prochlorococcus clone NCBI BioProject and associated metadata.<br /><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729" target="_blank">PRJNA377729</a><a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729" target="_blank">: </a><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729" target="_blank">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729</a></p></div>
Pro_ancestor
<div><p>Sequence reads were de-multiplexed and trimmed to remove sequencing barcodes. Trimmed reads were aligned to both the MIT9312 gene models (accession: NC_007577.1) and the draft EZ55 genome (Genbank accession TBD) using bowtie2 with sensitive end-to-end mode. Reads aligning to coding sequences in the MIT9312 gene models were counted with samtools idxstats. Reads aligning to the EZ55 draft genome were counted with HT-seq count.</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added links to NCBI BioProject page<br />
- replaced blanks with nd (no data)</p></div>
688162
Pro_ancestor
2017-04-24T13:41:55-04:00
2017-04-24T13:41:55-04:00
2023-07-07T16:10:26-04:00
urn:bcodmo:dataset:688162
Clones of Prochlorococcus MIT9312 mixed with clonal isolates of the heterotrophic "helper" bacterium Alteromonas EZ55 (P-ExpEv project)
Clones of Prochlorococcus MIT9312 mixed with clonal isolates of the heterotrophic "helper" bacterium Alteromonas EZ55 (P-ExpEv project).
false
Dyhrman, S. T., Morris, J. J. (2021) Clones of Prochlorococcus MIT9312 mixed with clonal isolates of the heterotrophic "helper" bacterium Alteromonas EZ55 (P-ExpEv project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-04-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.688162.1 [access date]
true
1
10.26008/1912/bco-dmo.688162.1
false
2017-04-24
Datapackage.json
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https://www.bco-dmo.org/dataset/688162/datapackage.json
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PDF
https://www.bco-dmo.org/dataset/688162/Dataset_description.pdf
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ISO 19115-2 (NOAA Profile)
https://www.bco-dmo.org/dataset/688162/iso
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688162
http://lod.bco-dmo.org/id/dataset/688162
2015-12 - 2015-12
2015-12
--12
2015
2015-12
--12
2015