Data · collection
Proteomic Signatures of Corals from Thermodynamic Reefs (NCEI Accession 0216077)
Listed in NASA Earthdata CMR
In this work, I took a protein profiling approach known as iTRAQ approach to characterize and quantify the proteins synthesized by 12 experimental coral samples.
Description
Specifically, corals were collected from an upwelling site in the Luzon Strait ("Houbihu;" 21°56â18.01ââN, 120°44â45.54ââE) and a non-upwelling "control" site in the nearby Taiwan Strait ("Houwan;"22°01'23.30"N, 120°41'18.29"E) and exposed to either highly variable (upwelling-simulating) or stable temperatures in the laboratory for seven days prior to sacrificing for protein analysis (the "Seriatopora hystrix variable temperature study" [SHVTS]).
In this submission, I have uploaded the proofs of the manuscript describing the proteomic data (Mayfield in press Microorganisms), two RAW files (SHVTS-A & SHVTS-B for iTRAQ batches A & B, respectively), two MZML (open-access mass spectrometry data) files (SHVTS-A.mzml & SHVTS-B.mzml), two MZID files (SHVTS-A.mzid & SHVTS-B.mzid), and a tab-delineated file that describes which samples were labelled with which iTRAQ tag ("Mayfield online supplemental data file").
Read the rest (2 more)
I have also uploaded the supplemental material that accompanies the Mayfield (in press) article since that is what readers interested in the specifics of the proteomic analysis pipeline should consult. The peak data were queried against a conceptually translated S. hystrix-Cladocopium dinoflagellate transcriptome described in Mayfield et al. (2016 Mol Ecol) and found here: symbiont.iis.sinica.edu.tw/s_hystrix/static/html/#stat.
Please note that all proteomic data represent a mix of multiple organisms (namely the anthozoan host and the dinoflagellate endosymbionts that inhabit their gastrodermal cells). All data analysis was conducted with Proteome Discoverer (Thermo-Fisher Scientific).
Links
Get the data
- ncei.noaa.gov /archive/accession/0216077 ↗
Navigate directly to the URL for a descriptive web page with download links.
download · from NASA CMR
- ncei.noaa.gov /archive/accession/download/216077 ↗
Navigate directly to the URL for data access and direct download.
download · from NASA CMR
- ncei.noaa.gov /archive/accession/oas/216077 ↗
Navigate directly to the URL for a descriptive web page with download links.
download · from NASA CMR
- ftp-oceans.ncei.noaa.gov /nodc/archive/arc0159/0216077 ↗
These data are available through the File Transfer Protocol (FTP). You may use any FTP client to download these data.
download · from NASA CMR
Documentation and papers
- MassIVE Metadata Record massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=558adcff310b48279b6692dbe3ea41c0 ↗
documentation · from NASA CMR
- doi.org /10.1242/jeb.071688 ↗
Mayfield, A.B., Chan, P.H., Putnam, H.P., Chen, C.S., Fan, T.Y. 2012. The effects of a variable temperature regime on the physiology of the reef-building coral Seriatopora hystrix: results from a labo
documentation · from NASA CMR
- doi.org /10.3390/microorganisms8081171 ↗
Mayfield, A.B. 2020. Proteomic Signatures of Corals from Thermodynamic Reefs. Microorganisms 8, 1171. https://doi.org/10.3390/microorganisms8081171
documentation · from NASA CMR
- Preview graphic ncei.noaa.gov/access/metadata/landing-page/bin/gfx?id=gov.noaa.nodc%3A0216077 ↗
preview image · from NASA CMR
Catalogue records · 2
- CMR record cmr.earthdata.nasa.gov/search/concepts/C2089376733-NOAA_NCEI.html ↗
catalogue entry · from NASA CMR
- CMR UMM-JSON cmr.earthdata.nasa.gov/search/concepts/C2089376733-NOAA_NCEI.umm_json ↗
metadata API · from NASA CMR
Topics
- Stated by source
- Coral Reefs · mass spectrometer · Not provided · Ocean Chemistry · swimmer/diver
- Inferred from text
- Mass spectrometry 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NASA Earthdata CMR | C2089376733-NOAA_NCEI | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[instrument].gcmd_instrument:mass-spectrometer | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[instrument].gcmd_instrument:swimmer-diver | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[measured_variable].gcmd:earth-science/oceans/ocean-chemistry | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[measured_variable].gcmd:earth-science/solid-earth/geomorphic-landforms-processes/coastal-landforms/coral-reefs | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| concepts[modality].local:modality:mass-spectrometry | enrichment · NASA CMR | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[platform].gcmd_platform:not-provided | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| description | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/Abstract |
| license_text | source · NASA CMR | connector:nasa_cmr@1.0.0 | |
| spatial | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/SpatialExtent |
| temporal | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/TemporalExtents |
| title | source · NASA CMR | connector:nasa_cmr@1.0.0 | /umm/EntryTitle |
| version_label | source · NASA CMR | connector:nasa_cmr@1.0.0 |