Stenvers, Vanessa; Hauss, Helena; Schmittmann, Lara; Bayer, Till; Havermans, Charlotte; Hentschel, Ute; Sweetman, Andrew K; Hoving, Henk-Jan T (2023): Transcriptome expression in Periphylla periphylla exposed to sediment plumes and increasing temperatures [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.962217
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Abstract:
This dataset comprises gene expression data in the deep pelagic jellyfish Periphylla periphylla exposed to anthropogenic disturbance. Specifically, we tested the effects of ocean warming and sediment plumes from deep-sea mining during ex situ experiments, using Periphylla collected in the Lurefjord and Sognefjord, Norway, in 2021. Gene expression is given in normalised counts for each expressed transcript (for both the temperature and suspended sediment separately). Moreover, this dataset lists all significantly expressed transcripts and their summary statistics (e.g. log2 fold change), as identified with Likelihood Ratio Tests (LRT) in DESeq2 (Love et al. 2014), in addition to transcript annotations performed with Trinotate v3.2.1 searching the Blastx, Blastp, Pfam, UniProt-SwissProt, GO, eggNOG and KEGG databases (Bryant et al. 2017).
Keyword(s):
Supplement to:
Stenvers, Vanessa; Hauss, Helena; Bayer, Till; Havermans, Charlotte; Hentschel, Ute; Schmittmann, Lara; Sweetman, Andrew K; Hoving, Henk-Jan T (2023): Experimental mining plumes and ocean warming trigger stress in a deep pelagic jellyfish. Nature Communications, 14(1), 7352, https://doi.org/10.1038/s41467-023-43023-6
Related to:
Stenvers, Vanessa; Hauss, Helena; Schmittmann, Lara; Bayer, Till; Havermans, Charlotte; Hentschel, Ute; Sweetman, Andrew K; Hoving, Henk-Jan T (2023): Microbial community composition associated with Periphylla periphylla exposed to sediment plumes and increasing temperatures. PANGAEA, https://doi.org/10.1594/PANGAEA.957395
Stenvers, Vanessa; Hauss, Helena; Schmittmann, Lara; Bayer, Till; Havermans, Charlotte; Hentschel, Ute; Sweetman, Andrew K; Hoving, Henk-Jan T (2023): Physiological and behavioural responses of the deep pelagic jellyfish Periphylla periphylla exposed to sediment plumes and increasing temperatures. PANGAEA, https://doi.org/10.1594/PANGAEA.957367
References:
Bryant, Donald M; Johnson, K; DiTommaso, Tia; Tickle, Timothy; Couger, Matthew Brian; Paytin-Dogru, Duygu; Lee, Tae J; Leigh, Nicholas D; Kuo, Tzu-Hsing; Davis, Francis G; Bateman, Joel; Bryant, Sevara; Guzikowski, Anna R (2017): A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. 18(3), 762-776, https://doi.org/10.1016/j.celrep.2016.12.063
Love, Michael; Huber, Wolfgang; Anders, Simon (2014): Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550, https://doi.org/10.1186/s13059-014-0550-8
Project(s):
Funding:
Horizon 2020 (H2020), grant/award no. 818123: Integrated Assessment of Atlantic Marine Ecosystems in Space and Time
Coverage:
Median Latitude: 56.347740 * Median Longitude: 0.211790 * South-bound Latitude: 47.250220 * West-bound Longitude: -10.104630 * North-bound Latitude: 61.100000 * East-bound Longitude: 5.585000
Date/Time Start: 2020-12-09T10:34:15 * Date/Time End: 2021-11-20T17:30:00
Minimum Elevation: -4427.2 m * Maximum Elevation: 0.0 m
Event(s):
Lurefjord_Norway_Periphylla_Sampling_1 * Latitude: 60.693000 * Longitude: 5.155000 * Date/Time Start: 2021-03-07T12:30:00 * Date/Time End: 2021-03-15T16:30:00 * Elevation Start: -470.0 m * Elevation End: 0.0 m * Location: Norwegian fjord
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Binary Object | Binary | Stenvers, Vanessa | Transcriptomic analysis | ||
| 2 | Binary Object (Media Type) | Binary (Type) | Stenvers, Vanessa | Transcriptomic analysis | ||
| 3 | Binary Object (File Size) | Binary (Size) | Bytes | Stenvers, Vanessa | Transcriptomic analysis | |
| 4 | File content | Content | Stenvers, Vanessa | Transcriptomic analysis |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Basic curation (CurationLevelB) * Processing Level: PANGAEA data processing level 1 (ProcLevel1)
Size:
2 data points
Data
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| 1 Binary | 2 Binary (Type) | 3 Binary (Size) [Bytes] | 4 Content |
|---|---|---|---|
| Stenvers-etal_2023_Periphylla_Transcriptomics.xlsx | application/vnd.openxmlformats-officedocument.spreadsheetml.sheet | 18.3 MBytes | Gene expression counts |