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| Status |
Public on Jun 20, 2017 |
| Title |
De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly |
| Organism |
coral metagenome |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: There is a dearth of knowledge regarding the molecular pathology of growth anomaly in corals. We investigated the gene expression profile of Montipora capitata metatranscriptomes from healthy and diseased (growth anomaly) coral colonies to elucidate differentially expressed genes.
Methods: mRNA profiles of coral tissue (including symbionts) were generated from three different tissue states: healthy, affected and unaffected. Healthy tissue was collected from coral colonies not affected by growth anomaly. Affected tissue was collected from coral growth anomaly lesions. Unaffected tissue was collected from coral colonies affected by growth anomaly.
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| Overall design |
Three distinct tissue types were sampled for this study: (1) healthy tissue from healthy corals, (2) diseased tissue from coral with growth anomaly, (3) apparently healthy tissue from coral with growth anomaly.
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| Contributor(s) |
Frazier M, Helmkampf M, Bellinger R, Geib S, Takabayashi M |
| Citation(s) |
28893194 |
| BioProject |
PRJNA377366 |
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| Submission date |
Apr 17, 2017 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Monika Frazier |
| E-mail(s) |
mfrazier@hawaii.edu
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| Organization name |
University of Hawaii at Hilo
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| Department |
Tropical Conservation Biology and Environmental Science
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| Street address |
200 West Kawili Street
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| City |
Hilo |
| State/province |
HI |
| ZIP/Postal code |
96720 |
| Country |
USA |
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| Platforms (1) |
| GPL23310 |
Illumina HiSeq 2000 (coral metagenome) |
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| Samples (27)
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| GSM2579605 |
Affected coral tissue from Kiholo, Hawaiʻi (Mcap_KA2) |
| GSM2579606 |
Affected coral tissue from Kiholo, Hawaiʻi (Mcap_KA3) |
| GSM2579607 |
Affected coral tissue from Kiholo, Hawaiʻi (Mcap_KA5) |
| GSM2579608 |
Healthy coral tissue from Kiholo, Hawaiʻi (Mcap_KH1) |
| GSM2579609 |
Healthy coral tissue from Kiholo, Hawaiʻi (Mcap_KH2) |
| GSM2579610 |
Healthy coral tissue from Kiholo, Hawaiʻi (Mcap_KH8) |
| GSM2579611 |
Unaffected coral tissue from Kiholo, Hawaiʻi (Mcap_KU2) |
| GSM2579612 |
Unaffected coral tissue from Kiholo, Hawaiʻi (Mcap_KU3) |
| GSM2579613 |
Unaffected coral tissue from Kiholo, Hawaiʻi (Mcap_KU5) |
| GSM2579614 |
Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA1) |
| GSM2579615 |
Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA2) |
| GSM2579616 |
Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA3) |
| GSM2579617 |
Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA4) |
| GSM2579618 |
Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA5) |
| GSM2579619 |
Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA6) |
| GSM2579620 |
Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH1) |
| GSM2579621 |
Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH2) |
| GSM2579622 |
Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH3) |
| GSM2579623 |
Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH4) |
| GSM2579624 |
Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH5) |
| GSM2579625 |
Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH6) |
| GSM2579626 |
Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU1) |
| GSM2579627 |
Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU2) |
| GSM2579628 |
Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU3) |
| GSM2579629 |
Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU4) |
| GSM2579630 |
Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU5) |
| GSM2579631 |
Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU6) |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE97888_Metatranscriptome_denovoassembly.fasta.gz |
167.8 Mb |
(ftp)(http) |
FASTA |
| GSE97888_Metatranscriptome_denovoassembly_isoforms_TPM.tsv.gz |
13.5 Mb |
(ftp)(http) |
TSV |
| GSE97888_Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv.gz |
8.0 Mb |
(ftp)(http) |
TSV |
| GSE97888_Metatranscriptome_qualityfiltered.fasta.gz |
47.7 Mb |
(ftp)(http) |
FASTA |
| GSE97888_Metatranscriptome_qualityfiltered_genes_FPKM.tsv.gz |
3.2 Mb |
(ftp)(http) |
TSV |
| GSE97888_Montiporacapitata_transcriptome.fasta.gz |
13.4 Mb |
(ftp)(http) |
FASTA |
| GSE97888_Montiporacapitata_transcriptome_genes_FPKM.tsv.gz |
732.1 Kb |
(ftp)(http) |
TSV |
| GSE97888_Montiporacapitata_transcriptome_isoforms_TPM.tsv.gz |
716.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data provided as supplementary file |
| Processed data are available on Series record |
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