Dataset: Supplementary Table 4B: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes

Name: Supplementary Table 4B: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes
Published: 2020-06-22
Keywords: Atlantis bank, transcriptomes, gene expression, gabbro, oceanic crust, metabolic pathways, oceans

Final no updates expectedDOI: 10.26008/1912/bco-dmo.812997.1Version 1 (2020-06-22)Dataset Type:Other Field Results

Principal Investigator, Contact: Virginia P. Edgcomb (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Karen Soenen (Woods Hole Oceanographic Institution)

Program: International Ocean Discovery Program (IODP)

Project: Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches (Subseafloor Lower Crust Microbiology)

Abstract

Supplementary Table 4B: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes. Samples taken on board of the R/V JOIDES Resolution between November 30, 2015 and January 30, 2016.

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Centroid: latitude: -32.70567, longitude: 57.278183
Temporal Extent: 2015-11-30 - 2016-01-30

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Methods

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. doi:10.1093/bioinformatics/btu170

Methods

Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., … Tiedje, J. M. (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research, 37(Database), D141–D145. doi:10.1093/nar/gkn879

Methods

Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., … Bateman, A. (2015). The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research, 44(D1), D279–D285. doi:10.1093/nar/gkv1344

Methods

Glassing, A., Dowd, S. E., Galandiuk, S., Davis, B., & Chiodini, R. J. (2016). Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathogens, 8(1). doi:10.1186/s13099-016-0103-7

Methods

Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. . (2001). Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen. Journal of Molecular Biology, 305(3), 567–580. doi:10.1006/jmbi.2000.4315

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Dataset: Supplementary Table 4B: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes

Final no updates expectedDOI: 10.26008/1912/bco-dmo.812997.1Version 1 (2020-06-22)Dataset Type:Other Field Results

Principal Investigator, Contact: Virginia P. Edgcomb (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Karen Soenen (Woods Hole Oceanographic Institution)

Program: International Ocean Discovery Program (IODP)

Project: Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches (Subseafloor Lower Crust Microbiology)

Abstract

Cite Dataset

Centroid: latitude: -32.70567, longitude: 57.278183
Temporal Extent: 2015-11-30 - 2016-01-30

XXX

Views

XX

Downloads

X

Citations

Related Datasets

No Related Datasets

Related Publications

Methods

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. doi:10.1093/bioinformatics/btu170

Methods

File(s)	Type	Description	Action
annotations.csv (29.22 KB)	Comma Separated Values (.csv)	A .csv data file associated with dataset 812997: Supplementary Table 4B - Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes.	Download

Supplemental File(s)	Type	Description	Action
sample_location_depth.xlsx (9.23 KB)	Octet Stream	A .xlsx file containing the location (latitude and longitude in decimal degrees)and the depth below seafloor (dbsf) of the samples.	Download

File(s)	Type	Description	Action
annotations.csv (29.22 KB)	Comma Separated Values (.csv)	A .csv data file associated with dataset 812997: Supplementary Table 4B - Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes.	Download

Supplemental File(s)	Type	Description	Action
sample_location_depth.xlsx (9.23 KB)	Octet Stream	A .xlsx file containing the location (latitude and longitude in decimal degrees)and the depth below seafloor (dbsf) of the samples.	Download

Dataset: Supplementary Table 4B: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes

Principal Investigator, Contact: Virginia P. Edgcomb (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Karen Soenen (Woods Hole Oceanographic Institution)

Program: International Ocean Discovery Program (IODP)

Project: Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches (Subseafloor Lower Crust Microbiology)

Abstract

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Dataset: Supplementary Table 4B: Annotations for contigs within transcriptome libraries for the eleven samples that were manually curated for selected metabolic processes

Principal Investigator, Contact: Virginia P. Edgcomb (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Karen Soenen (Woods Hole Oceanographic Institution)

Program: International Ocean Discovery Program (IODP)

Project: Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches (Subseafloor Lower Crust Microbiology)

Abstract

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