Dataset: Supplementary Table 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences, FPKM values

Name: Supplementary Table 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences, FPKM values
Published: 2020-07-01
Keywords: Atlantis bank, transcriptomes, gene expression, gabbro, oceanic crust, metabolic pathways, oceans

Final no updates expectedDOI: 10.26008/1912/bco-dmo.812936.1Version 1 (2020-07-01)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 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences: FPKM values. 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

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

Methods

Lagesen, K., Hallin, P., Rødland, E. A., Stærfeldt, H.-H., Rognes, T., & Ussery, D. W. (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research, 35(9), 3100–3108. doi:10.1093/nar/gkm160

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Dataset: Supplementary Table 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences, FPKM values

Final no updates expectedDOI: 10.26008/1912/bco-dmo.812936.1Version 1 (2020-07-01)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

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Views

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Downloads

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Methods

File(s)	Type	Description	Action
fpkm_values.csv (24.90 KB)	Comma Separated Values (.csv)	Data file associated with dataset 812936: Supplementary Table 4A - Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences: FPKM values	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
fpkm_values.csv (24.90 KB)	Comma Separated Values (.csv)	Data file associated with dataset 812936: Supplementary Table 4A - Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences: FPKM values	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 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences, FPKM values

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 4A: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences, FPKM values

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

ERDDAP

Metadata

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