ERDDAP > info > bcodmo_dataset_813173

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	Supplementary Table 4C: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data.		I   M	background			BCO-DMO	bcodmo_dataset_813173

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	access_formats	String	.htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute	NC_GLOBAL	acquisition_description	String	Rock material was crushed while still frozen in a Progressive Exploration Jaw Crusher (Model 150) whose surfaces were sterilized with 70% ethanol and RNase AWAY (Thermo Fisher Scientific, USA) inside a laminar flow hood. Powdered rock material was returned to the -80\u00b0C freezer until extraction. DNA was extracted from 20, 30, or 40 grams of powdered rock material, depending on the quantity of rock available. A DNeasy PowerMax Soil Kit (Qiagen, USA) was used following the manufacturer\u2019s protocol modified to included three freeze/thaw treatments prior to the addition of Soil Kit solution C1. Each treatment consisted of 1 minute in liquid nitrogen followed by 5 minutes at 65 \u00b0C. DNA extracts were concentrated by isopropanol precipitation overnight at 4\u00b0C. The low biomass in our samples required whole genome amplification (WGA) prior to PCR amplification of marker genes. Genomic DNA was amplified by Multiple Displacement Amplification (MDA) using the REPLI-g Single Cell Kit (Qiagen) as directed. MDA bias was minimized by splitting each WGA sample into triplicate 16 \u03bcL reactions after 1 hr of amplification and then resuming amplification for the manufacturer-specified 7 hrs (8 hrs total). DNA was also recovered from samples of drilling mud and drilling fluid (surface water collected during the coring process) for negative controls, as well as two \u201ckit control\u201d samples, in which no sample was added, to account for any contaminants originating from either the DNeasy PowerMax Soil Kit or the REPLI-g Single Cell Kit. Bacterial SSU rRNA gene fragments were PCR amplified from MDA samples and sequenced at Georgia Genomics and Bioinformatics Core (Univ. of Georgia). The primers used were: Bac515-Y and Bac926R. Dual-indexed libraries were prepared with (HT) iTruS (Kappa Biosystems) chemistry and sequencing was performed on an Illumina MiSeq 2 x 300 bp system with all samples combined equally on a single flow cell. Raw sequence reads were processed through Trim Galore [[http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/]](\\"http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/\]\\"), FLASH (ccb.jhu.edu/software/FLASH/) and FASTX Toolkit [[http://hannonlab.cshl.edu/fastx_toolkit/]](\\"http://hannonlab.cshl.edu/fastx_toolkit/\]\\") for trimming and removal of low quality/short reads. Quality filtering included requiring a minimum average quality of 25 and rejection of paired reads less than 250 nucleotides. Operational Taxonomic Unit (OTU) clusters were constructed at 99% similarity with the script pick_otus.py within the Quantitative Insights Into Microbial Ecology (QIIME) v.1.9.1 software and \u2018uclust\u2019. Any OTU that matched an OTU in one of our control samples (drilling fluids, drilling mud, extraction and WGA controls) was removed (using filter_otus_from_otu_table.py) along with any sequences of land plants and human pathogens that may have survived the control filtering due to clustering at 99% (filter_taxa_from_otu_table.py). As an additional quality control measure, genera that are commonly identified as PCR contaminants were removed. Unclassified OTUs were queried using BLAST against the GenBank nr database and further information about these OTUs is provided in the Supplementary Discussion text under the section \u201cTaxonomic diversity information from iTAGs.\u201d OTUs that could not be assigned to Bacteria or Archaea were removed from further analysis. For downstream analyses, any OTUs not representing more than 0.01% of relative abundance of sequences overall were removed as those are unlikely to contribute significantly to in situ communities. The OTU data table was transformed to a presence/absence table and the Jaccard method was used to generate a distance matrix using the dist.binary() function in the R package ade4.
attribute	NC_GLOBAL	awards_0_award_nid	String	709555
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1658031
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1658031
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_0_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Supplementary Table 4C: iTAG PI: Virginia Edgcomb Data Version 1: 2020-05-28
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_type	String	institution
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	dataset_current_state	String	Final and no updates
attribute	NC_GLOBAL	date_created	String	2020-05-28T12:54:12Z
attribute	NC_GLOBAL	date_modified	String	2020-07-09T16:05:24Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.813173.1
attribute	NC_GLOBAL	Easternmost_Easting	double	57.278183
attribute	NC_GLOBAL	geospatial_lat_max	double	-32.70567
attribute	NC_GLOBAL	geospatial_lat_min	double	-32.70567
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	57.278183
attribute	NC_GLOBAL	geospatial_lon_min	double	57.278183
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	geospatial_vertical_max	double	747.7
attribute	NC_GLOBAL	geospatial_vertical_min	double	10.7
attribute	NC_GLOBAL	geospatial_vertical_positive	String	down
attribute	NC_GLOBAL	geospatial_vertical_units	String	m
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/813173
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	DNA sequencing performed using the Illumina MiSeq 2 x 300 bp platform (Univ. of Georgia)
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	813183
attribute	NC_GLOBAL	instruments_0_description	String	General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Illumina MiSeq 2 x 300 bp platform
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, contmnt, data, dataset, depth, dmo, erddap, iTAG_OTU, iTAG_Paired_Contmnt_Rem, iTAG_Paired_QC, iTAG_Raw, latitude, longitude, management, metatr, Metatr_Paired_Contmnt_Rem, Metatr_Paired_QC, Metatr_Raw, Metatr_Reads_Remaining, oceanography, office, otu, paired, preliminary, raw, reads, rem, remaining, sample, Sample_ID, tag
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/813173/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/813173
attribute	NC_GLOBAL	Northernmost_Northing	double	-32.70567
attribute	NC_GLOBAL	param_mapping	String	{'813173': {'Latitude': 'flag - latitude', 'Depth': 'flag - depth', 'Longitude': 'flag - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/813173/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	WHOI
attribute	NC_GLOBAL	people_0_person_name	String	Virginia P. Edgcomb
attribute	NC_GLOBAL	people_0_person_nid	String	51284
attribute	NC_GLOBAL	people_0_role	String	Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	WHOI
attribute	NC_GLOBAL	people_1_person_name	String	Virginia P. Edgcomb
attribute	NC_GLOBAL	people_1_person_nid	String	51284
attribute	NC_GLOBAL	people_1_role	String	Contact
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	people_2_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_2_person_name	String	Karen Soenen
attribute	NC_GLOBAL	people_2_person_nid	String	748773
attribute	NC_GLOBAL	people_2_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	project	String	Subseafloor Lower Crust Microbiology
attribute	NC_GLOBAL	projects_0_acronym	String	Subseafloor Lower Crust Microbiology
attribute	NC_GLOBAL	projects_0_description	String	NSF abstract: The lower ocean crust has remained largely unexplored and represents one of the last frontiers for biological exploration on Earth. Preliminary data indicate an active subsurface biosphere in samples of the lower oceanic crust collected from Atlantis Bank in the SW Indian Ocean as deep as 790 m below the seafloor. Even if life exists in only a fraction of the habitable volume where temperatures permit and fluid flow can deliver carbon and energy sources, an active lower oceanic crust biosphere would have implications for deep carbon budgets and yield insights into microbiota that may have existed on early Earth. This is all of great interest to other research disciplines, educators, and students alike. A K-12 education program will capitalize on groundwork laid by outreach collaborator, A. Martinez, a 7th grade teacher in Eagle Pass, TX, who sailed as outreach expert on Drilling Expedition 360. Martinez works at a Title 1 school with ~98% Hispanic and ~2% Native American students and a high number of English Language Learners and migrants. Annual school visits occur during which the project investigators present hands on-activities introducing students to microbiology, and talks on marine microbiology, the project, and how to pursue science related careers. In addition, monthly Skype meetings with students and PIs update them on project progress. Students travel to the University of Texas Marine Science Institute annually, where they get a campus tour and a 3-hour cruise on the R/V Katy, during which they learn about and help with different oceanographic sampling approaches. The project partially supports two graduate students, a Woods Hole undergraduate summer student, the participation of multiple Texas A+M undergraduate students, and 3 principal investigators at two institutions, including one early career researcher who has not previously received NSF support of his own. Given the dearth of knowledge of the lower oceanic crust, this project is poised to transform our understanding of life in this vast environment. The project assesses metabolic functions within all three domains of life in this crustal biosphere, with a focus on nutrient cycling and evaluation of connections to other deep marine microbial habitats. The lower ocean crust represents a potentially vast biosphere whose microbial constituents and the biogeochemical cycles they mediate are likely linked to deep ocean processes through faulting and subsurface fluid flow. Atlantis Bank represents a tectonic window that exposes lower oceanic crust directly at the seafloor. This enables seafloor drilling and research on an environment that can transform our understanding of connections between the deep subseafloor biosphere and the rest of the ocean. Preliminary analysis of recovered rocks from Expedition 360 suggests the interaction of seawater with the lower oceanic crust creates varied geochemical conditions capable of supporting diverse microbial life by providing nutrients and chemical energy. This project is the first interdisciplinary investigation of the microbiology of all 3 domains of life in basement samples that combines diversity and "meta-omics" analyses, analysis of nutrient addition experiments, high-throughput culturing and physiological analyses of isolates, including evaluation of their ability to utilize specific carbon sources, Raman spectroscopy, and lipid biomarker analyses. Comparative genomics are used to compare genes and pathways relevant to carbon cycling in these samples to data from published studies of other deep-sea environments. The collected samples present a rare and time-sensitive opportunity to gain detailed insights into microbial life, available carbon and energy sources for this life, and of dispersal of microbiota and connections in biogeochemical processes between the lower oceanic crust and the overlying aphotic water column. About the study area: The International Ocean Discovery Program (IODP) Expedition 360 explored the lower crust at Atlantis Bank, a 12 Ma oceanic core complex on the ultraslow-spreading SW Indian Ridge. This oceanic core complex represents a tectonic window that exposes lower oceanic crust and mantle directly at the seafloor, and the expedition provided an unprecedented opportunity to access this habitat in the Indian Ocean.
attribute	NC_GLOBAL	projects_0_end_date	String	2020-01
attribute	NC_GLOBAL	projects_0_geolocation	String	SW Indian Ridge, Indian Ocean
attribute	NC_GLOBAL	projects_0_name	String	Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches
attribute	NC_GLOBAL	projects_0_project_nid	String	709556
attribute	NC_GLOBAL	projects_0_start_date	String	2017-02
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	Southernmost_Northing	double	-32.70567
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	latitude,longitude
attribute	NC_GLOBAL	summary	String	Supplementary Table 4C: Metatranscriptome data summary for cellular activities presented and statistics on sequencing and removal of potential contaminant sequences: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data. Samples taken on board of the R/V JOIDES Resolution between November 30, 2015 and January 30, 2016
attribute	NC_GLOBAL	title	String	Supplementary Table 4C: Statistics of reads retained through bioinformatic processing of iTAG data for the 11 samples and control samples and metatranscriptome data.
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	57.278183
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	Sample_ID		String
attribute	Sample_ID	bcodmo_name	String	sample
attribute	Sample_ID	description	String	Sample ID
attribute	Sample_ID	long_name	String	Sample ID
attribute	Sample_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Sample_ID	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	-32.70567, -32.70567
attribute	latitude	axis	String	Y
attribute	latitude	bcodmo_name	String	unknown
attribute	latitude	colorBarMaximum	double	90.0
attribute	latitude	colorBarMinimum	double	-90.0
attribute	latitude	description	String	Latitude of sample, south is negative
attribute	latitude	ioos_category	String	Location
attribute	latitude	long_name	String	Latitude
attribute	latitude	standard_name	String	latitude
attribute	latitude	units	String	degrees_north
variable	longitude		double
attribute	longitude	_CoordinateAxisType	String	Lon
attribute	longitude	_FillValue	double	NaN
attribute	longitude	actual_range	double	57.278183, 57.278183
attribute	longitude	axis	String	X
attribute	longitude	bcodmo_name	String	longitude
attribute	longitude	colorBarMaximum	double	180.0
attribute	longitude	colorBarMinimum	double	-180.0
attribute	longitude	description	String	Longitude of samples, west is negative
attribute	longitude	ioos_category	String	Location
attribute	longitude	long_name	String	Longitude
attribute	longitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	depth		double
attribute	depth	_CoordinateAxisType	String	Height
attribute	depth	_CoordinateZisPositive	String	down
attribute	depth	_FillValue	double	NaN
attribute	depth	actual_range	double	10.7, 747.7
attribute	depth	axis	String	Z
attribute	depth	bcodmo_name	String	depth
attribute	depth	colorBarMaximum	double	8000.0
attribute	depth	colorBarMinimum	double	-8000.0
attribute	depth	colorBarPalette	String	TopographyDepth
attribute	depth	description	String	Depth - meters below seafloor (mbsf)
attribute	depth	ioos_category	String	Location
attribute	depth	long_name	String	Depth
attribute	depth	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/DEPH/
attribute	depth	positive	String	down
attribute	depth	standard_name	String	depth
attribute	depth	units	String	m
variable	iTAG_Raw		int
attribute	iTAG_Raw	_FillValue	int	2147483647
attribute	iTAG_Raw	actual_range	int	29227, 810682
attribute	iTAG_Raw	bcodmo_name	String	unknown
attribute	iTAG_Raw	description	String	iTAG data - Raw reads
attribute	iTAG_Raw	long_name	String	I TAG Raw
attribute	iTAG_Raw	units	String	number of reads
variable	iTAG_Paired_QC		int
attribute	iTAG_Paired_QC	_FillValue	int	2147483647
attribute	iTAG_Paired_QC	actual_range	int	19196, 599653
attribute	iTAG_Paired_QC	bcodmo_name	String	unknown
attribute	iTAG_Paired_QC	colorBarMaximum	double	150.0
attribute	iTAG_Paired_QC	colorBarMinimum	double	0.0
attribute	iTAG_Paired_QC	description	String	iTAG data - paired reads after QC
attribute	iTAG_Paired_QC	long_name	String	I TAG Paired QC
attribute	iTAG_Paired_QC	units	String	number of reads
variable	iTAG_Paired_Contmnt_Rem		int
attribute	iTAG_Paired_Contmnt_Rem	_FillValue	int	2147483647
attribute	iTAG_Paired_Contmnt_Rem	actual_range	int	38, 39021
attribute	iTAG_Paired_Contmnt_Rem	bcodmo_name	String	unknown
attribute	iTAG_Paired_Contmnt_Rem	description	String	iTAG data - Paired reads surviving removal of potential contaminants matching sequences in control samples or known contaminants.
attribute	iTAG_Paired_Contmnt_Rem	long_name	String	I TAG Paired Contmnt Rem
attribute	iTAG_Paired_Contmnt_Rem	units	String	number of reads
variable	iTAG_OTU		byte
attribute	iTAG_OTU	_FillValue	byte	127
attribute	iTAG_OTU	actual_range	byte	8, 97
attribute	iTAG_OTU	bcodmo_name	String	unknown
attribute	iTAG_OTU	description	String	iTAG data - Number of OTUs at 99% identity
attribute	iTAG_OTU	long_name	String	I TAG OTU
attribute	iTAG_OTU	units	String	number of OTUs
variable	Metatr_Raw		int
attribute	Metatr_Raw	_FillValue	int	2147483647
attribute	Metatr_Raw	actual_range	int	13032452, 63348900
attribute	Metatr_Raw	bcodmo_name	String	unknown
attribute	Metatr_Raw	description	String	Metatranscriptome data - Raw reads from sequencing
attribute	Metatr_Raw	long_name	String	Metatr Raw
attribute	Metatr_Raw	units	String	number of reads
variable	Metatr_Paired_QC		int
attribute	Metatr_Paired_QC	_FillValue	int	2147483647
attribute	Metatr_Paired_QC	actual_range	int	5807873, 29212385
attribute	Metatr_Paired_QC	bcodmo_name	String	unknown
attribute	Metatr_Paired_QC	colorBarMaximum	double	150.0
attribute	Metatr_Paired_QC	colorBarMinimum	double	0.0
attribute	Metatr_Paired_QC	description	String	Metatranscriptome data - Paired reads after QC
attribute	Metatr_Paired_QC	long_name	String	Metatr Paired QC
attribute	Metatr_Paired_QC	units	String	number of reads
variable	Metatr_Paired_Contmnt_Rem		int
attribute	Metatr_Paired_Contmnt_Rem	_FillValue	int	2147483647
attribute	Metatr_Paired_Contmnt_Rem	actual_range	int	1724455, 16336790
attribute	Metatr_Paired_Contmnt_Rem	bcodmo_name	String	unknown
attribute	Metatr_Paired_Contmnt_Rem	description	String	Metatranscriptome data - Paired reads surviving removal of potential contaminants matching sequences in control samples or known contaminants.
attribute	Metatr_Paired_Contmnt_Rem	long_name	String	Metatr Paired Contmnt Rem
attribute	Metatr_Paired_Contmnt_Rem	units	String	number of reads
variable	Metatr_Reads_Remaining		float
attribute	Metatr_Reads_Remaining	_FillValue	float	NaN
attribute	Metatr_Reads_Remaining	actual_range	float	0.2344, 0.6815
attribute	Metatr_Reads_Remaining	bcodmo_name	String	unknown
attribute	Metatr_Reads_Remaining	description	String	Metatranscriptome data - Percent of original paired reads remaining
attribute	Metatr_Reads_Remaining	long_name	String	Metatr Reads Remaining
attribute	Metatr_Reads_Remaining	units	String	percentage (%)

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.