DOI: 10.5061/dryad.s7h44j1md
title: Data from: Geographic variation in diet, prey resources and exposure to parasites and saxitoxin in Steller sea lions in the Gulf of Alaska

description: Using 12S rRNA and mitochondrial cytochrome c oxidase subunit I (COI) gene
 metabarcoding, we examined diet composition, prey resources, and saxitoxin
 (STX) and parasite exposure in Steller sea lions (SSL) in the Gulf of
 Alaska in July and October 2022–2023 using 251 scat samples and 45
 seawater samples. SSL scat and water were sampled from a broad geographic
 area in the the Gulf of Alaska, from Southeast Alaska through Kodiak
 Island. The COI gene region was amplified with the Leray-XT primers and
 the 12S gene region was amplified with the MiFish-U primers. Data
 available here include: 1. SSL diet and parasite and saxitoxin exposure
 information from scat samples, including metadata (for each scat sample:
 collection location and date, host sex determined via molecular methods,
 saxitoxin level), unfiltered results of taxonomic groups detected in each
 scat sample for each gene region, and filtered results of prey species
 detected which were used in our published study in Frontiers in Marine
 Science. And 2. Taxonomic diversity of the nearshore waters of the Gulf
 Alaska for initial examination of geographic variation in the nearshore
 prey field for SSL in July (informed by the 12S gene region metabarcoding)
 for comparison to prey composition determined from SSL scat. 
 Information about other taxonomic groups of interest in water samples
 included geographic variation in saxitoxin-producing Alexandrium spp.,
 possible from COI gene metabarcoding which sampled well lower trophic
 levels.  Also included are 3. Information concerning reference
 databases used for bioinformatics for both gene regions and 4. raw
 sequence data for scat and water samples for each gene region (fastq
 files).
description: From manuscript: <strong>2.1 Sample
 collection and preparation</strong>
 <strong>2.1.1 SSL scat samples</strong>
 Both in the field and laboratory, a rigorous quality control
 protocol was followed to prevent contamination of samples from exogenous
 DNA (King et al., 2008; USFWS, 2022).  In July and October 2022 and 2023,
 251 scats were collected at 8 sites in 3 regions in the Gulf of Alaska:
 Cook Inlet, Kodiak Island, and PWS (Figure 1, Table 1).  Entire fresh
 scats (regardless of size or characteristics) were collected using clean,
 disposable gloves and spoon for each sample, placed in
 Ziploc<sup>®</sup> bags and stored at -20°C within 6 hr of
 collection (Thomas et al., 2022). Sample preparation
 followed protocols detailed for harbor seal diet metabarcoding studies
 (Thomas, 2015; Thomas et al., 2022).  To prepare samples for laboratory
 analysis, each frozen sample was partially thawed on a sterilized
 workspace and a ~4mL subsample was transferred to a 5mL cryovial using
 sterilize instruments and immediately stored at -80°C for STX analysis.
  The remaining sample was submerged in 95% molecular-grade ethanol in
 500mL or 1L Histoplex<sup>®</sup> jars lined with 1gal-sized
 paint strainers made of 200μm nylon mesh and then, after fully thawed,
 manually homogenized with a clean wooden tongue depressor by gentle
 stirring for ~3–5min per sample.  The paint strainer with hard-part and
 non-scat items (e.g., rocks or debris if present) was removed from the
 jar, placed in a Ziploc<sup>®</sup> bag, and archived at -20°C
 for future hard-part analysis.  The scat matrix ethanol mixture was stored
 at -20°C for 24 hr to allow the matrix to settle out of solution.  A
 clean, disposable pipette was used to transfer two subsamples of the
 matrix: 0.5mL to a 2mL cryovial (for DNA extraction) and 1mL to a 5mL
 cryovial (for archiving), which were topped off with 1.5mL and 3mL of
 fresh 95% molecular-grade ethanol (e.g., 1:3 ratio of matrix to ethanol),
 respectively, and stored at -80°C.  This procedure was used to ensure
 sample homogenization to maximize detection of diet items and reduce
 sample variance, as food items are not distributed equally within scat
 samples (Deagle et al., 2005). <strong>2.1.2
 Seawater samples to assess SSL prey field</strong>
 From 24 June–23 July 2023, seawater samples were collected via a
 1.7L Niskin bottle (Model 1010, General Oceanics, Inc., Miami, FL, USA) at
 a depth of 10m during Gulf-wide SSL population surveys.  Our goal for this
 sampling was to acquire initial data as a pilot study to determine if a
 fast, efficient seawater sampling protocol would provide useful data on
 nearshore fish assemblages as an efficient addition to our regular, annual
 SSL surveys.  A standard depth of 10m was chosen for the following
 reasons:  (1) Dives of adult female SSL from the western population were
 relatively shallow with median or average dive depths of 21–28m during
 summer and winter (Merrick and Loughlin, 1997; Lander et al., 2020); up to
 54% of dives of adult females were between 4–10m and &gt;90% were
 &lt;50m (Merrick and Loughlin, 1997).  (2) This depth allowed us to
 sample below the water’s surface but was shallow enough to allow quick,
 hand-deployment of the Niskin bottle; hand deploying to deeper depths,
 especially in strong currents, could be prohibitive. (3) We desired
 information on the nearshore environment and did not assume foraging areas
 or foraging depths of SSL; a rigorous, comprehensive study evaluating the
 utility of eDNA to study vertebrate diversity found equivalent information
 across 10–80m sampling depths suggesting vertical mixing may provide
 information on fish diversity from throughout the upper water column, even
 from surface water collections (Closek et al., 2019).
  Three 1.7L replicates per site were collected at 15 sites, at
 least 0.5km distant from SSL aggregations, from SEAK to Kodiak Island
 (Figure 1).  Seawater was filtered directly from the Niskin bottle in the
 field using a Smith-Root eDNA Citizen Scientist Sampler and 5µm
 self-preserving polyethersulfone filters (Smith-Root, Inc., Vancouver, WA,
 USA).  Five negative controls of distilled water were processed in
 triplicate at weekly intervals throughout the sampling period to test for
 contamination of the field sampling system.  Filters were stored in a
 cool, dry, and dark location until subsequent DNA extraction within 3
 months post sample collection. <strong>2.2 DNA
 metabarcoding</strong> <strong>2.2.1 DNA
 extraction</strong> All laboratory work for scat
 and seawater samples was performed at the Washington Department of Fish
 and Wildlife’s Molecular Genetics Laboratory (WDFW-MGL) in AirClean 600
 Workstations equipped with HEPA filtered air and UV light irradiation.
  Work surfaces and equipment were sterilized with 10% bleach and exposed
 to UV-C light for one hour to neutralize exogenous DNA.  Seawater filter
 DNA was extracted using DNeasy<sup>TM</sup> Blood &
 Tissue Kits (Qiagen, Hilden, Germany) following the methods of Pilliod et
 al. (2013) with one extraction negative control processed per batch of 47
 filters.  SSL scat DNA was extracted using QIAamp<sup>TM</sup>
 Fast DNA Stool Mini Kits (Qiagen) following a customized protocol for
 pinniped scat (Deagle et al., 2005) with one extraction negative control
 processed per batch of 23 scats. Library preparation -
  We assessed prey diversity using two genes, mitochondrial cytochrome c
 oxidase subunit I (COI) and 12S rRNA MiFish (12S) genes, to provide better
 biodiversity coverage.  The 12S rRNA MiFish-U primer was optimal for bony
 fishes (Actinopterygii) and informative of cartilaginous
 fishes (Chondrichthyes; Miya et al., 2015), whereas the COI primer
 amplifies all metazoans, including cephalopods (Arfin et al., 2023) which
 are potentially important SSL prey (Pitcher, 1981).  For pinniped scat
 diet studies, the COI gene (although a different fragment than used by in
 our study) has been used in particular to distinguish salmon species
 (Lewis, 2022; Thomas et al., 2022; Trzcinski et al., 2024).  The COI and
 12S genes were amplified in separate reactions.  The COI gene region was
 amplified with the Leray-XT primers (Wangensteen et al., 2018) and the 12S
 gene region was amplified with the MiFish-U primers (Miya et al., 2015).
  The Leray-XT primers amplified a 313bp gene fragment and included the
 forward primer mlCOIintF-XT 5′-GGWACWRGWTGRACWITITAYCCYCC-3′ (Wangensteen
 et al., 2018), modified from the original mlCOIintF primer developed by
 Leray et al. (2013), and the reverse primer jgHCO2198
 5′-TAIACYTCIGGRTGICCRAARAAYCA-3′ (Geller et al., 2013).  The MiFish-U
 primers amplified a 170bp gene fragment and included the forward primer
 5′-GTCGGTAAAACTCGTGCCAGC-3′ and the reverse primer
 5′-CATAGTGGGGTATCTAATCCCAGTTTG-3′ (Miya et al., 2015).  
 PCRs were performed in 30μL volumes using the Multiplex PCR Kit
 (Qiagen).  COI reactions contained 15μL (1X) of multiplex master mix,
 0.8μM of each primer and 2μL of template DNA with thermal cycling
 conditions as follows: 95°C for 10min, 35 cycles of 95°C for 60s, 50°C for
 60s, and 72°C for 60s, and a final extension of 72°C for 5min. 12S
 reactions contained 15μL (1X) of multiplex master mix, 2μM of each primer
 and 1μL of template DNA with thermal cycling conditions as follows: 95°C
 for 10min, 14 touchdown cycles of 94°C for 30s, 69.5-50°C for 30s, and
 72°C for 90s, 25 cycles of 94°C for 30s, 50°C for 30s, and 72°C for 45s,
 and a final extension of 72°C for 10min. A PCR negative and positive
 control were included on each 96-well PCR plate.  The negative control
 consisted of sterile molecular grade water in lieu of template DNA and
 kangaroo DNA was used as a positive amplification control.
 PCR products were size selected using
 Mag-Bind<sup>®</sup> TotalPure NGS (Omega Bio-tek, Inc.,
 Norcross, GA, USA) beads.  A ratio of beads to product of 0.8X was used
 for the COI amplicon and 1.2X was used for the 12S amplicon.  Sample
 amplicons were then indexed with Nextera DNA unique dual (UD) indexes
 (IDT<sup>®</sup> for Illumina<sup>®</sup>),
 normalized using the SequalPrep<sup>™</sup> Normalization
 Plate Kit (Invitrogen) and each 96-well plate was subsequently pooled.
  Plate libraries were bead cleaned at a 0.8X bead ratio, quantified with a
 Qubit<sup>®</sup> fluorometer (Life Technologies), and pooled
 by amplicon.  Amplicon libraries were quantified and normalized to 4nM
 prior to loading at a 1:1 12S to COI ratio on the
 NextSeq<sup>™</sup> 1000 platform with 25% PhiX Control v3
 Library (Illumina, Inc., San Diego, CA, USA).  Seawater filters were
 sequenced using the NextSeq<sup>™</sup> 1000 P1 (300 cycles)
 Reagent Kit for single end reads and scats were sequenced using the
 NextSeq<sup>™</sup> 1000 P1 (600 cycles) Reagent Kit for
 paired end reads (Illumina, Inc.). <strong>2.2.2
 Bioinformatics</strong> Amplicon sequence data
 were analyzed separately (COI and 12S) using either stand-alone QIIME 2
 (Bolyen et al., 2019) and DADA2 (Callahan et al., 2016) or with Tourmaline
 (https://github.com/aomlomics/tourmaline), a Snakemake pipeline that wraps QIIME 2 and DADA2, providing reproducible metabarcoding analysis.  Adapters and primers were trimmed from demultiplexed FASTQ reads using Cutadapt (Martin, 2011).  The program DADA2 was used to quality filter reads.  Reads were truncated to a common length (210bp for the COI amplicon and 160bp for the 12S amplicon) with a maximum number of expected errors=2, chimeras were removed (consensus method), and amplicon sequence variants (ASVs) were exported.   To assign COI taxonomy, a custom reference database was generated that included existing sequence data for published Alaska SSL prey observed in the Resource Assessment and Conservation Engineering (RACE) Gulf of Alaska summer biennial bottom trawl surveys (https://www.fisheries.noaa.gov/foss/f?p=215%3A28) from 2015–2023, the MIDORI database (Machida et al., 2017), and all mitochondrial COI sequences in the National Center for Biotechnology Information (NCBI) nucleotide database.  To assign 12S taxonomy, a rCRUX (Curd et al., 2024) generated reference database was used that included all 12S sequences in the NCBI nucleotide database, an additional custom database comprised of all Actinopterygii (bony fishes) mitogenomes (Gold et al., 2023), and sequences available for published SSL prey and for fishes and cephalopods in the RACE surveys.  If voucher specimen sequence data were publicly available, they were included in the reference library.  If sequences were identical, assignments were produced at a higher taxonomic resolution. Global taxonomic alignments between query and reference sequences were performed using the VSEARCH consensus taxonomy classifier (Rognes et al., 2016) and matches with ≥ 97% identity were retained.  Read counts for each operational taxonomic unit (OTU) per sample were tallied. <strong>2.3 Sex identification using SSL scat samples</strong> DNA extract from 250 scat samples was provided to the Alaska Department of Fish and Game's Gene Conservation Laboratory to determine SSL sex identification by adapting existing protocols (Lewis, 2022; Gard et al., 2024).  Briefly, sex-specific oligonucleotides developed for SSL were used to assess the presence of X- and Y-chromosomally linked genes (ZFX and SRY) in the scat DNA.  DNA was amplified on a GeneAmp™ PCR System 9700 with a Multiplex PCR Kit (Qiagen), 0.2μM of each primer, and 4μL of DNA using Gene Conservation Laboratory’s standard 14 cycle preamplification PCR protocol with thermal cycling conditions as follows: 95°C for 15min, 14 cycles of 95°C for 15s and 60°C for 4min.  The individual primers and probes from the two qPCR assays were then combined into a single 80X sex ID genotyping assay (16μM each probe, 72μM each primer).  Final concentrations of the probes and primers in the PCR reaction were 0.2µM and 0.9µM.  Genotypes were collected on an Applied Biosystems™ QuantStudio 12K Flex using their 2X TaqMan™ GTXpress™ Master Mix, 1X genotyping assay, and 2.5μL of 0.1X preamplification PCR product according to the PCR protocol of Schwarz et al. (2018).  Genotypes were scored at 42 cycles. <strong>2.4 Saxitoxin (STX) in SSL scat samples</strong>  In addition to scat samples from the current study, 8 samples from the Kenai Peninsula collected by the Alaska SeaLife Center (Jan–May 2017–2019) and 12 samples from SEAK (July 2016) were included.  STX in scat samples was measured by the Northwest Fisheries Science Center's Wildlife Algal-Toxin Research and Response Network (WARRN-West) laboratory, following the protocol of Lefebvre et al. (2022).  Briefly, the ~4mL raw scat samples provided to the lab were thawed slowly in a small cooler, stirred thoroughly, and ~1mL per sample was aliquoted into 14mL polypropylene screw-cap tubes (Falcon-BD).  For STX extraction, 50% methanol was added to samples in a 1:4 wt/v ratio (1 part sample, 3 parts solvent) and samples were vortexed.  Samples were homogenized for 60s using an Omni GLH 850 homogenizer and the homogenized sample was then centrifuged at 3,082xg (Jouan CR3i centrifuge) for 20min at 4°C.  The supernatant was added to a 0.22μm Durapore™ membrane filter (Millipore Ultrafree-MC centrifugal concentration device) and filtered in a desk-top microcentrifuge (AccuSpin Micro 17, Fisher Scientific) for 3min at 12,000rpm.  Sample extracts were stored at 4°C until analysis by enzyme-linked immunosorbent assay (ELISA). STX in samples was quantified using a commercially-available Abraxis saxitoxin ELISA kit (PN 52255B: Gold Standard Diagnostics, Horsham, PA).  Standards solutions provided in these kits were loaded along with the samples on plates and a standard curve was derived for each plate.  Manufacturer instructions were followed with modifications for matrix effects for marine mammal feces determined by Hendrix et al. (2021) with sample dilution of 1:50 filtered sample extract:sample diluent solution provided with the ELISA kit.  The ELISA kit was designed to measure STX with some limited cross-reactivity to several other paralytic shellfish poison (PSP) toxins.  Consequently, all PSP concentrations are listed as STX equivalents and may underestimate the presence of other congeners.   <strong>2.5 Statistics</strong> <strong>2.5.1 Diet and prey data summaries</strong> We included taxa for bony and cartilaginous fishes for the 12S data and for these fishes, cephalopods, and other potentially interesting taxa (e.g., parasitic worms) for the COI data.  For both metabarcoding datasets for scat samples, we performed the following minimum sequence threshold filtering steps prior to statistical analyses: (1) samples with &lt;20 total prey assigned reads were removed (Trzcinski et al., 2024), (2) OTUs were assigned into prey groups at the species level or at the genus level for groups in which significant assigned reads were only to genus level (Deagle et al., 2019), (3) global (summed across all samples) total assigned reads per prey group were calculated and groups with &lt;100 total assigned reads were removed, and (4) prey groups &lt;0.01% of the per sample proportion of total prey assigned reads were removed to normalize detection rates among samples which may vary in read depth (Pornon et al., 2016; Richardson et al., 2019) to assess region*season variation in diet. For seawater samples, all assigned fish reads were used without filtering data, and assigned reads for the three replicates per site were summed to provide sufficient sample size.
description: # Data from: Geographic variation in diet, prey resources and exposure to
 parasites and saxitoxin in Steller sea lions in the Gulf of Alaska Dataset
 DOI: [10.5061/dryad.s7h44j1md](https://doi.org/10.5061/dryad.s7h44j1md) ##
 Description of the data and file structure Data available here include: 1.
 SSL diet and parasite and saxitoxin exposure information from scat
 samples, including metadata (for each scat sample: collection location and
 date, host sex determined via molecular methods, saxitoxin level),
 unfiltered results of taxonomic groups detected in each scat sample for
 each gene region, and filtered results of prey species detected which were
 used in our published study in Frontiers in Marine Science. And 2.
 Taxonomic diversity of the nearshore waters of the Gulf Alaska for initial
 examination of geographic variation in the nearshore prey field for SSL in
 July (informed by the 12S gene region metabarcoding) for comparison to
 prey composition determined from SSL scat.  Information about other
 taxonomic groups of interest in water samples included geographic
 variation in saxitoxin-producing *Alexandrium* spp., possible from COI
 gene metabarcoding which sampled well lower trophic levels.  Also included
 are 3. Information concerning reference databases used for bioinformatics
 for both gene regions and 4. raw sequence data for scat and water samples
 for each gene region (fastq files).   Empty cells in tabular data files
 indicate either "unknown" or "not applicable".  Fastq
 zipped files open to the individual files directly, or to a folder by the
 same name as the filename or to a generic name (e.g., "test1"). 
 Open the folder to see the individual files included. ### Files and
 variables #### File: SSL_Diet.zip **Description:** Six files that describe
 results from Steller sea lion scat samples, including diet composition
 data and sample metadata, including host sex and saxitoxin levels. ***1.
 Metadata_SSL_Diet:*** metadata for SSL scat samples * WDFW_ID: Washington
 Dept Fish Wildlife ID * ADFG_ID: Alaska Dept Fish Game ID * GCL_ID: Gene
 Conservation Lab (ADFG) ID - for HostSex * WARRNWest_ID: WARRNWest (NOAA)
 ID - for STX (saxitoxin data) * CollectionDate: MO/DA/YR *
 CollectionLocation * CollectionRegion * HostSex: Determined by GCL *
 SexGenotype: Genotype assigned by GCL * SXTLevel (ng/g): Saxitoxin level;
 0 = BDL,Below Detection Limit (not detected in the sample at or above the
 minimum detection limit of the assay; ranged for 2.6-6 ng/g). * Species:
 Steller sea lion ***2. Metadata_SSL_Diet_LatLong:*** Latitude and
 Longitude for scat collection locations in SSL_Diet metadata *
 CollectionLocation * CollectionRegion * Lat, Long in decimal degrees *
 n_Scat: number of samples included per site in the study ***3.
 SSL_Diet_COI_LerayXT_All_Results:*** COI- #reads per taxonomic unit by
 sample (23MT083-23MT333,Postive and Negative Controls) ***4.
 SSL_Diet_COI_LerayXT_Filtered:*** COI - Final prey data included after
 filtering and prey grouping per sample * WDFW_ID: Washington Dept Fish
 Wildlife ID * ADFG_ID: Alaska Dept Fish Game ID * Group: Sex-Region-Season
 (M)ale/(F)Female*; (C)ook Inlet/(K)odiak/(P)rince William Sound;
 (J)uly/(O)ctober *unknown sex groups have no M or F designation *
 PreyGroup * SumofReads: #reads per preygroup for each sample ***5.
 SSL­_Diet_12S_MiFish-U_All_Results:*** MiFishU - as above for COI ***6.
 SSL­_Diet_12S_MiFish-U_Filtered:*** MiFishU - as above for COI #### File:
 Water_ADFG.zip **Description:** Four files concerning water samples -
 results and metadata ***1. Metadata_Water_ADFG:*** metadata for ADFG water
 samples * ADFG_ID: Alaska Dept Fish Game ID * WDFW_ID: Washington Dept
 Fish Wildlife ID * CollectionDate: MO/DA/YR * CollectionTime *
 CollectionLocation * CollectionRegion * SampleDepth(m): Depth at which the
 water sample was collected in meters * Lat,Long * WaterDepth(m): Depth of
 water in the area the sample was collected measured by sonar/depth finder
 from skiff * WaterTemp(C): Temperature of water at the surface (&lt;1m
 from surface) * Replicates: The number of replicates per
 CollectionLocation and SampleDepth ***2.
 Water_ADFG_COI_LerayXT_All_Results:*** COI - see above for SSL_Diet (few
 fish/cephalopod reads - no filtered data file) ***3.
 Water_ADFG_12S_MiFish-U_All_Results:*** MiFishU - see above for SSL_Diet
 ***4. Water_ADFG_12S_MiFish-U_10m:*** MiFishU - final results used - reads
 for samples collected at 10m sample depth summed across replicates per
 CollectionLocation and grouped into prey groups as in SSL_Diet * ADFG_ID:
 Alaska Dept Fish Game ID * CollectionLocation * PreyGroup * SumofReads:
 #reads per preygroup for collection location #### File:
 Reference_sequence_databases.zip **Description:** Four files describing
 the reference libraries used for bioinformatics for 12S MiFish-U and COI
 Leray-XT ***1. COI_LerayXT_SSL_Diet.fasta:*** Reference sequence database
 for COI LerayXT amplicons ***2. COI_LerayXT_SSL_Diet_Taxonomy.txt:***
 Taxonomic classification file for COI LerayXT amplicons ***3.
 12S_MiFish-U_SSL­_Diet.fasta:*** Reference sequence database for 12S
 MiFish-U amplicons ***4. 12S_MiFish-U_SSL­_Diet_Taxonomy.txt:*** Taxonomic
 classification file for 12S MiFish-U amplicons #### File:
 z_FASTQ_SSL_Diet_12S_MiFishU_PE_a.tar.gz (a-d) **Description:** Fastq raw
 sequence data - SSL_Diet: 12S MiFish-U, Paired end (PE) SSL scat data [2
 sequencing reads, (sequencing in the forward direction) and R2 (sequencing
 in the reverse direction)]. Note - In the fastq file are Illumina index
 adapters or sequence tags that identify each sample included for each read
 per sample using Nextera DNA unique dual (UD) indexes (IDT® for
 Illumina®): see
 [https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm](https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm) #### File: z_FASTQ_SSL_Diet_12S_MiFishU_PE_b.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_12S_MiFishU_PE_c.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_12S_MiFishU_PE_d.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_CO1_LerayXT_PE_a.tar.gz (a-g) **Description:** Fastq raw sequence data - SSL_Diet: COI, Paired end (PE) SSL scat data [2 sequencing reads, (sequencing in the forward direction) and R2 (sequencing in the reverse direction)]. Note - In the fastq file are Illumina index adapters or sequence tags that identify each sample included for each read per sample using Nextera DNA unique dual (UD) indexes (IDT® for Illumina®): see [https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm](https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm) #### File: z_FASTQ_SSL_Diet_CO1_LerayXT_PE_b.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_CO1_LerayXT_PE_c.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_CO1_LerayXT_PE_d.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_CO1_LerayXT_PE_e.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_CO1_LerayXT_PE_f.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_SSL_Diet_CO1_LerayXT_PE_g.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_Water_ADFG_12S_MiFishU_SE_a.tar.gz (a-c) **Description:** Fastq raw sequence data - Water samples: 12S MiFish-U, single end (SE) water data [1 sequencing read, R1 (sequencing in the forward direction only)] . Note - In the fastq file are Illumina index adapters or sequence tags that identify each sample included for each read per sample using Nextera DNA unique dual (UD) indexes (IDT® for Illumina®): see [https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm](https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm) #### File: z_FASTQ_Water_ADFG_12S_MiFishU_SE_b.tar.gz **Description:** continuation of (a) above #### File: z_FASTQ_Water_ADFG_12S_MiFishU_SE_c.tar.gz **Description:** continuation of (a) above #### File: z_FASTQ_Water_ADFG_CO1_LerayXT_SE_a.tar.gz (a-d) **Description:** Fastq raw sequence data - Water samples: COI, single end (SE) water data [1 sequencing read, R1 (sequencing in the forward direction only)] . Note - In the fastq file are Illumina index adapters or sequence tags that identify each sample included for each read per sample using Nextera DNA unique dual (UD) indexes (IDT® for Illumina®): see [https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm](https://support-docs.illumina.com/SHARE/AdapterSequences/Content/SHARE/AdapterSeq/Illumina_DNA/IDTIlluminaUDIndexes.htm) #### File: z_FASTQ_Water_ADFG_CO1_LerayXT_SE_b.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_Water_ADFG_CO1_LerayXT_SE_c.tar.gz **Description:** Continuation of (a) above #### File: z_FASTQ_Water_ADFG_CO1_LerayXT_SE_d.tar.gz **Description:** Continuation of (a) above