coral metagenome
collection_date
2014-12-11
env_broad_scale
Ocean
env_local_scale
coral tissue
isolate
S. Capella 2
env_medium
marine photic zone
geo_loc_name
USA:United States Virgin Islands,South Capella
host
Orbicella franksi
lat_lon
18.2659 N 64.8661 W
depth
23.77
host_taxid
48499
samp_collect_device
corer
samp_mat_process
Preserved using RNAlater and stored at -20C
nucl_acid_ext
Extraction occurred at the U.S. Geological Survey Environmental Microbiology Laboratory in St. Petersburg, FL. DNA was extracted from approximately 0.05g (50-60 µL) of coral tissue sample using MO BIO PowerSoil DNA Isolation Kit protocol (_https://www.qiagen.com/us/resources/resourcedetail?id=5c00f8e4-c9f5-4544-94fa-653a5b2a6373&lang=en) adapted to include Sunagawa modification. Step 8 in notebook was added (centrifuge for two minutes at maximum speedc of centrifuge, around 16,000 X g typically, at room temperature and transfer 250µL of the supernatant into a 2mL collection tube) between steps 6 and 7 of handbook per Sungawa protocol. Step 10 in notebook was added (Centrifugure for five minutes at 23,000 X g at 4¡C and quickly transfer supernatant to a new 1.5 mL collection tube, working in order) per Sungawa protocol. Step 11 in notebook was added (Centrifugure for five minutes at 23,000 X g at 4¡C and quickly transfer supernatant to a new 1.5 mL collection tube, working in reverse) per Sungawa protocol. All subsequent steps of notebook correspond with n-2 of handbook.
target_gene
16S rRNA
target_subfragment
V4
pcr_primers
FWD (515F):5_ GTGCCAGCMGCCGCGGTAA, REV (806RB):5_ GGACTACNVGGGTWTCTAAT
seq_meth
Illumina MiSeq v2 chemistry producing paired-end 250 bp reads
BioSampleModel
MIMARKS.survey
BioSampleModel
MIGS/MIMS/MIMARKS.host-associated