EMOBON_PiEGetxo_Wa_2
marine plankton metagenome
ENA first public
2024-11-11
INSDC center name
European Marine Biological Resource Centre
INSDC status
public
Submitter Id
EMOBON00036
amount or size of sample collected
10
broad-scale environmental context
marine biome [ENVO:00000447];estuarine biome [ENVO:01000020]
chlorophyll
2.29
chlorophyll method
HPLC (Alliance HPLC System) following the method described by Zapata et al. 2000
collection date
2021-08-24
conductivity
46.4582
conductivity method
EXO2 multiparameter sonde
depth
1
dna concentration
36.2
environmental medium
seawater [ENVO:00002149]; coastal sea water [ENVO:00002150]; surface water [ENVO:00002042]
geographic location (country and/or sea)
Spain
geographic location (latitude)
43.338583
geographic location (locality)
Abra de Bilbao
geographic location (longitude)
-3.014639
geographic location (ocean)
North Atlantic Ocean
geographic location (region and locality)
Bay of Biscay
library reads sequenced
86491718
local environmental context
marine pelagic feature [ENVO:01000044];marine water body [ENVO:00001999];harbor[ENVO:00000463]
mock_eu
DDC_AAABOSDA_4_HMGW5DSX3.UDI213
mock_pr
DDC_AAAAOSDA_4_HMGW5DSX3.UDI201
nucleic acid amplification
metag
nucleic acid extraction
https://www.protocols.io/view/cryogrinding-protocol-mecanic-lysis-of-planktonic-n92ldyq88l5b/v1; https://www.protocols.io/view/rna-dna-extraction-from-plankton-natural-samples-u-eq2lynz2qvx9/v1; https://www.fishersci.com/shop/products/nucleospin-rna-ii-740955-250/NC0707522; https://www.mn-net.com/lysis-buffer-ra1-740961
obs_id
PiEGetxo
pH
7.8
pcr conditions
DNA Polymerase:taq Q5;NoPCRs:2;PCRvolume:30;Nocycles:10
pcr primers
metag
ph method
EXO2 multiparameter sonde
pigments
B-caroten: 0.04;α-caroten 0.005;chlorophyll b: 0.224;Lutein: 0.009;Zeaxanthin: 0.016;Diatoxanthin: 0;Aloxanthin: 0.038;Anteraxanthin: 0;Dinoxanthin: 0;Diadinoxanthin: 0.106;Hfu: 0.032;Violaxanthin: 0;Neoxanthin: 0;Prasinoxanthin: 0;Fucoxanthin: 0.278;Bfu: 0;Peridinin: 0.289;chlorophyll C1: 0.04;chlorophyll C2: 0.236
pigments method
HPLC (Alliance HPLC System) following the method described by Zapata et al. 2000
project name
EMOBON
relevant standard operating procedures
Prod_ILL_BqADN_NEBUII_151_v4; Bq NEB Next Ultra II
salinity
33.16
salinity method
EXO2 multiparameter sonde
sample collection device
Niskin
sample material processing
WaSOP 1
sample name
EMOBON00036
sample storage location
BBEBB, freezer 12
sample storage temperature
-80
scientific_name
marine plankton metagenome
sea subsurface temperature
20.73
sea subsurface temperature method
EXO2 multiparameter sonde
sea surface temperature
20.73
sea surface temperature method
EXO2 multiparameter sonde
sequence quality check
manual
sequence_batch
Batch1
sequence_batch_rundate
Batch1_220622
sequencing method
Illumina NovaSeq 6000
size-fraction lower threshold
3
size-fraction upper threshold
200
source material identifiers
EMOBON_PiEGetxo_Wa_210824_3um_2
status
sample
subsurface salinity
33.16
subsurface salinity method
EXO2 multiparameter sonde
target gene
metag
target subfragment
metag
tidal stage
low
tidal stage information
low_tide
total depth of water column
10
turbidity
0