2024-11-11
ENA first public
ERC000024
ENA-CHECKLIST
European Marine Biological Resource Centre
INSDC center name
public
INSDC status
ERS20568959
SRA accession
EMOBON00062
Submitter Id
0.41
µmol/L
ammonium
segmented continuous-flow autoanalyzer
ammonium method
5
L
amount or size of sample collected
marine biome [ENVO:00000447];marine pelagic biome [ENVO:01000023];mediterranean sea biome[ENVO_01000047]
broad-scale environmental context
1.71
µg/L
chlorophyll
spectrofluorometry
chlorophyll method
2021-08-31
collection date
46.07
mS/cm
conductivity
CTD SBE911plusV2
conductivity method
25.0316
g/m3
density
CTD SBE911plusV2
density method
0
m
depth
EMOBON metagenome water sample from station NRMCB collected on 2021-08-31 size fraction 3-200um
description
4.607
µmol/kg
dissolved oxygen
SBE 43
dissolved oxygen method
12.7
ng/µl
dna concentration
seawater [ENVO:00002149]; coastal sea water [ENVO:00002150]; surface water [ENVO:00002042]
environmental medium
Italy
geographic location (country and/or sea)
40.800139
DD
geographic location (latitude)
Naples Gulf
geographic location (locality)
14.25
DD
geographic location (longitude)
Mediterranean Sea - Western Basin
geographic location (ocean)
Tyrrhenian Sea
geographic location (region and locality)
94643683
library reads sequenced
marine pelagic feature [ENVO:01000044];marine water body [ENVO:00001999];costal water body [ENVO:02000049]
local environmental context
DDC_AAABOSDA_4_HMGW5DSX3.UDI213
mock_eu
DDC_AAAAOSDA_4_HMGW5DSX3.UDI201
mock_pr
0.01
µmol/L
nitrate
segmented continuous-flow autoanalyzer
nitrate method
0.05
µmol/L
nitrite
segmented continuous-flow autoanalyzer
nitrite method
metag
nucleic acid amplification
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
nucleic acid extraction
NRMCB
obs_id
marine plankton metagenome
organism
phytoplankton: 4.46E+06; diatoms: 2.76E+06; dinoflagellates: 7.25E+04; coccolitrophores: 0.00E+00; other flagellates: 1.63E+06
organism count
phytoplankton; diatoms; dinoflagellates; coccolithophores; other flagellates: Utermöhl (Phytoplankton) Sedimentation Chamber
organism count method
DNA Polymerase:taq Q5;NoPCRs:2;PCRvolume:30;Nocycles:10
pcr conditions
metag
pcr primers
SBE27
ph method
0,51
µg/L
phaeopigments
spectrofluorometry
phaeopigments method
0.1
µmol/L
phosphate
segmented continuous-flow autoanalyzer
phosphate method
1,2505
µg/L
pigments
this is not pigments but fluorescense. WetLabs ECO-FL
pigments method
EMOBON
project name
Prod_ILL_BqADN_NEBUII_151_v4; Bq NEB Next Ultra II
relevant standard operating procedures
37.9887
psu
salinity
CTD SBE911plusV2
salinity method
Niskin
sample collection device
Wa SOP1
sample material processing
Casotti minus80
sample storage location
-80
°C
sample storage temperature
marine plankton metagenome
scientific_name
26.8072
ºC
sea subsurface temperature
CTD SBE911plusV2
sea subsurface temperature method
26.8119
ºC
sea surface temperature
CTD SBE911plusV2
sea surface temperature method
manual
sequence quality check
Batch1
sequence_batch
Batch1_220622
sequence_batch_rundate
Illumina NovaSeq 6000
sequencing method
0.31
µmol/L
silicate
segmented continuous-flow autoanalyzer
silicate method
3
µm
size-fraction lower threshold
200
µm
size-fraction upper threshold
EMOBON_NRMCB_Wa_210831_3um_1
source material identifiers
sample
status
37.9916
psu
subsurface salinity
CTD SBE911plusV2
subsurface salinity method
metag
target gene
metag
target subfragment
no_tide
tidal stage information
EMOBON_NRMCB_Wa_23
title
75
m
total depth of water column
0.2925
FTU
turbidity
Turner Cyclops 7 turb
turbidity method