EMOBON_NRMCB_Wa_29
marine plankton metagenome
ENA first public
2024-11-11
INSDC center name
European Marine Biological Resource Centre
INSDC status
public
Submitter Id
EMOBON00066
ammonium
0.41
ammonium method
segmented continuous-flow autoanalyzer
amount or size of sample collected
5
broad-scale environmental context
marine biome [ENVO:00000447];marine pelagic biome [ENVO:01000023];mediterranean sea biome[ENVO_01000047]
chlorophyll
1.71
chlorophyll method
spectrofluorometry
collection date
2021-08-31
conductivity
46.07
conductivity method
CTD SBE911plusV2
density
25.0316
density method
CTD SBE911plusV2
depth
0
dissolved oxygen
4.607
dissolved oxygen method
SBE 43
dna concentration
10.75
environmental medium
seawater [ENVO:00002149]; coastal sea water [ENVO:00002150]; surface water [ENVO:00002042]
geographic location (country and/or sea)
Italy
geographic location (latitude)
40.800139
geographic location (locality)
Naples Gulf
geographic location (longitude)
14.25
geographic location (ocean)
Mediterranean Sea - Western Basin
geographic location (region and locality)
Tyrrhenian Sea
library reads sequenced
67900169
local environmental context
marine pelagic feature [ENVO:01000044];marine water body [ENVO:00001999];costal water body [ENVO:02000049]
mock_pr
DDC_AAAAOSDA_1_HMNJKDSX3.UDI201
nitrate
0.01
nitrate method
segmented continuous-flow autoanalyzer
nitrite
0.05
nitrite method
segmented continuous-flow autoanalyzer
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
NRMCB
organism count
phytoplankton: 4.46E+06; diatoms: 2.76E+06; dinoflagellates: 7.25E+04; coccolitrophores: 0.00E+00; other flagellates: 1.63E+06
organism count method
phytoplankton; diatoms; dinoflagellates; coccolithophores; other flagellates: Utermöhl (Phytoplankton) Sedimentation Chamber
pcr conditions
DNA Polymerase:taq Q5;NoPCRs:2;PCRvolume:30;Nocycles:10
pcr primers
metag
ph method
SBE27
phaeopigments
0,51
phaeopigments method
spectrofluorometry
phosphate
0.1
phosphate method
segmented continuous-flow autoanalyzer
pigments
1,2505
pigments method
this is not pigments but fluorescense. WetLabs ECO-FL
project name
EMOBON
relevant standard operating procedures
Prod_ILL_BqADN_NEBUII_151_v4; Bq NEB Next Ultra II
salinity
37.9887
salinity method
CTD SBE911plusV2
sample collection device
Niskin
sample material processing
Wa SOP1
sample name
EMOBON00066
sample storage location
Casotti minus80
sample storage temperature
-80
scientific_name
marine plankton metagenome
sea subsurface temperature
26.8072
sea subsurface temperature method
CTD SBE911plusV2
sea surface temperature
26.8119
sea surface temperature method
CTD SBE911plusV2
sequence quality check
manual
sequence_batch
Batch1
sequence_batch_rundate
Batch1_220712
sequencing method
Illumina NovaSeq 6000
silicate
0.31
silicate method
segmented continuous-flow autoanalyzer
size-fraction lower threshold
0.2
size-fraction upper threshold
3
source material identifiers
EMOBON_NRMCB_Wa_210831_0.2um_2
status
sample
subsurface salinity
37.9916
subsurface salinity method
CTD SBE911plusV2
target gene
metag
target subfragment
metag
tidal stage information
no_tide
total depth of water column
75
turbidity
0.2925
turbidity method
Turner Cyclops 7 turb