EMOBON_NRMCB_Wa_2
marine plankton metagenome
ENA first public
2024-11-11
INSDC center name
European Marine Biological Resource Centre
INSDC status
public
Submitter Id
EMOBON00057
ammonium
1.73
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
1.66
chlorophyll method
spectrofluorometry
collection date
2021-06-21
conductivity
56.5917
conductivity method
CTD SBE 19plusV2
density
25.2822
density method
CTD SBE 19plusV2
depth
0
dissolved oxygen
4.7913
dissolved oxygen method
SBE 43
dna concentration
9.41
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
85203137
local environmental context
marine pelagic feature [ENVO:01000044];marine water body [ENVO:00001999];costal water body [ENVO:02000049]
mock_eu
DDC_AAABOSDA_4_HMGW5DSX3.UDI213
mock_pr
DDC_AAAAOSDA_4_HMGW5DSX3.UDI201
nitrate
0.64
nitrate method
segmented continuous-flow autoanalyzer
nitrite
0.09
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: 7.22E+06; diatoms: 3.72E+06; dinoflagellates: 2.33E+05; coccolitrophores: 0.00E+00; other flagellates: 3.27E+06
organism count method
phytoplankton; diatoms; dinoflagellates; coccolithophores; other flagellates: Utermöhl (Phytoplankton) Sedimentation Chamber
pH
8.227
pcr conditions
DNA Polymerase:taq Q5;NoPCRs:2;PCRvolume:30;Nocycles:10
pcr primers
metag
ph method
SBE18
phaeopigments
0,61
phaeopigments method
spectrofluorometry
phosphate
0.09
phosphate method
segmented continuous-flow autoanalyzer
pigments
1,2959
pigments method
this is not pigments but fluorescense. chl Turner Design Cyclops 7C)
project name
EMOBON
relevant standard operating procedures
Prod_ILL_BqADN_NEBUII_151_v4; Bq NEB Next Ultra II
salinity
37.5864
salinity method
CTD SBE 19plusV2
sample collection device
Niskin
sample material processing
Wa SOP1
sample name
EMOBON00057
sample storage location
Casotti minus80
sample storage temperature
-80
scientific_name
marine plankton metagenome
sea subsurface temperature
25.0217
sea subsurface temperature method
CTD SBE 19plusV2
sea surface temperature
25.0217
sea surface temperature method
CTD SBE 19plusV2
sequence quality check
manual
sequence_batch
Batch1
sequence_batch_rundate
Batch1_220622
sequencing method
Illumina NovaSeq 6000
silicate
0.8
silicate method
segmented continuous-flow autoanalyzer
size-fraction lower threshold
3
size-fraction upper threshold
200
source material identifiers
EMOBON_NRMCB_Wa_210621_3um_2
status
sample
subsurface salinity
37.5934
subsurface salinity method
CTD SBE 19plusV2
target gene
metag
target subfragment
metag
tidal stage information
no_tide
total depth of water column
75
turbidity
0.4101
turbidity method
Turner Cyclops 7 turb