2024-11-11
ENA first public
ERC000024
ENA-CHECKLIST
European Marine Biological Resource Centre
INSDC center name
public
INSDC status
ERS20568957
SRA accession
EMOBON00056
Submitter Id
1.73
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
1.66
µg/L
chlorophyll
spectrofluorometry
chlorophyll method
2021-06-21
collection date
56.5917
mS/cm
conductivity
CTD SBE 19plusV2
conductivity method
25.2822
g/m3
density
CTD SBE 19plusV2
density method
0
m
depth
EMOBON metagenome water sample from station NRMCB collected on 2021-06-21 size fraction 3-200um
description
4.7913
µmol/kg
dissolved oxygen
SBE 43
dissolved oxygen method
8.29
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)
81490002
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
0.64
µmol/L
nitrate
segmented continuous-flow autoanalyzer
nitrate method
0.09
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: 7.22E+06; diatoms: 3.72E+06; dinoflagellates: 2.33E+05; coccolitrophores: 0.00E+00; other flagellates: 3.27E+06
organism count
phytoplankton; diatoms; dinoflagellates; coccolithophores; other flagellates: Utermöhl (Phytoplankton) Sedimentation Chamber
organism count method
8.227
pH
DNA Polymerase:taq Q5;NoPCRs:2;PCRvolume:30;Nocycles:10
pcr conditions
metag
pcr primers
SBE18
ph method
0,61
µg/L
phaeopigments
spectrofluorometry
phaeopigments method
0.09
µmol/L
phosphate
segmented continuous-flow autoanalyzer
phosphate method
1,2959
µg/L
pigments
this is not pigments but fluorescense. chl Turner Design Cyclops 7C)
pigments method
EMOBON
project name
Prod_ILL_BqADN_NEBUII_151_v4; Bq NEB Next Ultra II
relevant standard operating procedures
37.5864
psu
salinity
CTD SBE 19plusV2
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
25.0217
ºC
sea subsurface temperature
CTD SBE 19plusV2
sea subsurface temperature method
25.0217
ºC
sea surface temperature
CTD SBE 19plusV2
sea surface temperature method
manual
sequence quality check
Batch1
sequence_batch
Batch1_220622
sequence_batch_rundate
Illumina NovaSeq 6000
sequencing method
0.8
µmol/L
silicate
segmented continuous-flow autoanalyzer
silicate method
3
µm
size-fraction lower threshold
200
µm
size-fraction upper threshold
EMOBON_NRMCB_Wa_210621_3um_1
source material identifiers
sample
status
37.5934
psu
subsurface salinity
CTD SBE 19plusV2
subsurface salinity method
metag
target gene
metag
target subfragment
no_tide
tidal stage information
EMOBON_NRMCB_Wa_1
title
75
m
total depth of water column
0.4101
FTU
turbidity
Turner Cyclops 7 turb
turbidity method