EPT-14_W_3_B12
insect metagenome
Megabarcoding of single Insect (Ephemeroptera, Plecoptera, Trichoptera) specimen
ENA first public
2025-10-30
INSDC center name
UDE
INSDC status
public
Submitter Id
W_3_B12
accessRights
Open Access. You are free to share and adapt under the following terms: You must give appropriate credit , provide a link to the license, and indicate if changes were made . You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
adapter_forward
AATGATACGGCGACCACCGAGATCTACAC
adapter_reverse
CAAGCAGAAGACGGCATACGAGAT
ampliconSize
205
amplificationReactionVolume
10
annealingTemp
58
assay_name
fwh (megabarcoding)
assay_type
other: DNA megabarcoding - single specimen barcoding using high troughput sequencing
associated_resource
Additional Image Data: DOI: 10.5281/zenodo.15966820
barcoding_pcr_appr
two-step PCR
bibliographicCitation
Will be added upon release.
checkls_ver
1
code_repo
https://github.com/PhilippMRehsen/EPT-14_code
collection date
2022
commercial_mm
DreamTaq Green PCR Master Mix, Thermo Fisher Scientific
demux_max_mismatch
0
demux_tool
Demultiplexer v1.2
geographic location (country and/or sea)
Germany
inhibition_check
The extracts were tested using a serial dilusion approach (1:10, 1:50, 1:100, 1:200), followed by 40 cycles of PCR and visual evaluation via gel electrophoresis. In case undiluted samples didn't show visual bands after gel electrophoresis, samples were repeated using a 1:200 dilution.
inhibition_check_0_1
1
institution
University of Duisburg-Essen
institutionID
https://ror.org/04mz5ra38
instrument
NovaSeq6000
lib_layout
paired end
license
https://creativecommons.org/licenses/by/4.0/
merge_min_overlap
5
merge_tool
APSCALE v1.7.1
min_len_cutoff
195
min_len_tool
APSCALE v1.7.1
mod_date
2025-07-31 00:00:00
neg_cont_0_1
1
otu_clust_cutoff
98
otu_clust_tool
v2.22.1 (using APSCALE v1.7.1)
otu_db
BOLD
otu_seq_comp_appr
BOLDigger v2.1.3
pcr2_amplificationReactionVolume
10
pcr2_annealingTemp
61
pcr2_commercial_mm
DreamTaq Green PCR Master Mix, Thermo Fisher Scientific
pcr2_cond
initial denaturation:95_3;denaturation:95_0.5;annealing:61_0.5;elongation:72_1;final elongation:72_10;10
pcr2_cycles
10
pcr2_dna_vol
2
pcr_0_1
1
pcr_cond
initial denaturation:95_3;denaturation:95_0.5;annealing:58_1.5;elongation:72_1;final elongation:72_10;40
pcr_cycles
40
pcr_dna_vol
1
pcr_primer_conc_forward
10
pcr_primer_conc_reverse
10
pcr_primer_forward
GGDACWGGWTGAACWGTWTAYCCHCC
pcr_primer_name_forward
fwhF2
pcr_primer_name_reverse
fwhR2n
pcr_primer_reference_forward
https://doi.org/10.3897/mbmg.1.14625
pcr_primer_reference_reverse
https://doi.org/10.3897/mbmg.1.14625
pcr_primer_reverse
GTRATWGCHCCDGCTARWACWGG
pcr_primer_vol_forward
0.2
pcr_primer_vol_reverse
0.2
pcr_rep
0
pos_cont_0_1
0
project_contact
philipp.rehsen@uni-due.de
project_id
exstream_germany_boye_2022_EPT14
recordedBy
Philipp M. Rehsen | Mia S. Honka | Mikko Impiö | Iris Madge Pimentel | Florian Leese | Arne J. Beermann
recordedByID
https://orcid.org/0009-0003-0156-457X | | https://orcid.org/0000-0001-7672-3000 | https://orcid.org/0000-0002-8252-7660 | https://orcid.org/0000-0002-5465-913X | https://orcid.org/0000-0003-0403-0322
rightsHolder
Aquatic Ecosystem Research - University of Duisburg Essen, Germany
sample name
W_3_B12
scientific_name
insect metagenome
screen_contam_method
Taxa detected in negative controls were checked and labwork of samples on the same plate as negatice controls with high read numbers were re-done (starting with the extracts) and sequenced an additional time.
screen_nontarget_method
Samples returning non-target species (i.e., species not belonging to Ephemeroptera, Plecoptera or Trichoptera species) were removed in the creation of the final dataset
screen_other
see corresponging paper
seq_kit
NovaSeq6000 2 x 150 bp
sequencing_location
Azenta Life Sciences (Leipzig, Germany)
sop_bioinformatics
https://github.com/DominikBuchner/demultiplexer | https://github.com/DominikBuchner/apscale/ | https://github.com/DominikBuchner/BOLDigger3
sterilise_method
Sterile labware kits used for each individual sample, all lab surfaces cleaned with 80% ethanol prior to extraction and PCR set up, single-use gloves were used during all steps in the lab.
study_factor
effect of multiple stressors (added salinity and increased temperature) on benthic macroinvetebrates (Ephemeroptera, Plecoptera, Trichoptera) in an outdoor field mesocosm experiment.
targetTaxonomicAssay
invertebrate
targetTaxonomicScope
invertebrate
target_gene
COI
target_subfragment
see fwhF2, fwhR2n primer
tax_assign_cat
sequence similarity
tax_class_collapse
98%: species level, 95%: genus level, 90%: family level, 85%: order level, <85%: class level
tax_class_id_cutoff
75
tax_class_query_cutoff
75
thermocycler
Blue-Ray Biotech, TurboCycler
trim_method
cutadapt v4.4 (using APSCALE v1.7.1)