SAMN37694358
External Id
University of Helsinki
INSDC center name
2023-10-13T00:50:20.127Z
INSDC first public
2023-10-13T00:50:20.127Z
INSDC last update
SRS19075004
INSDC secondary accession
live
INSDC status
MIMS.me
NCBI submission model
MIGS/MIMS/MIMARKS.plant-associated
NCBI submission model
MIMS.me.plant-associated.6.0
NCBI submission package
SRS19075004
SRA accession
2017-05-08
collection_date
Keywords: GSC:MIxS;MIMS:6.0
description
Pine sapling samples (stem, needles and buds separately) were collected from a yard experiment setting (Helsinki, Finland) aiming to reveal diurnal variation in pine-related methane-emissions. To evaluate potential within-plant methane production and oxidation, plant-associated methanogens and methanotrophs were analyzed via probe-targeted metagenomics. Probes were designed to target functional genes mcrA, coding for the methyl coenzyme-M reductase (methanogens); pmoA, coding for the particulate methane monooxygenase (methanotrophs); and mmoX, coding for the soluble methane monooxygenase (methanotrophs).
design_description
Pinus sylvestris
env_broad_scale
buds from a Pinus sylvestris sapling
env_local_scale
conifer tree
env_medium
7011-JK-4_019_S1_L005_R1_001.fastq.gz
filename
7011-JK-4_019_S1_L005_R2_001.fastq.gz
filename2
7478-JK-3_019_S1_L005_R1_001.fastq.gz
filename3
7478-JK-3_019_S1_L005_R2_001.fastq.gz
filename4
fastq
filetype
Finland: Helsinki
geo_loc_name
Pinus sylvestris
host
Illumina NovaSeq 6000
instrument_model
60.23 N 25.02 E
lat_lon
SC19_pine_C_bu
library_id
paired
library_layout
Padlock probes capture method
library_selection
Metagenomic
library_source
Targeted-Capture
library_strategy
plant metagenome
http://purl.obolibrary.org/obo/NCBITaxon_1297885
organism
ILLUMINA
platform
Probe-targeted sequencing of CH4- and N-cycling microbes within pine samplings
title
SC19_pine_C_bu
title