2025-09-11
ENA first public
ERC000020
ENA-CHECKLIST
Scotland's Rural College - Aberdeen Campus
INSDC center name
public
INSDC status
ERS26104521
SRA accession
ms00743
Submitter Id
Forward overhang: 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG; Reverse overhang: 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
adapters
environmental system determined by an organism
broad-scale environmental context
N/A
chimera check software
controlled glasshouse
climate environment
2021-09-06
collection date
96 pooled culturable isolates from Sugarbeet grown in Silt Clay Loam from Shropshire
description
rhizosphere environment
environmental medium
Sugarbeet
experimental factor
United Kingdom
geographic location (country and/or sea)
52.4936865
DD
geographic location (latitude)
-2.4788747
DD
geographic location (longitude)
3
months
host age
Sugarbeet
host common name
flowering
host life stage
Degas
host subspecific genetic lineage
3555
host taxid
plant-associated environment
local environmental context
N/A
multiplex identifiers
plant-associated environment
negative control type
https://www.novogene.com/eu-en/resources/blog/a-beginners-guide-to-16s-18s-its-amplicon-metagenomic-sequencing/?_gl=1*zg303z*_up*MQ..*_gs*MQ..&gclid=CjwKCAjw24vBBhABEiwANFG7y_L5jjZFt1XnOwrf0qRG07FrSPv8bvD-aqDeyMYkG-ytGAiddyaqpBoCgrEQAvD_BwE&gbraid=0AAAAApRAw_nj7fjNvzzuoPTcLafmAJU-A
nucleic acid amplification
Boil (15 min.) and freeze cells in Tris 40mM, EDTA 0.4 mM, 0.4% Triton-X
nucleic acid extraction
soil metagenome
organism
95 C for 3 minutes; 25 cycles of 95 C for 30 seconds, 55 C for 30 seconds, 72 C for 30 seconds; 72 C for 5 minutes; Hold at 4 C
pcr conditions
Forward: 5' GTGCCAGCMGCCGCGGTAA; Reverse: 5' CCGTCAATTCCTTTGAGTTT
pcr primers
root
plant body site
N/A
plant product
rhizosphere environment
positive control type
UK Crop Microbiome Cryobank
project name
Rothamsted Research Station
reference for biomaterial
agmicrobiomebase.org
relevant electronic resources
0.5
g
sample volume or weight for DNA extraction
soil metagenome
scientific_name
software
sequence quality check
NovaSeq
sequencing method
16S
target gene
SU-SC-SH-04
title