Genome sequencing of Harvard Forest soil isolates - SRA

SRX19837942: Genome sequencing of Harvard Forest soil isolates
1 OXFORD_NANOPORE (MinION) run: 624,643 spots, 4.9G bases, 4.2Gb downloads

Design: MinION sequencing libraries were prepared using the Ligation Sequencing Kit SQK-LSK-109 (ONT, Oxford, UK). Between 6-8 isolates were multiplexed per sequencing run using the Native Barcoding Expansion Kit EXP-NBD104 (ONT, Oxford, UK). We skipped the Covaris g-TUBE shearing step to target long fragment DNA. Starting with 1 g of DNA per isolate, samples were prepped with the NEBNext FFPE DNA Repair Mix and NEBNext Ultra II End Repair/dA-Tailing kits (New England Biolabs, Ipswich, MA, USA), and DNA cleanup was performed using Ampure XP beads (Beckman Coulter, Pasadena, CA, USA). 150 ng of each barcoded sample was pooled for a final library of 700-1000 ng, and adapters were ligated to the sample with Blunt/TA ligase (New England Biolabs, Ipswich, MA, USA). The long fragment buffer was used in an extended 10 minute incubation at 37 C to enrich for high molecular weight DNA. The flow cell was primed using the Flow Cell Priming Kit (ONT, Oxford, UK). Approximately 15 fmols of the pooled library, sequencing buffer, and loading beads were mixed and then loaded through Spot-On port of the flow cell. Sequencing runs completed after 72 hours, and high accuracy base calling was performed on the raw fast5 data with the ONT software Guppy v4.5.4 or v6.1.1 (Oxford Nanopore Technologies, 2021).

Submitted by: University of Massachusetts Amherst

Study: Betaproteobacteria Ralstonia spp. clade Genome sequencing and assembly

PRJNA944978 • SRP430325 • All experiments • All runs

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To better define microbial responses to warming, we study microorganisms from an ongoing soil warming experiment at the Harvard Forest Long-term Ecological Research (LTER) site where, for over three decades, soils are continuously heated 5 degreesC above ambient temperatures. Bacteria are isolated from soils, genotyped, and genomes sequenced.

Sample:

SAMN33771265 • SRS17196833 • All experiments • All runs

Organism: Ralstonia sp. GP174

Library:

Name: GP174

Instrument: MinION

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: SINGLE

Runs: 1 run, 624,643 spots, 4.9G bases, 4.2Gb

Run	# of Spots	# of Bases	Size	Published
SRR24035319	624,643	4.9G	4.2Gb	2023-03-31

ID:: 27194844

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