ArticleGigaScience2022
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 2 syntheses or guidelines pooled it, 44 citations in OpenAlex.
- Type Genomics: A Framework for Integrating Genomic Data into Biodiversity and Taxonomic Research.Systematic biology · 2025Guideline
- A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution.The Journal of heredity · 2023Pooled it
- A T2T Genome of the Lobed-Lip Iguazu Joana (Crenicichla tuca) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes.Genome biology and evolution · 2026Article
- Ambient temperature storage of individual parasitic nematode larvae for whole genome sequencing.PLoS neglected tropical diseases · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Assessment of DNA Variations From Two In Vivo Skeletal Muscle Disorder Mouse Models Using Complementary Square-Wave Voltammetry and LC-MS/MS Analysis.Chembiochem : a European journal of chemical biology · 2026Article
- Article
- Comparing Minimally Lethal Sampling Methods for Genomics in the Eastern Oyster (Ecology and evolution · 2026Article
- From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe.Molecular ecology resources · 2026Review
- Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes.GigaScience · 2026Article
- Targeted sequencing and iterative assembly of near-complete genomes.Nature communications · 2025Article
- The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.Frontiers in science · 2025Article
- Development of a qPCR molecular diagnostic assay for the detection of kiwi Eimeria species and its application to determine tissue-specificity of species causing coccidiosis in North Island brown kiwi (Apteryx mantelli).Parasitology research · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- Combination of Sample Preservation Approaches and DNA Extraction Methods for Long-Read Sequencing of Nudibranchs' Genomes.Ecology and evolution · 2025Article
- Long-read sequencing and genome assembly of natural history collection samples and challenging specimens.Genome biology · 2025Article
- Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.GigaScience · 2025Article
- Perish the thawed? EDTA reduces DNA degradation during extraction from frozen tissue.PloS one · 2025Article
- The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.BMC genomics · 2024Review
- The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 12 institutions in 7 countries.
Funding
Abstract
backgroundStudies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.
resultsWe find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.
conclusionWe provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.