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DRX360805: Illumina MiniSeq paired end sequencing of SAMD00448215
1 ILLUMINA (Illumina MiniSeq) run: 1.5M spots, 107.7M bases, 40.7Mb downloads

Submitted by: ARIMA_GEN
Study: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
show Abstracthide Abstract
Studies 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. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we 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 (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.
Sample: Arima-HiC on zebra finch muscle tissue, no preservative, 6hr 4C storage, rep1
SAMD00448215 • DRS239909 • All experiments • All runs
Library:
Instrument: Illumina MiniSeq
Strategy: Hi-C
Source: GENOMIC
Selection: Restriction Digest
Layout: PAIRED
Construction protocol: Arima-HiC
Spot descriptor:
forward19  reverse

Runs: 1 run, 1.5M spots, 107.7M bases, 40.7Mb
Run# of Spots# of BasesSizePublished
DRR3749041,474,082107.7M40.7Mb2022-05-16

ID:
21821237

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