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Wednesday, July 29, 2020

A HiFi View: Sequencing the Gut Microbiome with Highly Accurate Long Reads

Whether you are seeking to characterize microbial diversity in the gut, or distinguish between pathogenic and commensal bacteria on the skin, full-length 16S rRNA sequencing using PacBio systems is a valuable tool for metagenomics studies, according to microbiology researchers in a recent webinar. The HiFi advantage. With HiFi sequencing, every read yields 7-9 complete genes. PacBio microbiology expert Meredith Ashby (@AshbyMere) began the webinar by highlighting some of the strengths of the Sequel II System in metagenomics research.  One of the biggest advantages is the ability to do gene prediction directly on high-quality HiFi reads, without the need for any…

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Thursday, July 23, 2020

Sequencing 101: What’s the Value of Sequencing Full-length RNA Transcripts?

The study of genomics has revolutionized our understanding of science, but the field of transcriptomics grew with the need to explore the functional impacts of genetic variation. While different tissues in an organism may share the same genomic DNA, they can differ greatly in what regions are transcribed into RNA and in their patterns of RNA processing. By reviewing the history of transcriptomics, we can see the advantages of RNA sequencing – using a full-length transcript approach – become clearer. Reaching for the Transcriptome Even before genome sequencing became commonplace, scientists were able to measure gene expression activity using hybridization…

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Tuesday, July 21, 2020

Review: How Long-Read Sequencing Is Revealing Unseen Genomic Variation

“We are now embarking on an era where all genetic variation in an individual will be completely discovered,” write Glennis Logsdon (@glennis_logsdon), Mitchell Vollger (@mrvollger), and Evan Eichler in a recent Nature Reviews Genetics paper. “Hundreds and ultimately thousands of new human reference genomes will be produced.”  A decade ago that would have sounded impossible, but today this bold proclamation is widely accepted in the genomics community — a telling sign of the remarkable innovation that has driven genome sequencing in recent years. In their review, the University of Washington scientists give credit for much of these accomplishments to advancements in…

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Friday, July 17, 2020

New Isoform Phasing Technique Traces Parental-Progeny Differences in Maize

It’s not unusual for progeny to outperform their parents, and it’s often the goal in plant breeding. But tracing the molecular basis of such heterosis can be difficult, especially in diploid species with high genetic diversity and allele-specific expression like maize. Cold Spring Harbor scientists have tackled the challenge using the PacBio Iso-Seq method and a new tool, IsoPhase. As reported in Nature Communications Biology, Bo Wang, Doreen Ware, and colleagues performed an isoform-level phasing study in maize using the temperate line B73 and the tropical line Ki11, as well as their reciprocal crosses (B73 × Ki11; Ki11 × B73),…

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Tuesday, July 7, 2020

Sequencing 101: From DNA to Discovery – The Steps of SMRT Sequencing

Starting a sequencing project can be daunting. First of all, there are several types of sequencing technologies, each based on unique processes. At PacBio, we use a technology called Single Molecule, Real-Time (SMRT) Sequencing.   Learn how SMRT Sequencing works in this short video:   Although each sequencing project is unique, there are five main steps to go from DNA to discovery with SMRT Sequencing:   Step 1: Sample Prep Similar to cooking, for the best results, start with the best ingredients. The ideal sequencing starter is high molecular weight DNA. There are plenty of kits on the market that…

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Wednesday, July 1, 2020

Don’t Sweat The Small Stuff: Low DNA Input Workflow Enables Sequencing of the Smallest Species

Tackling larger and larger genomes has been an attractive pursuit for many scientists as sequencing technologies improve at rapid rates. But what about the other end of the spectrum — the tiny organisms that comprise much of the diversity of life?  An obvious obstacle to decoding the DNA of small organisms such as insects, nematodes and other arthropods is collecting enough of it to actually sequence (usually multiple micrograms worth). Until recently, the solution was to pool DNA from many of these tiny creatures to create a representative sample, and extrapolate the biology of the individual constituents from there. But…

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