Tag: iso-seq

Kinnex launch promises to revolutionize RNA research

RNA sequencing (RNA-seq) has become an indispensable tool for analyzing transcriptomes across all domains of life that can reveal insights about biology and disease. While the genome remains relatively constant for most species over brief time scales, the transcriptome –the sum total of expressed messenger RNA (mRNA) transcripts – varies…

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A HiFi movement: Transcript isoform resolved RNA sequencing

The books of life are fascinating yet challenging reads, owing to the complexity of the underlying biological processes and their alterations that lead to disease. Thanks to highly accurate HiFi long-read sequencing, we are now seeing fundamental changes in our ability to print, read and comprehend this most exciting literature….

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Powered by PacBio: Selected publications for October 2023

PacBio HiFi sequencing technology continues to play an increasingly pivotal role in advancing critical research across the life sciences. In this blog series, we explore some of the latest and most exciting scientific papers and preprints that demonstrate the power of HiFi sequencing in unraveling new insights in areas as…

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Three new RNA kits | Scientist Live

PacBio has announced it has begun taking orders for its new Kinnex RNA kits, which increase throughput for full-length RNA, single-cell RNA, and 16S rRNA sequencing on the firm’s long-read sequencing systems to enable large-scale studies at a resolution difficult to attain with short-read RNA sequencing. “The new family of…

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Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo

Introduction The non-random packaging of chromatin within the nucleus is a universal feature of eukaryotic genomes. The three-dimensional (3D) spatial organization of chromatin could be partitioned at different levels based on the interaction frequency between two given loci in the genome. Advances in sequencing technologies have led to the identification…

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PacBio announces expansion of Kinnex RNA kits, HiFi sequencing in full-length RNA, single-cell RNA and 16S rRNA applications.

Based on the MAS-Seq concatenation method, these three new assemblies can significantly increase throughput in RNAi applications. MENLO PARK, CA., October 31, 2023 /PRNewswire/ – PacBio (NASDAQ: PACB), a leading developer of high-quality, high-fidelity sequencing solutions, today announced that it has begun accepting orders for its innovative Kinnex RNA kits,…

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Pacific Biosciences of California, Inc. (NASDAQ:PACB) Q3 2023 Earnings Call Transcript

Pacific Biosciences of California, Inc. (NASDAQ:PACB) Q3 2023 Earnings Call Transcript October 30, 2023 Pacific Biosciences of California, Inc. beats earnings expectations. Reported EPS is $-0.26, expectations were $-0.3. Operator: Good afternoon, everyone, and welcome to the PacBio Third Quarter 2023 Earnings Conference Call. All participants will be in a…

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Q3 2023 Pacific Biosciences of California Inc Earnings Call

Participants Christian O. Henry; President, CEO & Director; Pacific Biosciences of California, Inc. Susan G. Kim; CFO; Pacific Biosciences of California, Inc. Todd Friedman; Former Director of IR; Pacific Biosciences of California, Inc. Daniel Gregory Brennan; MD and Senior Tools & Diagnostics Analyst; TD Cowen, Research Division Eve Burstein Jack…

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PacBio Announces Kinnex RNA Kits, Further Scaling HiFi Sequencing in Full-Length RNA, Single-Cell RNA and 16S rRNA Applications

Building on the MAS-Seq Concatenation Method, These Three New Kits can Significantly Increase Throughput in RNA Applications MENLO PARK, Calif., Oct. 31, 2023 /PRNewswire/ — PacBio (NASDAQ: PACB), a leading developer of high-quality, highly accurate sequencing solutions, today announced it has begun taking orders for its groundbreaking Kinnex RNA kits, which…

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Characterization and analysis of the muscle transcriptome in black Tibetan sheep (Ovis aries) by hybrid sequencing of PacBio Iso-seq

Author links open overlay panelZhanyue Wu a b, Lei Zhuang a b, Mingyi Yan a b c, Wenwen Ren a b, Sayed Haidar Abbas Raza d e, Waleed Al Abdulmonem f, Ruqaih S. Alghsham g, Yousef Mesfer Alharbi h, Sen Wu a b c Show more doi.org/10.1016/j.smallrumres.2023.107093Get rights and content…

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Powered by PacBio: Selected publications for August 2023

Want to know what PacBio users have been up to? In this summary, get the latest on some of the hottest scientific publications to incorporate PacBio sequencing methods. Selections from the month of August 2023 include papers on human genomics, Mendelian genetics, and rare disease research. Read the bullet points,…

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Iso-Seq method outperforms other long-read methods in benchmarking consortium study

A benchmarking of long-read RNA sequencing methods and analysis tools The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) consortium, an initiative to systematically evaluate methods for transcript identification and quantification, recently released their final assessment of long-read sequencing technologies and tools in the preprint “Systematic assessment of long-read RNA-seq methods…

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A HiFi movement : Isoform-resolved cell atlases

Cellular cartography has been just as important for biologists to navigate the complex topography of living systems as was the mapping of the earth’s landscapes for explorers hundreds of years ago. While much has been learned about cellular identities and functions through gene expression analysis, one of the main drivers…

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Identification of bromelain subfamily proteases encoded in the pineapple genome

C1A protease family genes in the pineapple MD2 v2 genome Presence of either the C1 peptidase or I29 inhibitor domains were used as a signature to identify genes belonging to the C1A protease gene family9. 71 C1A genes were identified (AcC1A1–AcC1A71), and were distributed across 17 pineapple chromosomes (Fig. 1,…

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Beyond borders: The 2023 Discoveries Roadshow ignites curiosity worldwide

Scientific breakthroughs are rarely achieved in isolation. They require collaboration, cutting-edge techniques, and a platform where scientists can come together to exchange knowledge and explore groundbreaking tools. And that’s exactly what the 2023 PacBio Discoveries Roadshow delivered… The 2023 Roadshow in the Americas and Europe left a lasting impression.  The…

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Cracking cancer: Using long-read RNA sequencing for cancer neoantigen discovery

When developing effective personalized immunotherapies, such as cancer vaccines, a pivotal factor lies in uncovering tumor neoantigens that can serve as crucial therapeutic targets. Traditionally, neoantigen discovery heavily relied on short-read sequencing technology, with a predominant focus on neoantigens resulting from single-nucleotide variants (SNVs). However, recent advancements have unveiled the…

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An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

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The Biostar Herald for Thursday, May 11, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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A Better Telescope Gazing at the Transcriptome

Jason Underwood, PhDPacBio In the middle of 2022, the world saw the first image from the Webb Space Telescope, a new cutting-edge instrument certain to unlock new secrets about the universe. That first infrared image showed a tiny sliver of a universe with thousands of galaxies with brightness and clarity…

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The power of accurate long-read RNA sequencing for fusion gene detection in cancer research

  pbfusion is a new software tool for detecting gene fusions and other transcriptional abnormalities in PacBio Iso-Seq data. The advancement of cancer research depends on the ability to accurately detect the molecular changes driving the initiation, progression, and evolution of tumors. In particular, gene fusions can lead to transcriptional…

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Long-read sequencing: the key to a more complete cancer transcriptome

Uncover the mysteries of RNA dysregulation in cancer Our understanding of the complex biology of cancers is currently limited by the sequencing technology that we have available. For example, a study previously published in Science Advances showed that short-read based RNA-seq approaches only capture a faction of RNA isoforms that…

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Single-Cell RNA Isoform Sequencing Picks up Steam as Long-Read Technologies Improve

NEW YORK – Riding the wave of recent technological advancements in long-read sequencing, single-cell RNA isoform analysis has not only become feasible but is snowballing into a thriving field. The approach, based on the ability of long-read platforms to capture full-length transcriptomes, allows scientists to take a closer looker at…

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Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

The 18-genome data package To investigate the genome inversion landscape of Asian rice from a population structure perspective, we first combined a set of 16 previously published high-quality genomes32,33,34 that represent the K = 15 population structure of O. sativa, plus the largest Xian/indica (XI) admixed subpopulation (XI-adm: Minghui 63 (MH63)) to…

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nf-core/isoseq: Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing

doi: 10.1093/bioinformatics/btad150. Online ahead of print. Affiliations Expand Affiliations 1 The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG. 2 Wobble Genomics, University of Edinburgh, Edinburgh, EH25 9RG. Item in Clipboard Sébastien Guizard et al. Bioinformatics. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/bioinformatics/btad150. Online ahead…

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Number of gigabases necesary for Iso-seq-PacBio

Number of gigabases necesary for Iso-seq-PacBio 0 Dear Biostars community, I’m currently working on a sequencing project and we are interested in using long-reads sequencing, specifically Iso-seq with PacBio to make a general survey of mRNA isoforms of Arabidopsis roots. Considering that Arabidopsis genome is around 3.2Gbases, I’d like to…

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A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk

Chromosomal-scale genome assembly and full spidroin gene set of T. clavata To explore dragline silk production in T. clavata, we sought to assemble a high-quality genome of this species. Thus, we first performed a cytogenetic analysis of T. clavata captured from the wild in Dali City, Yunnan Province, China, and…

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PacBio to Expand MAS-Seq Technology to 16S rRNA and Bulk RNA-Seq Solutions

End-to-End Solutions Planned to Support Key Customer Applications With Increased Cost Flexibility on Long-Read Sequencing Systems MENLO PARK, Calif., Feb. 7, 2023 /PRNewswire/ — PacBio (NASDAQ: PACB), a leading developer of high-quality, highly accurate sequencing solutions, today announced the commencement of a program intended to expand Multiplexed Arrays Sequencing (MAS-Seq)…

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PacBio to Expand MAS-Seq Techn

MENLO PARK, Calif., Feb. 7, 2023 End-to-End Solutions Planned to Support Key Customer Applications With Increased Cost Flexibility on Long-Read Sequencing Systems MENLO PARK, Calif., Feb. 7, 2023 /PRNewswire/ — PacBio (NASDAQ: PACB), a leading developer of high-quality, highly accurate sequencing solutions, today announced the commencement of a program intended…

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Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines

The gene expression of Mamu-E is regulated by extensive alternative splicing that is conserved among HLA-E isoforms To accurately define Mamu-E transcript structures, we aimed to use high-quality, full-length transcript sequences obtained by long-read transcriptome sequencing41. Since the sequences of MHC genes are very similar, it was critical that we…

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Gene fusion detection and characterization in long-read cancer transcriptome sequencing data with FusionSeeker | Cancer Research

Gene fusions are prevalent in a wide array of cancer types with different frequencies. Long-read transcriptome sequencing technologies, such as PacBio, Iso-Seq, and Nanopore direct RNA sequencing, provide full-length transcript sequencing reads, which could facilitate detection of gene fusions. In this work, we developed a method, FusionSeeker, to comprehensively characterize…

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Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

. 2022 Mar 3;220(3):iyac017. doi: 10.1093/genetics/iyac017. Affiliations Expand Affiliations 1 Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA. 2 Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA. Item in Clipboard Hope M Healey et al. Genetics. 2022. Show details Display options Display options…

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What are the steps of an full lengh RNA seq annotation method?

What are the steps of an full lengh RNA seq annotation method? 0 I have read a few papers, some of them used GenMark, or PacBios proprietary Iso-Seq pipeline but as I’m just a Bachelor’s student I am having trouble understanding how exactly it works. Can some one roughly explain…

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How does PacBio Iso-Seq annotation compare to other pipelines?

How does PacBio Iso-Seq annotation compare to other pipelines? 1 I have no experience in annotation RNA seq data (or genome assembly) but I’ve spent the last weeks ploughing through some papers and looking at manuals. I am wondering why it seems so common that e.g. proprietary pipelines of sequencers…

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How does PacBio Iso -Seq Annotation compare to other pipelines?

How does PacBio Iso -Seq Annotation compare to other pipelines? 1 I have no experience in annotation or assembly but I’ve spent the last weeks ploughing through some papers and looking at manuals. I am wondering why it seems so common that e.g. proprietary pipelines of sequencers are not used?…

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