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    LongBench - cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

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    Sold by: Richie Lab, Walter and Eliza Hall Institute of Medical Research 
    Open data
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    Deployed on AWS
    LongBench is a comprehensive benchmark dataset of the latest long-read transcriptomics technologies from Oxford Nanopore (ON) and Pacific Biosciences, alongside a comparison with next-generation sequencing from Illumina. We generated bulk and single-cell libraries from lung cancer cell lines which include different cancer subtypes to capture real biological variation. To further compare and assess sequencing platform performance, Sequins and SIRVs (Set 4) synthetic spike-ins have been included.

    Overview

    LongBench is a comprehensive benchmark dataset of the latest long-read transcriptomics technologies from Oxford Nanopore (ON) and Pacific Biosciences, alongside a comparison with next-generation sequencing from Illumina. We generated bulk and single-cell libraries from lung cancer cell lines which include different cancer subtypes to capture real biological variation. To further compare and assess sequencing platform performance, Sequins and SIRVs (Set 4) synthetic spike-ins have been included.

    Features and programs

    Open Data Sponsorship Program

    This dataset is part of the Open Data Sponsorship Program, an AWS program that covers the cost of storage for publicly available high-value cloud-optimized datasets.
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    Pricing

    This is a publicly available data set. No subscription is required.

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    Usage information

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    Delivery details

    AWS Data Exchange (ADX)

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    Open data resources

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    How to use
    To access these resources, reference the Amazon Resource Name (ARN) using the AWS Command Line Interface (CLI). Learn more 
    Description
    Bulk, single-cell, and single-nucleus RNA-seq data from the LongBench project, covering eight human lung cancer cell lines. Bulk sequencing (FASTQ) was performed on ONT PCR-cDNA, ONT direct RNA (including pod5 files for RNA modification analysis), PacBio Kinnex, and Illumina platforms. Single-cell and single-nucleus sequencing (FASTQ) was performed on ONT PCR-cDNA, PacBio Kinnex, and Illumina platforms. Aligned reads (BAM), variant calls (VCF), and processed gene expression data are also provided, along with reference genome annotations (GTF and FASTA).
    Resource type
    S3 bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::longbench-data
    AWS region
    ap-southeast-2
    AWS CLI access (No AWS account required)
    aws s3 ls --no-sign-request s3://longbench-data/

    Resources

    Vendor resources

    View this dataset on Github 

    Support

    Contact

    mritchie@wehi.edu.au 

    Managed By

    Richie Lab, Walter and Eliza Hall Institute of Medical Research

    How to cite

    LongBench - cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches was accessed on DATE from https://registry.opendata.aws/longbench .

    License

    CC BY-4.0