Open data
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Deployed on AWS
The Singapore Nanopore Expression (SG-NEx) project is an international collaboration to generate reference transcriptomes and a comprehensive benchmark data set for long read RNA-Seq. Transcriptome profiling is done using Nanopore PCR-cDNA sequencing (PCR-cDNA), Nanopore amplification-free cDNA sequencing (direct cDNA), Nanopore direct sequencing of native RNA (direct RNA), PacBio IsoSeq, and short read RNA-Seq. The SG-NEx core data includes 5 of the most commonly used cell lines and it is extended with additional cell lines and samples that cover a broad range of human tissues. All core samples are sequenced with at least 3 high quality replicates. For a subset of samples spike-in RNAs are used and matched m6A profiling data is available.
Overview
The Singapore Nanopore Expression (SG-NEx) project is an international collaboration to generate reference transcriptomes and a comprehensive benchmark data set for long read RNA-Seq. Transcriptome profiling is done using Nanopore PCR-cDNA sequencing (PCR-cDNA), Nanopore amplification-free cDNA sequencing (direct cDNA), Nanopore direct sequencing of native RNA (direct RNA), PacBio IsoSeq, and short read RNA-Seq. The SG-NEx core data includes 5 of the most commonly used cell lines and it is extended with additional cell lines and samples that cover a broad range of human tissues. All core samples are sequenced with at least 3 high quality replicates. For a subset of samples spike-in RNAs are used and matched m6A profiling data is available.
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.
Pricing
This is a publicly available data set. No subscription is required.
Legal
Content disclaimer
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Delivery details
AWS Data Exchange (ADX)
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Open data resources
Available with or without an AWS account.
- How to use
- To access these resources, reference the Amazon Resource Name (ARN) using the AWS Command Line Interface (CLI). Learn more
- Description
- Nanopore and PacBio long read RNA Seq data and matched short read RNA-Seq from the Singapore Nanopore Expression Project (SG-NEx). The data includes raw signal data (fast5), basecalled reads (fastq), aligned reads (bam), processed data for RNA modification detection (json), reference genome annotation files (gtf and fa) and sample metadata (txt).
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::sg-nex-data
- AWS region
- ap-southeast-1
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://sg-nex-data/
- Description
- Nanopore long read RNA Seq data from the Singapore Nanopore Expression Project (SG-NEx). The data includes raw signal data (blow5), converted from raw signal data (fast5).
- Resource type
- S3 bucket
- Amazon Resource Name (ARN)
- arn:aws:s3:::sg-nex-data-blow5
- AWS region
- ap-southeast-1
- AWS CLI access (No AWS account required)
- aws s3 ls --no-sign-request s3://sg-nex-data-blow5/
Resources
Vendor resources
Support
Contact
Managed By
The Genome Institute of Singapore (https://www.a-star.edu.sg/gis )
How to cite
The Singapore Nanopore Expression Data Set was accessed on DATE from https://registry.opendata.aws/sgnex .