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metagenomics of human oral microbiome (SRR8114030)
Run | Spots | Bases | Size | GC Content | Data Status | Published |
---|---|---|---|---|---|---|
SRR8114030 | 9.6M | 2.4G | 995.7MB | 53.7% | Public | 2019-03-26 |
This run has variable number of reads per spot
Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
---|---|---|---|---|---|---|---|
SRX4940482 | M11.5-V1-saliva-metaG | Illumina | WGS | METAGENOMIC | RANDOM | PAIRED |
Biosample | Sample Description | Organism | Links |
---|---|---|---|
SAMN09837438 (SRS3984278) | human oral metagenome | bioproject/289586 |
Bioproject | SRA Study | Title |
---|---|---|
PRJNA289586 | SRP072561 | Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus |
Recent evidence from high-resolution molecular studies suggests links between microbial dysbiosis in the gastrointestinal tract and a number of complex chronic diseases including diabetes mellitus. The present study forms a pilot study for the larger Luxembourg-based Diabetes Multiplex Family Study (MUST). Within the pilot study, we investigate the interplay of the gastrointestinal microbiota, lifestyle and genetic background in an observational study of families with two or more individuals affected by type 1 diabetes mellitus. Faecal samples which have undergone comprehensive biomolecular extractions are currently analysed using a multi-omics approach. Anthropometric data, including demographics, medical history, health status, medication, and dietary habits of all study participants were collected and are integrated with molecular data.
SRA archive data is normalized by the SRA load process and used by the SRA Toolkit to read and produce formats like FASTQ, SAM, etc. The default toolkit configuration enables it to find and retrieve SRA runs by accession.
Public SRA files are now available from GCP and AWS cloud platforms as well as from NCBI. Access to most data in the cloud requires a user account with the cloud service provider. The user’s account will incur costs for cloud compute or to copy data outside of the specified cloud service region.
Type | Version | Created | Size | Location | Name | Free Egress | Access Type |
---|---|---|---|---|---|---|---|
SRA Normalized | 1 | 2018-10-26 | 995.7MB | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8114030/SRR8114030 | worldwide | anonymous |
SRA Lite | 1 | 2020-06-20 | 601.2MB | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR008/114/SRR8114030.sralite.1 | worldwide | anonymous |
AWS | s3://sra-pub-zq-7/SRR8114030/SRR8114030.sralite.1 | s3.us-east-1 | aws identity | ||||
GCP | gs://sra-pub-zq-102/SRR8114030/SRR8114030.zq.1 | gs.us-east1 | gcp identity |
The original files submitted to SRA. These files may require specific software to open, read and interpret data.
Type | Version | Created | Size | Location | Name | Free Egress | Access Type |
---|---|---|---|---|---|---|---|
fastq | 1 | 2020-02-11 | 660.6MB | AWS | s3://sra-pub-src-3/SRR8114030/M11.5-V1-saliva-metaG.preprocessed.R1.fastq.gz | - | Use Cloud Data Delivery |
fastq | 1 | 2020-02-11 | 661.9MB | AWS | s3://sra-pub-src-3/SRR8114030/M11.5-V1-saliva-metaG.preprocessed.R2.fastq.gz | - | Use Cloud Data Delivery |
fastq | 1 | 2020-02-11 | 18.0MB | AWS | s3://sra-pub-src-3/SRR8114030/M11.5-V1-saliva-metaG.preprocessed.SE.fastq.gz | - | Use Cloud Data Delivery |
Egress - term used by cloud providers to describe cost (charged to the user) of moving data outside of the storage region
Free Egress column indicates where the data can be accessed without an egress charge:
- worldwide - can be downloaded from anywhere for free
- s3.us-east-1 - is free to access from machines running in Amazon's us-east-1 region, access from other regions or transport outside of AWS will require paying egress charges
- gs.US - is free to access from machines running in Google’s gs.US region, access from other regions or transport outside of GCP will require paying egress charges
Access Type - describes whether a cloud service user account is necessary for data access. "anonymous" access means general public access
Name - column provides either a link to free download location at NCBI or a URL for the cloud provider storage location. Either s3:// for Amazon or gs:// for Google storage
In order to support large scale (hyper parallel) data analyses SRA data is now available at GCP and AWS with few caveats:
- SRA data is copied to the cloud from NCBI. There may be a lag between availability from NCBI and from CSP (cloud service providers).
- To access public data user account with the cloud service provider is required. Your account will incur costs for cloud compute and/or to copy data (either archival or results of your compute) outside of the specified cloud service region.
- Distribution of protected data is signed by NIH account and requires user to operate in the same region as the data.
SRA has also begun to provide access to originally submitted source files:
- not all files have been validated by SRA;
- not all source files have been made available for different reasons (contaminations cleared on load but unsuitable for publishing, some subjects consented to share their virus but not their own genome, public health pipelines putting hospitals or plants id in their system in file name etc);
- the volume of this type of data a much larger and it is not used as often so we will keep most of it on tape or "cold" storage in cloud. As a result, the data may not be available instantly and restore requests will be served on first-come first-served basis and cost of restore may be charged to your user account.
Please visit SRA Data Delivery service to request Sequence Read Archive (SRA) data to be delivered to an Amazon Web Services (AWS) or Google Cloud Platform (GCP) bucket of your choice.