| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
DRR222484 |
84.3k | 24.9Mbp | 20.5M | 63% | 2020-04-16 | public |
This run has 1 read per spot:
| ̅L=296, σ=91.4, 100% |
- Legend
Technical read Application Read L=4, 100% Length is 4, 100% spots contain this read ̅L=165, σ=92.8, 66% Average length is 165, standard deviation is 92.8, 66% spots contain this read
| Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
|---|---|---|---|---|---|---|---|
| DRX212769 | Ion Torrent | AMPLICON | TRANSCRIPTOMIC | RT-PCR | SINGLE |
| Biosample | Sample Description | Organism | Links |
|---|---|---|---|
| SAMD00220073 (DRS137657) | Family 2 | Felis catus | PRJDB9676 |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJDB9676 | DRP006030 | Identification of novel alleles and structural haplotypes of major histocompatibility complex class I and DRB genes in domestic cat (Felis catus) by a newly developed NGS-based genotyping method |
Peripheral white blood cells (PWBCs) were obtained from 20 related domestic cats from two families and five unrelated cats (A6, A116, A165, A176 and A214). Each family was composed of ten cats representing three generations that were considered suitable for investigating the FLA allele and haplotype segregation. We first used the five unrelated cats to elucidate the alleles and specificity of expressed FLA-I loci in PWBCs and then used the 20 related cats for the NGS-based genotyping of expressible FLA-I and FLA-DRB loci. We have identified and presented novel alleles for the FLA-I and FLA-DRB genes and provided some further insights into the development of the NGS-based genotyping method at the RNA expression level, phylogenetic relationships and haplotype structures of FLA-I and FLA-DRB alleles and haplotypes in 20 cats from two families. This FLA polymorphism information could be useful as a standard internal control to establish the feline MHC genetic background for the benefit of biomedical research into disease associations such as infectious disease and autoimmune diseases in veterinary medical field.
SRA archive 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 | Size | Location | Name | Free Egress | Access Type |
|---|---|---|---|---|---|
| SRA Normalized | 19,984 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/DRR222484/DRR222484 | worldwide | anonymous |
| SRA Lite | 6,450 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/DRR000/222/DRR222484/DRR222484.lite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-8/DRR222484/DRR222484.lite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-107/DRR222484/DRR222484.lite.1 | gs.us-east1 | gcp identity |
- Egress and Access: what does it mean?
-
Egress
term used by cloud providers to describe cost (charged to the user) of moving data outside of the storage region Free Egresscolumn 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 Typedescribes whether a cloud service user account is necessary for data access. "anonymous" access means general public access Namecolumn 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
- Why is SRA data in the cloud?
-
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 comute) 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 files have been copied to cloud locations (recovering it from NCBI tape system takes time ).
- 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 resore may be charged to your user account.
- What is "Cloud Data Delivery"?
-
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.