| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
SRR3213608 |
45.7M | 9.2Gbp | 5.8G | 50.3% | 2017-02-01 | public |
This run has 2 reads per spot:
| L=101, 100% | L=101, 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 |
|---|---|---|---|---|---|---|---|
| SRX1621002 | Swordfish heart | Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED |
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMN04526262 (SRS1329767) | This sample represents RNA that was used for an RNA-seq experiment comparing heart transcriptomes from seven different species (white shark, shortfin mako, great hammerhead, yellow stingray, swordfish, ocean surgeonfish, and hogfish). This project was conducted to compare elasmobranchs (sharks and rays) to teleost fishes while also looking to see whether there are genes under convergent evolution or expression patterns in three regionally endothermic species (white shark, shortfin mako, and swordfish) relative to strictly ectothermic fishes (hogfish, ocean surgeonfish, great hammerhead, and yellow stingray). | Xiphias gladius |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJNA313962 | SRP071340 | RNA-seq of heart tissue from 7 fish species, including four elasmobranchs (white shark, shortfin mako, great hammerhead, and yellow stingray) and three teleost species (swordfish, hogfish, and ocean surgeonfish) Raw sequence reads |
RNA-seq was conducted on heart tissue from white shark (Carcharodon carcharias), shortfin mako (Isurus oxyrinchus), great hammerhead (Sphyrna mokarran), yellow stingray (Urobatis jamaicensis), swordfish (Xiphias gladius), hogfish (Lachnolaimus maximus), and ocean surgeonfish (Acanthurus bahianus). Heart transcriptomes were assembled in order to determine differences in gene content between elasmobranchs and teleost fishes as well as between regional endothermic species (white shark, mako, and swordfish) and pure ectotherms (great hammerhead, yellow stingray surgeonfish, and hogfish). We identified cases where positive selection was acting on the elasmobranch lineage and genes that had functional differences between elasmobranchs and teleosts with a focus on immune genes.
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 | 5,642,096 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3213608/SRR3213608 | worldwide | anonymous |
| SRA Lite | 2,269,177 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR003/213/SRR3213608/SRR3213608.sralite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-8/SRR3213608/SRR3213608.sralite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-101/SRR3213608/SRR3213608.noqual.1 | gs.us-east1 | gcp identity |
Original format
The original files submitted to SRA. These files may require specific software to open, read and interpret data.
| Type | Size | Location | Name | Free Egress | Access Type |
|---|---|---|---|---|---|
| fastq | 4,233,682 Kb | AWS | s3://sra-pub-src-8/SRR3213608/1431_2708_5173_N_swordfish_TGACCA_R1.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 4,258,000 Kb | AWS | s3://sra-pub-src-5/SRR3213608/1431_2708_5173_N_swordfish_TGACCA_R2.fastq.gz | - | Use Cloud Data Delivery |
- 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.