| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
SRR2032208 |
52.1M | 10.4Gbp | 6.5G | 49.4% | 2015-08-04 | public |
This run has 2 reads per spot:
| L=100, 100% | L=100, 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 |
|---|---|---|---|---|---|---|---|
| SRX1032652 | RNA130408JP_A5_514 | Illumina | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED |
Design:
| Biosample | Sample Description | Organism | Links |
|---|---|---|---|
| SAMN03610089 (SRS940314) | Austrofundulus limnaeus | PRJNA272154 |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJNA272154 | SRP058458 | Transcriptome of Austrofundulus limnaeus embryos |
Austrofundulus limnaeus is an annual killifish that inhabits ephemeral ponds in coastal desert and savanna regions of Venezuela. These fish survive in ephemeral habitats by producing drought-tolerant embryos that can enter into a state of metabolic depression termed diapause. The adults are highly hypoxia tolerant and eurythermal. The embryos are tolerant of extreme environmental stresses and can survive for months without oxygen or water. This species is an excellent model for studying the mechanisms that control cellular growth and proliferation, phenotypic plasticity during development, and tolerance to environmental stress. Studies of this organism could lead to new strategies for preventing cellular damage associated with heart attack and stroke, and provide novel insights into stem cell biology and regenerative medicine.
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 | 6,373,313 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2032208/SRR2032208 | worldwide | anonymous |
| SRA Lite | 2,648,322 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/032/SRR2032208/SRR2032208.sralite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-8/SRR2032208/SRR2032208.sralite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-102/SRR2032208/SRR2032208.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 | 362,671 Kb | AWS | s3://sra-pub-src-9/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_005.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 369,296 Kb | AWS | s3://sra-pub-src-10/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_007.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 360,640 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_008.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 359,526 Kb | AWS | s3://sra-pub-src-11/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_010.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 359,591 Kb | AWS | s3://sra-pub-src-10/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_012.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 357,209 Kb | AWS | s3://sra-pub-src-9/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_002.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 345,545 Kb | AWS | s3://sra-pub-src-9/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_005.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 346,332 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_008.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 340,271 Kb | AWS | s3://sra-pub-src-9/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_010.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 347,058 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_011.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 344,012 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_012.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 13,693 Kb | AWS | s3://sra-pub-src-13/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_014.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 362,512 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_013.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 361,235 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_009.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 355,830 Kb | AWS | s3://sra-pub-src-10/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_007.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 344,083 Kb | AWS | s3://sra-pub-src-13/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_006.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 346,672 Kb | AWS | s3://sra-pub-src-11/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_004.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 340,921 Kb | AWS | s3://sra-pub-src-11/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_003.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 339,480 Kb | AWS | s3://sra-pub-src-13/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R2_001.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 14,136 Kb | AWS | s3://sra-pub-src-10/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_014.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 374,924 Kb | AWS | s3://sra-pub-src-10/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_013.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 360,200 Kb | AWS | s3://sra-pub-src-9/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_011.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 375,481 Kb | AWS | s3://sra-pub-src-10/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_009.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 358,606 Kb | AWS | s3://sra-pub-src-13/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_006.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 360,806 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_004.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 358,734 Kb | AWS | s3://sra-pub-src-14/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_003.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 372,196 Kb | AWS | s3://sra-pub-src-11/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_002.fastq.gz | - | Use Cloud Data Delivery |
| fastq | 357,648 Kb | AWS | s3://sra-pub-src-9/SRR2032208/RNA130408JP_A5_514_AGTTCC_L002_R1_001.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.
Taxonomy Analysis
- Unidentified reads: 33.83%
- Identified reads: 66.17%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Austrofundulus limnaeus | species | 47.3 | 4,930,478 | |
| Bacteria | Bacteria | superkingdom | 18.6 | 1,942,604 | |
| Bacteria | Firmicutes | phylum | 0.2 | 25,527 | |
| Bacteria | Pseudomonas sp. NBRC 111131 | species | 0.1 | 12,312 | |
| Eukaryota | Homininae | subfamily | 0.1 | 8,816 | |
| Bacteria | Burkholderia | genus | 0.1 | 7,741 | |
| Eukaryota | Salmo salar | species | 0.1 | 6,318 | |
| Eukaryota | Kryptolebias marmoratus | species | 0.1 | 5,348 | |
| Bacteria | Clostridioides difficile | species | 0.0 | 4,842 | 1.2 |
- How to read results?
Results show distribution of reads mapping to specific taxonomy nodes as a percentage of total reads within the analyzed run. In cases where a read maps to more than one related taxonomy node, the read is reported as originating from the lowest shared taxonomic node. So when a read maps to two species belonging to the same genus, it is assigned at the genus level. Sequence reads from a single organism will map to several taxonomy nodes spanning the organism’s lineage. The number of reads mapping to higher level nodes will typically be greater than those that map to terminal nodes.
STAT results are proportional to the size of sequenced genomes. Given a mixed sample containing several organisms at equal copy number, proportionally more reads originate from the larger genomes. This means that the percentages reported by STAT will reflect genome size and must be considered against the genomic complexity of the sequenced sample.
- How can I query this analysis data?
Please take a look at NCBI SRA Cloud-based Taxonomy Analysis Table