| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
SRR090452 |
288.4k | 151.0Mbp | 341.8M | 43.1% | 2012-03-01 | public |
This run has 2 reads per spot:
| L=4, 100% | ̅L=520, σ=103.6, 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 |
|---|---|---|---|---|---|---|---|
| SRX033004 | EM | LS454 | FL-cDNA | TRANSCRIPTOMIC | cDNA | SINGLE |
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMN00139521 (SRS140304) | Gills were sampled from 10 fish. Total RNA was extracted using TRizol (Invitrogen, Cergy-Pontoise, France) according to the manufacturer's instructions. Total RNA yield was estimated by using a Nanodrop 1000 spectrophotometer (Labtech, Palaiseau, France) and RNA quality was checked with an Agilent Bioanalyzer (Agilent Technologies, Massy, France). Only good quality total RNA (RNA Integrity Number (RIN)>8) were selected. Total RNA from 10 extractions were pooled to minimize the impact of biological variance and to have a large quantity necessary to the library preparation. This pool was purified with the NucleoSpin® RNA II kit (Macherey-Nagel, Hoerdt, France) according to the protocol "Clean-up of RNA from reaction mixtures". This purification was made from 200µg of the Total RNA mix and the elution was done twice with 70µl H2O (2 successives elutions). mRNA were then isolated from 250µg of total RNA using the Nucleotrap® mRNA kit (Macherey-Nagel, Hoerdt, France) as described in the manufacturer's manual, except for the elution procedure (40µl prewarmed (68°C) H2O for 40µl Oligo(dT) latex beads used, 3 rounds of elution). Quality of mRNA and depletion in ribosomal RNA were checked with the Agilent Bioanalyzer (Agilent Technologies, Massy, France). Different isolations of mRNA were made per sample, pooled and then ethanol precipitated overnight (2 vol of cold absolute ETOH, 1/10 vol of 3M pH5.2 Sodium Acetate and 20µg of glycogen). Double stranded cDNA were prepared as described by Leroux et al. [2010] using a modified protocol of the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Cergy-Pontoise, France). Briefly, a modified primer (5' GAGAGAGAGACTGGAG(T)16VN 3') containing the GsuI restriction site and methylated dCTP (10mM dm5CTP, Fermentas, Saint-Remy-les-Chevreuse, France) were used during the first strand cDNA synthesis. First strand was synthesized from 3µg of mRNA. Next steps (second strand synthesis, RNase I digestion, phenol/chloroform extraction and ethanol precipitation) were proceeded according to the manufacturer's instructions. Pellets were resuspended in 9µl of water. 5 independent synthesis were made for each sample and pooled in order to obtain a total of 3.2µg. Then, the double-stranded cDNA was digested by GsuI (5U) to remove the polyA tail for 90min at 30°C. cDNAs were quantified using Quant-iT PicoGreen kit (Invitrogen, Cergy-Pontoise, France). | Oncorhynchus mykiss |
| SRA Study | Title |
|---|---|
| SRP004756 | Characterization of rainbow trout gonads, brains and gills deep cDNA repertoires using a 454-Titanium sequencing approach |
Background Rainbow trout, Oncorhynchus mykiss, is an important worldwide aquaculture species and in addition to its commercial interest, it is also a model research organism of considerable scientific importance. Because of the lack of a currently available whole genome sequence in that species, genomic analysis have been often slowed down by the limited knowledge available on it transcriptome. Using next generation sequencing (NGS) technologies we aimed to complement this knowledge by providing new tissue-specific cDNA repertoires from different rainbow trout tissues using the 454-Titanium technology. Results Several non-normalized cDNA libraries were constructed from testis, ovaries, brains and gills rainbow trout samples and these different libraries were sequenced in 10 separate half-runs of 454-Titanium. Overall we produced a total of 3 millions good quality sequences (testis: 1.234.260, ovaries: 738.510, brains: 481.363 and gills: 613.223) with an average size of 328 bp representing more than 1 Gb of expressed sequence information.
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 | 333,815 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR090452/SRR090452 | worldwide | anonymous |
| SRA Lite | 284,414 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR000/090/SRR090452/SRR090452.lite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-9/SRR090452/SRR090452.lite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-109/SRR090452/SRR090452.lite.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 |
|---|---|---|---|---|---|
| sff | 908,513 Kb | AWS | s3://sra-pub-src-13/SRR090452/F6VG15V02.sff | - | 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: 24.17%
- Identified reads: 75.83%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Salmo salar | species | 74.8 | 112,973 |
- 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