Illumina HiSeq 2500 paired end sequencing; Subtle effects of radiation on embryo development of the 3-spined stickleback(ERR3281056)
| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
ERR3281056 |
11.5M | 2.9Gbp | 1.2G | 51.9% | 2020-02-05 | public |
This run has 2 reads per spot:
| L=125, 100% | L=125, 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
| Name | Value |
|---|---|
| ENA-FIRST-PUBLIC | 2020-02-04 |
| ENA-LAST-UPDATE | 2019-04-15 |
| Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
|---|---|---|---|---|---|---|---|
| ERX3307855 | HighExposure_Rep2_p | Illumina | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED |
Design:
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMEA5567544 (ERS3369569) | Protocols: Adult sticklebacks were kept in artificial reproduction conditions in order to generate the in vitro fertilized embryos. Four couples were used to generate the embryos. 104 embryos were used for next generation sequencing analyses. 3 replicates of pool of 4 to 10 embryos per condition were used for NGS analyses. Each embryo was placed in individual glass tube and waterborne exposed to 3 mL of a radioactive solution of 0.1, 1 and 10 mGy/day using 32P and artificial water. These doses encompass the chronic low (0.1 mGy/day) and medium (1 mGy/day) doses encountered in the environment at Chernobyl 30 years after the accident, and the initial high dose to fish after the accident (10 mGy/day). These doses span the protection threshold of ecosystems set at 10 uGy/h (0.24 mGy/day). Control embryos were kept in clean artificial water. The embryos were exposed for 10 days and euthanized according to schedule 1 of the Home Office Licence (ASPA, 1986) using tricaine methanesulfonate (Sigma). Total RNAs were extracted using the High Pure RNA Tissue kit (Roche Diagnostics Ltd, West Sussex, U.K.) according to the supplier's instructions. RNA quality and integrity was evaluated using a bioanalyzer. RNA integrity numbers ranged from 7.4 to 9.5. mRNA-seq libraries were prepared for each pool using the Illumina TruSeq mRNA library kit following standard protocols. | Gasterosteus aculeatus |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJEB32176 | ERP114823 | Subtle effects of radiation on embryo development of the 3-spined stickleback |
Following serious accidents at the Chernobyl and Fukushima nuclear power plants in 1986 and 2011 respectively, local flora and fauna have been chronically exposed to environmental radiation for many years . However, little is known about the environmental effects of low doses of radiation on aquatic organisms. The present study assesses the effect of an environmentally relevant dose range of radiation (Control: 0, Low (L): 0.1, Medium (M): 1 and High (H): 10 mGy/day) of waterborne 32P on early life stages of the 3-spined stickleback, Gasterosteus aculeatus. Here we assess the global effects on gene regulation on the embryo development of fish suffering from differing levels of environmental radiation to identify significantly altered transcriptional networks as a result of sustained radiation exposure.
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 Lite | 707,929 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/ERR003/3281/ERR3281056/ERR3281056.lite.2 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-3/ERR3281056/ERR3281056.lite.2 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-102/ERR3281056/ERR3281056.lite.2 | gs.us-east1 | gcp identity | ||
| SRA Normalized | 1,171,533 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR3281056/ERR3281056 | worldwide | anonymous |
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 | 848,677 Kb | AWS | s3://sra-pub-src-5/ERR3281056/150810_D00248_0109_BC7FL8ANXX_4_IL-TP-018_2.sanfastq.gz.1 | - | Use Cloud Data Delivery |
| fastq | 825,309 Kb | AWS | s3://sra-pub-src-5/ERR3281056/150810_D00248_0109_BC7FL8ANXX_4_IL-TP-018_1.sanfastq.gz.1 | - | Use Cloud Data Delivery |
- Egress and Access: what does it mean?
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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"?
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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: 8.36%
- Identified reads: 91.64%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Gasterosteus aculeatus aculeatus | subspecies | 90.4 | 2,606,151 | |
| Eukaryota | Pungitius pungitius | species | 0.7 | 21,404 | |
| Bacteria | Pantoea vagans | species | 0.3 | 7,416 | 1.5 |
| Bacteria | Escherichia coli | species | 0.2 | 4,812 | 0.9 |
| Bacteria | Terrabacteria group | 0.0 | 362 | ||
| Bacteria | Pseudomonadales | order | 0.0 | 228 | |
| Viruses | Human respirovirus 1 | species | 0.0 | 10 |
- 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