| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
SRR6912044 |
35.6M | 8.9Gbp | 4.9G | 48.8% | 2018-04-30 | 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
| Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
|---|---|---|---|---|---|---|---|
| SRX3859973 | Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED |
| Biosample | Sample Description | Organism | Links |
|---|---|---|---|
| SAMN08811253 (SRS3102534) | Xiphophorus maculatus | PRJNA447434 |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJNA447434 | SRP136668 | Waveband Specific Transcriptional Control of Select Genetic Pathways in Xiphophorus maculatus Skin |
Changes in the transcriptional profiles of Xiphophorus maculatus skin was assessed by RNA-Seq after exposure to fluorescent (i.e., FL, 4,100K or “cool white”), or narrow wavelength regions of light between 300-600 nm (i.e., 50 nm or 10 nm regions, herein termed ”wavebands”). Exposure to varied 50 nm wavebands allowed identification of waveband specific transcriptional modulation within gene sets representing discrete functional pathways within Xiphophorus skin. For example, exposure to either 350-400 or 450-500 nm wavebands resulted in opposite transcriptional effects in necrosis and apoptosis gene sets that predict selective differential suppression or activation of these pathways (i.e., 350-400 nm; necrosis suppression, apoptosis activation, and 450-500 nm; apoptosis suppression, necrosis activation). Further investigation of waveband specific transcription employing successive 10 nm waveband exposures within the genetically responsive 500-550 nm waveband show; (a) greater numbers of genes may be transcriptionally modulated after 10 nm exposures, than observed for either 50 nm or FL exposures. (b) the 10 nm wavebands incite greater functional specificity than either 50 nm or FL exposures. (c) The principal genetic effects of FL are primarily due to the 30 nm between 500 to 530 nm. Overall design: Xiphophorus maculatus fish were exposed to 4,100K fluorescent light, 50 nm wavelength window (waveband) between 300 to 600 nm wavelength region, or 10 nm waveband between 500 and 550 nm wavelength region. Gene expression were profiled by mRNA-Seq following exposure to each type of light exposre and were compared to the baseline gene expression (i.e., no light 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 Normalized | 4,744,439 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6912044/SRR6912044 | worldwide | anonymous |
| SRA Lite | 2,246,739 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR006/912/SRR6912044.sralite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-2/SRR6912044/SRR6912044.sralite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-105/SRR6912044/SRR6912044.zq.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 | 10,794,886 Kb | AWS | s3://sra-pub-src-5/SRR6912044/XMB_105b.ac_M12mo_S_0pt_BC_2015-04-30_1.fastq | - | Use Cloud Data Delivery |
| fastq | 10,794,886 Kb | AWS | s3://sra-pub-src-5/SRR6912044/XMB_105b.ac_M12mo_S_0pt_BC_2015-04-30_2.fastq | - | 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: 6.84%
- Identified reads: 93.16%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Xiphophorus maculatus | species | 92.6 | 8,238,833 | |
| Bacteria | Bacteria | superkingdom | 0.4 | 32,813 | |
| Eukaryota | Poecilia | genus | 0.2 | 15,132 | |
| Bacteria | Firmicutes | phylum | 0.0 | 568 | |
| Bacteria | Proteobacteria | phylum | 0.0 | 333 |
- 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