| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
SRR6639055 |
14.0M | 1.4Gbp | 235.2M | 47.5% | 2018-06-13 | public |
| Reference | Length | Coverage | Unaligned |
|---|---|---|---|
| Felis_catus_6.2 | 2.4Gbp | 0.57x | .00% |
This run has 1 read per spot:
| 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 |
|---|---|---|---|---|---|---|
| SRX3626707 | Illumina | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE |
| Biosample | Sample Description | Organism | Links |
|---|---|---|---|
| SAMN08432504 (SRS2893809) | Felis catus | PRJNA432069 |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJNA432069 | SRP131692 | Transcriptome profiling of alphaherpesvirus-infected cells treated with the HIV-integrase inhibitor raltegravir reveals profound and specific alterations in host transcription. |
Purpose: To study the effects of raltegravir treatment for corneal cells on host gene expression during FHV-1 infection and in uninfected cells. Method: For examination of effects in infected cells, corneal cells were infected with FHV-1 for 2 hours and treated with raltegravir or DMSO for 2 h. For examination of effects in uninfected cells, corneal cells were infected with FHV-1 for 2 h. Data was analyzed using a standard pipeline. Follow up of results were done with SYBR green based qPCR and functional assays where relevant. Results: In infected cells, we identifed 399 differentially expressed genes following raltegravir therapy. Many of these genes had functions as anti-angiogenic factors and in metabolic pathways. In contrast, in uninfected cells, only 27 genes were identified as differentially regulated by raltegravir, with little overlap with those modulated during infection and little shared biological functions. This indicates that raltegravir is unlikely to induce side effects in vivo. Conclusion: Our study represents the first, to our knowledge, use of RNAseq technology to study the effects of an antiviral on host gene expression during a virus infection. We conclude that such methodology will be useful in future studies to identify bystander effects of drug treatment. Overall design: RNAseq analysis of gene expression of antiviral treated, FHV-1 infected or uninfected corneal cells. For each sample, 3 independent biological replicates were performed
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 | 229,743 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6639055/SRR6639055 | worldwide | anonymous |
| SRA Lite | 66,503 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR006/639/SRR6639055.sralite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-6/SRR6639055/SRR6639055.sralite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-105/SRR6639055/SRR6639055.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 |
|---|---|---|---|---|---|
| bam | 664,169 Kb | AWS | s3://sra-pub-src-4/SRR6639055/2C.bam | - | 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.
| Alignment | Reads | Bases | Fraction |
|---|---|---|---|
| Primary | 14.0M | 1.4Gbp | 100% |
| Alternate | 413.7k | 41.1Mbp | 2.92% |