Illumina HiSeq 2500 paired end sequencing; Scottish Blackface x Texel sheep transcriptome and gene expression atlas.(ERR2074059)
| Run | Spots | Bases | Size | Published | Access Type |
|---|---|---|---|---|---|
ERR2074059 |
4.4M | 1.1Gbp | 507.1M | 2017-08-10 | public |
| Name | Value |
|---|---|
| ENA-FIRST-PUBLIC | 2017-08-04 |
| ENA-LAST-UPDATE | 2018-11-16 |
| Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
|---|---|---|---|---|---|---|---|
| ERX2133175 | SHPL5Cae | Illumina | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED |
Design:
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMEA5218168 (ERS2107142) | caecum from a female one week old texel x blackface lamb, OAR_RI_L5 | Ovis aries |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJEB19199 | ERP021182 | RNA sequencing of tissues and cell types from Texel x Scottish Blackface sheep for transcriptome annotation and expression analysis. |
Sheep are an important source of meat, milk and fibre globally. To support functional annotation of the sheep genome we have produced a high-resolution atlas of gene expression from a comprehensive set of tissues and cell types from Texel x Scottish Blackface crossbred individuals. RNA-Seq libraries were generated by Edinburgh Genomics from tissues and cells representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The dataset includes 352 medium depth (>25 million reads per sample) mRNA-Seq stranded libraries (125 base pairs paired-end) and 74 high depth (>100 million reads per sample) total RNA-Seq stranded libraries (125 base pairs paired-end). This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact emily.clark@roslin.ed.ac.uk or faang-dcc@ebi.ac.uk to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle.
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 | 279,095 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/ERR002/074/ERR2074059.sralite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-1/ERR2074059/ERR2074059.sralite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-105/ERR2074059/ERR2074059.zq.1 | gs.us-east1 | gcp identity |
- 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?
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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.