De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX Titanium Platform of 454 pyrosequencing(SRR087417)
| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
SRR087417 |
383.9k | 197.7Mbp | 456.9M | 41.2% | 2011-04-26 | public |
This run has 2 reads per spot:
| L=4, 100% | ̅L=511, σ=91.7, 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 |
|---|---|---|---|---|---|---|---|
| SRX035761 | Jatropha 454 Normalized cDNA from 5 tissues | LS454 | FL-cDNA | TRANSCRIPTOMIC | unspecified | SINGLE |
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMN00188808 (SRS150508) | Jatropha curcas |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJNA79875 | SRP004898 | De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX Titanium Platform of 454 pyrosequencing |
Jatropha curcas L. is an important non edible oilseed crop with promising future in biodiesel production. However, factors like oil quantity, quality, toxicity of seed cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier we have cloned 7,009 unigenes by sequencing 12,084 ESTs from the developing seeds of J. curcas using Sanger's method. In order to expedite the process of gene discovery, we have undertaken high throughput 454 pyrosequencing of the cDNA fragments prepared from roots, mature leaves, flowers, developing seeds, and embryos of the same species. Here we report the assembly of 17,457 transcripts from 381,957 reads with an average read length of 343 bases. Average length of the assembled transcripts was 916 bp. About 30% of the assembled transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX result revealed that 2,589 of these transcripts represent full length genes. The assembled transcripts were validated by RT-PCR analysis of 28 randomly selected transcripts, and the results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways. This included 56 genes coding for 29 enzymes and proteins involved in oil biosynthesis. This is a significant outcome of the current study because cloned genes are essential for genetic manipulation of the oil biosynthesis pathway in jatropha to make it an ideal biodiesel crop.
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 | 446,152 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR087417/SRR087417 | worldwide | anonymous |
| SRA Lite | 378,665 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR000/087/SRR087417/SRR087417.lite.1 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-9/SRR087417/SRR087417.lite.1 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-109/SRR087417/SRR087417.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 | 1,199,974 Kb | AWS | s3://sra-pub-src-12/SRR087417/Jatropha%20curcas%20454%20sequencing%20data.sff | - | 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?
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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.
Taxonomy Analysis
- Unidentified reads: 5.51%
- Identified reads: 94.49%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Jatropha curcas | species | 94.3 | 186,429 |
- 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