Illumina HiSeq 2000 paired end sequencing; RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 15 days (D15) and 20 days (D20) shading treatment after pollination, against 15 DAP, 20 DAP untreated controls. The purple-grain wheat were grown under natural field conditions at Shandong Agricultural University Experimental Station (36169 N, 117169 E), Taian, China during Octubor, 2015 to June, 2016.(ERR2146870)
| Run | Spots | Bases | Size | GC content | Published | Access Type |
|---|---|---|---|---|---|---|
ERR2146870 |
20.3M | 6.1Gbp | 2.9G | 56.4% | 2018-03-27 | public |
This run has 2 reads per spot:
| L=150, 100% | L=150, 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 | 2018-03-26 |
| ENA-LAST-UPDATE | 2018-11-16 |
| Experiment | Library Name | Platform | Strategy | Source | Selection | Layout | Action |
|---|---|---|---|---|---|---|---|
| ERX2203403 | L20_2_p | Illumina | RNA-Seq | TRANSCRIPTOMIC | PCR | PAIRED |
| Biosample | Sample Description | Organism |
|---|---|---|
| SAMEA104326262 (ERS1951240) | Protocols: Having cut both side of embryo and another, the pericarp of the seed were stripped and frozen in liquid nitrogen and stored at 80oC until RNA extraction. Plants of purple-grain wheat line Luozhen No.1 were grown under natural field conditions at Shandong Agricultural University Experimental Station (36169 N, 117169 E), Taian, China during October, 2015 to June, 2016. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. Total RNAs were extracted from pericarp of purple-grain wheat using an RNeasy Plant Mini Kit (Cat. No. 74904, Qiagen, Valencia, CA, USA). At least 500 ng total RNA was extracted from each material used for library construction. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the quality control steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000. | Triticum aestivum |
| Bioproject | SRA Study | Title |
|---|---|---|
| PRJEB22854 | ERP104568 | RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 15 days (D15) and 20 days (D20) shading treatment after pollination, against 15 DAP, 20 DAP untreated controls. The purple-grain wheat were grown under natural field conditions at Shandong Agricultural University Experimental Station (36169 N, 117169 E), Taian, China during Octubor, 2015 to June, 2016. |
Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. But little is known about molecular mechanism of anthocyanin biosynthesis. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced four pericarp cDNA libraries, D15 (15 DAP), D20 (20 DAP) of shading treatment, and L15 (15 DAP), L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000. After quality control, raw reads are filtered into clean reads which will be aligned to the reference sequences. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio, and proceed with downstream analysis including gene and isoform expression, deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection. Further, we also perform deep analysis based on different expression genes, including Gene Ontology (GO) enrichment analysis, Pathway enrichment analysis, cluster analysis, and finding transcriptor factor.
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 | 1,485,202 Kb | NCBI | https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/ERR002/2146/ERR2146870/ERR2146870.lite.2 | worldwide | anonymous |
| AWS | s3://sra-pub-zq-6/ERR2146870/ERR2146870.lite.2 | s3.us-east-1 | aws identity | ||
| GCP | gs://sra-pub-zq-106/ERR2146870/ERR2146870.lite.2 | gs.us-east1 | gcp identity | ||
| SRA Normalized | 2,864,308 Kb | AWS | https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR2146870/ERR2146870 | 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 | 1,820,775 Kb | AWS | s3://sra-pub-src-3/ERR2146870/L20_2_1.fq.gz.1 | - | Use Cloud Data Delivery |
| EBI | http://ftp.sra.ebi.ac.uk/vol1/run/ERR214/ERR2146870/L20_2_1.fq.gz | worldwide | anonymous | ||
| fastq | 2,049,685 Kb | AWS | s3://sra-pub-src-3/ERR2146870/L20_2_2.fq.gz.1 | - | Use Cloud Data Delivery |
| EBI | http://ftp.sra.ebi.ac.uk/vol1/run/ERR214/ERR2146870/L20_2_2.fq.gz | worldwide | anonymous |
- 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: 20.34%
- Identified reads: 79.66%
Strong signals
| SuperKingdom | Organism | Rank | %% | Kbp | Coverage |
|---|---|---|---|---|---|
| Eukaryota | Aegilops tauschii subsp. tauschii | subspecies | 77.5 | 4,708,214 | |
| Eukaryota | Brachypodium distachyon | species | 0.3 | 18,088 | |
| Eukaryota | rosids | 0.3 | 17,909 | ||
| Eukaryota | Alternaria alternata | species | 0.3 | 16,149 | 0.5 |
| Bacteria | Streptomyces | genus | 0.2 | 14,089 | |
| Eukaryota | Botrytis cinerea | species | 0.2 | 9,640 | 0.2 |
| Bacteria | Escherichia coli | species | 0.2 | 9,476 | 1.8 |
| Bacteria | Klebsiella pneumoniae | species | 0.1 | 4,499 | 0.8 |
| Eukaryota | Panicum hallii | species | 0.1 | 4,364 |
- 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