Run Browser : Browse : Sequence Read Archive : NCBI/NLM/NIH

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR1161521	6.8M	1.4Gbp	895.6M	49.2%	2015-07-22	public

Quality graph (bigger)(smaller)

240

Phred quality score

This run has 2 reads per spot:

L=101, 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
SRX670826		Illumina	RNA-Seq	TRANSCRIPTOMIC	unspecified	PAIRED

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Total RNA was extracted from each sample using the RNeasyTM Plant Mini Kit following the manufactures instructions (Qiagen, Valencia, CA) and the RNA integrity was measured with an RNA 6000 Nano LabchipTM on the Agilent 2100 BioanalyzerTM (Agilent Technologies, Santa Clara, CA). Using the mRNA-Seq Sample Prep Kit (Illumina, protocol version 1004898 Rev. D, September 2009), the mRNA-Seq library was generated using 10 µg total RNA from each of the twelve samples; it was purified using poly-T oligonucleotide-attached magnetic beads and fragmented using divalent cations under elevated temperature. Using reverse transcriptase and random hexamer primers, first strand cDNA copies of the mRNA fragments were generated. The second strand cDNA was then synthesized using DNA Polymerase I and RNaseH. Using the Multiplexing Sample Preparation Oliogonucleotide KitTM, the Illumina adaptors were added by ligation and a fragment size of approximately 200bp was isolated via gel purification. The libraries generated were enriched by 18 PCR cycles. Using the InvitrogenTM Qubit® Fluorometer (Life Technologies, Carlsbad, CA), the concentrations of the libraries were determined, and purity and size of the libraries were measured using the DNA 1000 kitTM on the Agilent 2100 BioanalyzerTM (Agilent Technologies, Santa Clara, CA). An equimolar amount of each library was pooled and diluted with EB buffer (Qiagen, Valencia, CA) to 10 nM for preparation for paired-end Illumina GAIIx sequencing.

Biosample	Sample Description	Organism	Links
SAMN02566651 (SRS675422)	Meristem tissue	Lolium perenne	PRJNA222646

Bioproject	SRA Study	Title
PRJNA222646	SRP044151	Lolium perenne strain:P226/135/16 Transcriptome or Gene expression

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Perennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. De novo transcriptome assembly of the inbred genotype created 186,141 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,627 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,946 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,996 transcripts with a Pfam protein domain and 2,357 putative secreted proteins. To evaluate the reference transcriptome we targeted the high-affinity K+ transporter gene family and found multiple orthologs. Our study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.

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	337,246 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/161/SRR1161521/SRR1161521.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-6/SRR1161521/SRR1161521.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-102/SRR1161521/SRR1161521.zq.1	gs.us-east1	gcp identity
SRA Normalized	874,588 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1161521/SRR1161521	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	501,657 Kb	AWS	s3://sra-pub-src-12/SRR1161521/P226_135_16_meristem_pair_end_2.txt.bz2	-	Use Cloud Data Delivery
fastq	513,674 Kb	AWS	s3://sra-pub-src-9/SRR1161521/P226_135_16_meristem_pair_end_1.txt.bz2	-	Use Cloud Data Delivery

Egress and Access: what does it mean?

Egressterm used by cloud providers to describe cost (charged to the user) of moving data outside of the storage region

Free Egress column 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: 92.69%
Identified reads: 7.31%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Brachypodium distachyon	species	3.7	50,964
Eukaryota	Oryza brachyantha	species	0.6	7,609
Eukaryota	Setaria italica	species	0.5	7,403
Eukaryota	Sorghinae	subtribe	0.5	6,901
Eukaryota	Pentapetalae		0.3	3,847
Eukaryota	Bilateria		0.2	2,932
Bacteria	Bacteria	superkingdom	0.1	1,915
Viruses	Ryegrass mosaic virus	species	0.0	116
Viruses	Barley yellow dwarf virus-PAV	species	0.0	45

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

How taxonomy analysis is done?: A fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next generation sequence submissions

De novo assembly of perennial ryegrass transcriptome using an RNA-seq strategy(SRR1161521)

SRA archive data

Original format

Taxonomy Analysis

Strong signals

Intensity graph

	View: biological readstechnical readsquality scoresadvanced options Hide Reads base space color space show separated reads quality score with bases show clipped show 4 channel quality scorewith bases Intensity graph Signals table
	Intensity graph