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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR3159236	1.9M	879.1Mbp	641.8M	42.3%	2017-01-25	public

Quality graph (bigger)(smaller)

240

Phred quality score

This run has 2 reads per spot:

̅L=243, σ=26.4, 100%

L=212, 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
SRX1569471	C1.2	Illumina	RNA-Seq	TRANSCRIPTOMIC	size fractionation	PAIRED

Show designHide design

"RNA from pea node 2 axillary buds was extracted using a TRIzol extraction method and then purified using RNeasy MinElute cleanup kit (Qiagen). RiboZeroTM Magnetic (Plant leaf) kit (Epicentre) was used to remove rRNA from 3.81 lg of each of the samples. The removal of rRNA was confirmed using a 2100 BioAnalyser (Agilent Technologies).The RNA libraries were prepared using the ScriptSeqTM V2 RNA Seq Library Preparation kit (Epicentre), except for the following changes: the samples were incubated in the first step for 5 minutes at the lower temperature of 70 deg C to reduce RNA fragmentation, the cDNA was purified using the MinElute kit (Qiagen), and the ScriptSeqTM Index primers 1, 8, 9, 10, 11 and 12 (Epicentre) were used as adaptors. Strand-specificity was not utilized. Size selection was performed by running the purified libraries on an agarose gel and excising a band of RNA between 350-550bps long. This was then purified using the QIAquick Gel Extraction kit (Qiagen). The QubitTM dsDNA HS Assay was used to quantify the RNA in each library. Four libraries were pooled for each sequencing run, with each library contributing 1.75 ng of RNA. The pooled libraries were prepared for sequencing using a MiSeq Desktop Sequencer (Illumina) and run on a 150 or 250 paired-end cycle cartridge."

Biosample	Sample Description	Organism	Links
SAMN04412739 (SRS1259490)		Pisum sativum	PRJNA308776

Bioproject	SRA Study	Title
PRJNA308776	SRP068822	Pisum sativum cultivar:Torsdag Raw sequence reads

Abstract:

RNA-seq using RNA from garden pea axillary buds

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	626,787 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3159236/SRR3159236	worldwide	anonymous
SRA Lite	221,297 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR003/159/SRR3159236/SRR3159236.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-8/SRR3159236/SRR3159236.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-101/SRR3159236/SRR3159236.noqual.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
fastq	450,010 Kb	AWS	s3://sra-pub-src-6/SRR3159236/Sample9_S3_L001_R1_001.fastq.gz	-	Use Cloud Data Delivery
fastq	385,876 Kb	AWS	s3://sra-pub-src-6/SRR3159236/Sample9_S3_L001_R2_001.fastq.gz	-	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: 52.43%
Identified reads: 47.57%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Pisum sativum	species	29.4	258,147
Eukaryota	Medicago truncatula	species	8.2	71,833
Eukaryota	Cicer arietinum	species	5.2	45,464
Eukaryota	Glycine max	species	1.7	15,189
Eukaryota	Lathyrus	genus	0.7	6,338
Eukaryota	Phaseolus	genus	0.7	5,946
Eukaryota	Vigna	genus	0.5	4,707
Eukaryota	Arachis	genus	0.5	4,171
Eukaryota	malvids		0.3	2,967

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

Pisum sativum cultivar:Torsdag Raw sequence reads: Sample Control 1 hour(SRR3159236)

Abstract:

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