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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR1009171	643.3k	354.6Mbp	805.1M	43.4%	2014-03-13	public

Quality graph (bigger)(smaller)

040

Phred quality score

This run has 2 reads per spot:

L=4, 100%

̅L=547, σ=84.7, 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
SRX352443	Good quality cork	LS454	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE

Show designHide design

Biological sample Phellogenic tissue was collected from 10 mature cork oaks under cork production (estimated age 50-70 years) in Southern Portugal. The sample was taken at the time of cork harvest, in the period of end July-beginning August 2011, by scratching the inside of the plank (the so-called cork belly, corresponding to the torn out phellogen) immediately after the separation of the cork plank from the tree stem, and freezing in liquid nitrogen right after the collection. Five samples were taken from cork oaks producing good quality cork and five samples from trees with bad quality cork were retained for analysis. cDNA preparation The quality of total RNA was verified on Agilent 2100 Bioanalyzer with the RNA 6000 Pico Kit (agilent Technologies, Waldbronn, Germany) and the quantity assessed by fluorimetry with the Quant-iT RiboGreen RNA kit (Invitrogen, CA, USA). A fraction of 0.5-2 micrograms of each pool of total RNA was used as starting material for cDNA synthesis with the MINT cDNA synthesis kit (Evrogen, Moscow, Russia), a strategy based on the SMART double-stranded cDNA synthesis methodology with amplification of polyA mRNA molecules using a modified template-switching approach that allows the introduction of known adapter sequences to both ends of the first strand cDNA. The synthesis were also done with a modified oligodT containing a restriction site for Bsgl to eliminate these tails and, in that way, minimize the interference of a A homopolymers during the 454 sequencing run. Non-normalized cDNA was quantified by fluorescence and sequence in 454 GS FLX Titanium according to the standard manufacturer’s instructions (Roche-454 Life Sciences, Bradford, CT, USA) at Biocant (Cantanhede, Portugal).

Biosample	Sample Description	Organism	Links
SAMN02351106 (SRS481410)	pool of five trees that produce good quality cork	Quercus suber	Transcriptional profiling of phellogenic tissue PRJNA218509

Bioproject	SRA Study	Title
PRJNA218509	SRP030001	Quercus suber Transcriptome or Gene expression

Abstract:

The present work establishes a comparison of phellogenic genes differentially expressed during the development of cork of good and bad quality making use of Roche 454-pyrosequencing.

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	786,242 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1009171/SRR1009171	worldwide	anonymous
SRA Lite	647,916 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/009/SRR1009171/SRR1009171.lite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-9/SRR1009171/SRR1009171.lite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-109/SRR1009171/SRR1009171.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	2,078,751 Kb	AWS	s3://sra-pub-src-10/SRR1009171/CB.sff	-	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: 86.44%
Identified reads: 13.56%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Maloideae	subfamily	3.4	12,223
Eukaryota	Populus	genus	2.6	9,145
Eukaryota	Euphorbiaceae	family	1.8	6,506
Eukaryota	Morus notabilis	species	1.8	6,305
Eukaryota	Gossypium	genus	1.7	5,856
Eukaryota	Rosoideae	subfamily	1.5	5,323
Eukaryota	Rhamnaceae	family	1.4	4,896
Eukaryota	Fabales	order	1.2	4,201
Eukaryota	Sapindales	order	0.9	3,244

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

Good vs bad quality cork: high-throughput sequence of phellogenic tissue(SRR1009171)

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