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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR1659054	33.6M	6.7Gbp	4.5G	51%	2014-12-03	public

Quality graph (bigger)(smaller)

241

Phred quality score

This run has 2 reads per spot:

L=100, 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
SRX765337	B423LI_lane4	Illumina	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED

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"Tissue was harvested immediately after euthanasia. Approximately 100 mg of tissue was flash-frozen in liquid nitrogen and stored at -80 degrees Celsius until RNA was extracted. Frozen tissue was pulverized using a mortar and pestle, and total RNA was extracted using TRIzol RNA Isolation methods (Life Technologies). Quantitative and qualitative RNA assessments were made using Nanodrop (Thermo Scientific) and Bioanalyzer 2100 (Agilent ) using the RNA 6000 Nano chip. A 2-ug total RNA sample was suspended in 10 uL of DEPC-treated water. Total RNA was depleted of rRNA and the libraries were prepared using the TruSeq stranded total RNA sample preparation kit for human/mouse/rat (Illumina). The sizes of the libraries were determined on a Bioanalyzer 2100 (Agilent) using the DNA1000 chip and quantifiedon aQubit 2.0 using the broad range DNA assay (Invitrogen). Libraries were diluted to 2 uM and pooled. The pooled libraries were quantified again, this time using the Qubit high sensitivity assay, to recheck concentrations.Prepared samples were loaded into six lanes on a high output flow cell ??at a concentration of 7 pM and cluster generation was performed usinga cBot (Illumina). The flowcell was runonan IlluminaHiSeq 2500 (2X100 High Output)."

Biosample	Sample Description	Organism	Links
SAMN03201488 (SRS749649)	liver tissue isolated for directional mRNASeq to assist in genome annotation	Bison bison	PRJNA257088

Bioproject	SRA Study	Title
PRJNA257088	SRP050120	Bison bison bison isolate:TAMUID 2011002044 Genome sequencing and assembly

Abstract:

American bison Whole Genome Sequence

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	1,709,282 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/659/SRR1659054/SRR1659054.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-8/SRR1659054/SRR1659054.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-107/SRR1659054/SRR1659054.noqual.1	gs.us-east1	gcp identity
SRA Normalized	4,423,866 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1659054/SRR1659054	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	1,972,206 Kb	AWS	s3://sra-pub-src-14/SRR1659054/B423LI_CGATGT_L004_R2_001.fastq.bz2	-	Use Cloud Data Delivery
fastq	1,904,082 Kb	AWS	s3://sra-pub-src-11/SRR1659054/B423LI_CGATGT_L004_R1_001.fastq.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: 11.19%
Identified reads: 88.81%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Bovinae	subfamily	86.7	5,819,462
Eukaryota	Bison bison bison	subspecies	11.1	743,663
Eukaryota	Bos	genus	1.1	75,910
Eukaryota	Callithrix jacchus	species	0.7	47,936
Eukaryota	Bos taurus	species	0.3	19,363
Eukaryota	Bubalus bubalis	species	0.3	17,269
Eukaryota	Bos mutus	species	0.2	15,570
Eukaryota	Aotus nancymaae	species	0.2	14,593
Eukaryota	Saimiriinae	subfamily	0.1	7,869

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

directional RNA-Seq of Bison bison: adult female liver: Sample B423LI(SRR1659054)

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