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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR592699	16.4M	1.7Gbp	985.3M	46.7%	2012-12-14	public

Quality graph (bigger)(smaller)

241

Phred quality score

This run has 2 reads per spot:

L=51, 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
SRX195404		Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED

Show designHide design

library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar-codes were used, one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed.

Biosample	Sample Description	Organism
SAMN01765705 (SRS369337)	Adult (0.5-1.5 years old) transgenic zebrafish, Tg(aanat2:EGFP)Y8, which express enhanced green fluorescent protein (EGFP) in the pineal gland under the control of the aanat2 regulatory regions, were used. Fish were raised under 12-hr light:12-hr dark (LD) cycles, in a temperature controlled room, and transferred to constant darkness (DD) for tissue collection. Fish were anesthetized in 1.5 mM Tricane (Sigma), sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time (CT) 14, pineal glands were collected at 4-hr intervals for 48 hours (12 time points identified as CT 14, 18, 22, 2, 6, 10, 14b, 18b, 22b, 2b, 6b and 10b). Pools of 20 pineal glands were prepared at each time-point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (QIAGEN), according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall, 12 libraries (12 time points) were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics). On average, ~30 million paired-end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points (CTs 22, 2, 6, 10, 18b, 2b, 6b, 10b) and 2 x 50 base pairs for the remaining time points (CTs 14, 18, 14b and 22b).	Danio rerio

Bioproject	SRA Study	Title
PRJNA177642	SRP016132	Danio rerio Transcriptome or Gene expression

Abstract:

Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.

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	962,163 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR592699/SRR592699	worldwide	anonymous
SRA Lite	443,368 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR000/592/SRR592699/SRR592699.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-8/SRR592699/SRR592699.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-101/SRR592699/SRR592699.noqual.1	gs.us-east1	gcp identity

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: 58.18%
Identified reads: 41.82%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp	Coverage
Eukaryota	Danio rerio	species	41.5	691,968	0.5
Bacteria	Pelomonas	genus	0.1	2,478
Eukaryota	Sinocyclocheilus	genus	0.1	2,439
Bacteria	unclassified Burkholderiales		0.0	443
Viruses	Suid herpesvirus 1	species	0.0	249

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

Zebrafish pineal gland CT18(SRR592699)

Abstract:

SRA archive data

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