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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR1298698	31.4M	2.9Gbp	1.8G	45%	2015-07-22	public

Quality graph (bigger)(smaller)

240

Phred quality score

This run has 2 reads per spot:

̅L=94, σ=5.9, 100%

L=0

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
SRX551505	CG_15d	Illumina	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE

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Oyster whole body tissue was collected from 15 randomly sampled oysters each from CGX, CF3L (unchallenged controls), GX, and F3L (challenged resistant and susceptible oysters) at days 1, 5, 15, and 30 following challenge with the bacterial pathogen Roseovarius crassostreae and stored in RNAlater® until time of RNA isolation. All RNA molecules >200 nucleotides were purified using Qiagen RNAeasy Mini Kit. Samples were checked for RNA purity using a Nanodrop 8000 spectrophotometer and a subset of the extracts were checked using an Agilent 2100 Bioanalyzer. Due to limitations in funding, control non-challenged susceptible (CF3L) oysters were not included in the sequencing analysis, but RNA samples are available for future sequencing. Equal amounts of total RNA from 5 oysters from each treatment and time point (excluding C3FL) were pooled for a total of 12 experimental samples (3 treatments x 4 time points). Samples of RNA were selectively enriched for poly-A containing mRNA and cDNA libraries for sequencing were prepared using the Illumina mRNA-Seq-8 Sample Prep Kit. The cDNA libraries were sequenced on the Illumina GAIIx platform (1 lane per sample for a total of 12 lanes, Genome Quebec, Canada). Raw sequencing reads of 108 bp were pooled, processed, and filtered for contamination of mitochondrial and ribosomal sequences by mapping to all Crassostrea spp. rRNA and mtDNA in NCBI Genbank database. Reads were filtered for vector sequences by mapping to Univec (ftp://ftp.ncbi.nih.gov/pub/univec) using bowtie2. Low-complexity artifacts were removed, and Illumina adapters and the 5’-ends of reads were trimmed using the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Adaptive trimming was performed on reads using the btrim software package. Reads less than 20 bp in length were discarded

Biosample	Sample Description	Organism	Links
SAMN02797581 (SRS619214)		Crassostrea virginica	PRJNA248114

Bioproject	SRA Study	Title
PRJNA248114	SRP042090	Crassostrea virginica strain:GX3 and F3L Transcriptome or Gene expression

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The American oyster Crassostrea virginica, an ecologically and economically important estuarine organism, can suffer high mortalities due to infectious diseases. The goals of this research were to provide insights into: 1) the responses of American oysters to pathogenic challenge, and 2) potential mechanisms of resistance or susceptibility to infectious diseases.

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	733,981 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/298/SRR1298698/SRR1298698.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-5/SRR1298698/SRR1298698.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-106/SRR1298698/SRR1298698.zq.1	gs.us-east1	gcp identity
SRA Normalized	1,799,968 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1298698/SRR1298698	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	8,455,730 Kb	AWS	s3://sra-pub-src-14/SRR1298698/GX_15d_qc.fq	-	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: 93.74%
Identified reads: 6.26%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Crassostrea gigas	species	5.5	163,179
Eukaryota	Crassostrea virginica	species	0.4	11,735
Bacteria	Enterobacteriaceae	family	0.2	4,464
Eukaryota	Deuterostomia		0.1	4,303
Bacteria	Terrabacteria group		0.0	231

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

Transcriptome of American oysters, Crassostrea virginica, in response to bacterial challenge: Insights into potential mechanisms of disease resistance(SRR1298698)

SRA archive data

Original format

Taxonomy Analysis

Strong signals

Intensity graph

	View: biological readstechnical readsquality scoresadvanced options Hide Read 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