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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR3193132	19.2M	959.7Mbp	704.6M	44.9%	2016-03-03	public

Quality graph (bigger)(smaller)

241

Phred quality score

This run has 1 read per spot:

L=50, 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
SRX1603965	E4 larval wing 1500uM AA ID number 28	Illumina	RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE

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Caterpillars were purchased from Carolina Biological supplies and arrived as second instar (Batch 1). Each caterpillar was reared individually in a plastic container with holes poked in the top to ensure air-flow. At the beginning of the experiment, 5g of diet was weighed out and placed into each container and 100µl of 1500µM of Anacardic acid was added to the diet. The chemical was thoroughly mixed into the diet. Wing discs were dissected from caterpillars in the final instar early 4th larval stage (2 days post-molt). Prior to harvest, larvae were weighed. The thorax, including the first abdominal segment, was harvested and placed immediately in RNAlater® (Ambion) and stored at 4°C for at least 48 hours prior to dissection. All tissues were weighed and processed using an electric homogenizer followed by RNA isolation using isopropanol. Concentration of RNA was measured using a ND-1000 spectrophotometer (NanoDrop products, Wilmington, DE) (A260/A280 >1.8) and integrity was assessed using electrophoresis on a formaldehyde-agarose gel. The RNA samples were diluted in water to a concentration of 25ng/µl in 50µl. All fore and hind wing discs were pooled for each larva prior to RNA extraction. RNA from 5 individual larvae was diluted and pooled (in total four biological replicates of 5 pooled individuals).

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Program	Version
CLC Genomics Workbench	6.5.1

Biosample	Sample Description	Organism	Links
SAMN04524096 (SRS1317507)	larval wing tissue	Vanessa cardui	PRJNA284000

Bioproject	SRA Study	Title
PRJNA284000	SRP059310	Vanessa cardui Transcriptome or Gene expression

Abstract:

Investigate temporal patterns of gene expression during wing color pattern development.

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	276,524 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR003/193/SRR3193132.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-2/SRR3193132/SRR3193132.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-103/SRR3193132/SRR3193132.zq.1	gs.us-east1	gcp identity
SRA Normalized	688,128 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR3193132/SRR3193132	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	2,970,919 Kb	AWS	s3://sra-pub-src-7/SRR3193132/10215X28_130809_SN141_0714_BD2BKYACXX_2.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: 96.41%
Identified reads: 3.59%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Papilionoidea	superfamily	3.5	33,201
Eukaryota	Pyraloidea	superfamily	0.7	7,130
Eukaryota	Bombycoidea	superfamily	0.4	4,051

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

Vanessa cardui early 4th instar larval wing transcriptome (reared on artificial diet supplied with 1500uM Anacardic acid)(SRR3193132)

Abstract:

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