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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR1556028	46.6M	9.4Gbp	5.4G	48.6%	2014-09-15	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
SRX684729	C2b	Illumina	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED

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We isolated total RNA from above ground seedling tissue (30-40 mg per seedling) using Direct-zol RNA Mini-Prep following manufacturer’s instructions (Zymo Research Corporation, Irvine, CA), and DNase-treated total RNA with Turbo DNA-free (Applied Biosystems/Ambion, Austin, TX, USA). DNase-treated RNA was extracted from 12 individuals for RNA-sequencing – two individuals from each of three damage-treated and control maternal lines. We prepared RNA-seq libraries using Illumina TruSeq RNA Sample Preparation Kit following manufacturer’s instructions (Illumina Incorporated, San Diego, CA, USA). We Illumina indexed and sequenced (100 bp paired end reads) the twelve libraries on four hiSeq2500 lanes (six samples per lane, each sample run in two lanes). Reads from each of our twelve samples were mapped to the M. guttatus 2.0 reference genome (http://www.phytozome.net/mimulus_er.php) using the CLC Large Gap Read Mapping algorithm. We used genome annotations to guide the mapping of reads that spanned introns. Reads mapped to 24,919 of 27,851 annotated transcripts. Down-stream differential expression analyses were based on quantification of reads mapped to the 24,919 annotated genes.

Biosample	Sample Description	Organism
SAMN03001969 (SRS687846)		Erythranthe guttata

Bioproject	SRA Study	Title
PRJNA258667	SRP045683	Erythranthe guttata strain:RIL 94 Transcriptome or Gene expression

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This study compared gene expression in the progeny of damaged and undamaged plants to determine the extent to which parental environment alters offspring gene expression. The progeny of damaged plants not only show differential gene expression, but also increased trichome density.

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	2,293,781 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/556/SRR1556028/SRR1556028.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-2/SRR1556028/SRR1556028.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-101/SRR1556028/SRR1556028.zq.1	gs.us-east1	gcp identity
SRA Normalized	5,320,022 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1556028/SRR1556028	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	6,801,730 Kb	AWS	s3://sra-pub-src-14/SRR1556028/MimC2b.fastq.gz	-	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: 33.14%
Identified reads: 66.86%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Erythranthe guttata	species	66.5	6,234,752
Eukaryota	Sesamum indicum	species	0.1	9,329
Eukaryota	fabids		0.1	7,124
Eukaryota	Brassiceae	tribe	0.0	4,355
Bacteria	Bacteria	superkingdom	0.0	4,131
Eukaryota	Solanaceae	family	0.0	2,174
Bacteria	Firmicutes	phylum	0.0	429
Bacteria	Actinobacteria	phylum	0.0	311
Bacteria	Proteobacteria	phylum	0.0	286

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

RIL94 C2b Transcriptome(SRR1556028)

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