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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR1043177	26.8M	5.4Gbp	3.5G	42.6%	2013-12-04	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
SRX387250	Whole plant - PE reads	Illumina	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED

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RNA-seq libraries from 6 week old whole plants were prepared from total RNA using the Illumina RNAseq sample prep multiplex protocol (not strand specific) according to manufacturers instructions. Briefly, Poly-A mRNA were purified using oligo (dT) primed magnetic beads and chemically fragmented into smaller pieces. Cleaved fragments were converted to double-stranded cDNA using random hexamer primers. After purification and end-repair, the cDNA fragments were ligated to Illumina paired-end sequencing adapters which contain sample specific indexes to allow for sequencing of multiple libraries on a single lane of an Illumina flowcell. Following this, fragments were purified, size selected on a gel, and then amplified by PCR to obtain the final library. The final libraries were then pooled in equal quantities with other libraries for sequencing on the Illumina HiSeq-2000 platform.

Biosample	Sample Description	Organism	Links
SAMN02429707 (SRS511151)	New RNA-seq reads from whole plant used to supplement available RNA-seq reads, to create a new transcriptome assembly with new method of assembly.	Nicotiana benthamiana	Nicotiana benthamiana genome page PRJNA188486

Bioproject	SRA Study	Title
PRJNA188486	SRP018508	Nicotiana benthamiana Transcriptome or Gene expression

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Goals: To enable interrogation of the transcriptome of Nicotiana benthamiana. Relevance: N. benthamiana is used for many different types of research including gene silencing, metabolic engineering, plant-microbe interactions, protein-protein interactions and gene function studies due to its excellent properties for rapid transient expression. The ability to interrogate its transcriptome bioinformatically would greatly facilitate design and assessment of experiments related to these fields.

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	3,397,968 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1043177/SRR1043177	worldwide	anonymous
SRA Lite	1,370,889 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/043/SRR1043177/SRR1043177.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-5/SRR1043177/SRR1043177.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-103/SRR1043177/SRR1043177.zq.1	gs.us-east1	gcp identity

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	1,046,072 Kb	AWS	s3://sra-pub-src-10/SRR1043177/Whole1.run1.R1.fastq.gz	-	Use Cloud Data Delivery
fastq	1,049,424 Kb	AWS	s3://sra-pub-src-9/SRR1043177/Whole1.run1.R2.fastq.gz	-	Use Cloud Data Delivery
fastq	1,096,445 Kb	AWS	s3://sra-pub-src-9/SRR1043177/Whole2.run1.R1.fastq.gz	-	Use Cloud Data Delivery
fastq	1,101,135 Kb	AWS	s3://sra-pub-src-11/SRR1043177/Whole2.run1.R2.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: 38.52%
Identified reads: 61.48%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Nicotiana	genus	60.3	3,232,307
Eukaryota	Nicotiana tabacum	species	1.0	56,221
Eukaryota	Nicotiana sylvestris	species	0.9	46,199
Eukaryota	Nicotiana tomentosiformis	species	0.5	26,604
Eukaryota	Lycopersicon	subgenus	0.4	19,114
Eukaryota	Solanum tuberosum	species	0.3	16,856
Eukaryota	Capsicum annuum	species	0.3	16,758
Bacteria	Gammaproteobacteria	class	0.1	4,204
Eukaryota	malvids		0.1	3,006

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

Nicotiana benthamiana Whole plant RNA-seq paired-end reads(SRR1043177)

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