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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR1265955	30.1M	6.0Gbp	4.0G	48.9%	2014-05-09	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
SRX529363		Illumina	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED

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Total RNAs were extracted from the blood of an additionally acquired vulture using Trizol LS Reagent (Ambion, TX) according to the manufacturer’s instructions. RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 LabChip kit (Agilent Technologies, CA). Ahead of cDNA library construction, the 2ug of total RNA was treated with DNase I, and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Subsequently, the library was sequenced using an Illumina HiSeq2500 sequencer (Illumina, CA) that was set to rapid run mode. Cluster generation, followed by 2×100 cycle sequencing reads, separated by a paired-end turnaround, which were performed on the instrument. Image analysis was performed using the HiSeq control Software version 1.8.4.

Biosample	Sample Description	Organism
SAMN02739871 (SRS599045)		Aegypius monachus

Bioproject	SRA Study	Title
PRJNA245779	SRP041562	Aegypius monachus Transcriptome or Gene expression

Abstract:

PGI, National Museum of Korea, and collaborators are working on the Cinereous Vulture whole transcriptome sequencing and analysis.

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	1,531,034 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR001/265/SRR1265955/SRR1265955.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-1/SRR1265955/SRR1265955.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-104/SRR1265955/SRR1265955.zq.1	gs.us-east1	gcp identity
SRA Normalized	3,950,036 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1265955/SRR1265955	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	383,920 Kb	AWS	s3://sra-pub-src-14/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_007.fastq.gz	-	Use Cloud Data Delivery
fastq	390,689 Kb	AWS	s3://sra-pub-src-14/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_006.fastq.gz	-	Use Cloud Data Delivery
fastq	388,971 Kb	AWS	s3://sra-pub-src-10/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_005.fastq.gz	-	Use Cloud Data Delivery
fastq	396,002 Kb	AWS	s3://sra-pub-src-13/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_004.fastq.gz	-	Use Cloud Data Delivery
fastq	394,661 Kb	AWS	s3://sra-pub-src-14/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_003.fastq.gz	-	Use Cloud Data Delivery
fastq	400,259 Kb	AWS	s3://sra-pub-src-12/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_002.fastq.gz	-	Use Cloud Data Delivery
fastq	397,506 Kb	AWS	s3://sra-pub-src-13/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_001.fastq.gz	-	Use Cloud Data Delivery
fastq	199,540 Kb	AWS	s3://sra-pub-src-12/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_008.fastq.gz	-	Use Cloud Data Delivery
fastq	365,648 Kb	AWS	s3://sra-pub-src-13/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_007.fastq.gz	-	Use Cloud Data Delivery
fastq	372,547 Kb	AWS	s3://sra-pub-src-9/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_006.fastq.gz	-	Use Cloud Data Delivery
fastq	369,616 Kb	AWS	s3://sra-pub-src-13/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_005.fastq.gz	-	Use Cloud Data Delivery
fastq	381,826 Kb	AWS	s3://sra-pub-src-14/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_004.fastq.gz	-	Use Cloud Data Delivery
fastq	379,099 Kb	AWS	s3://sra-pub-src-13/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_003.fastq.gz	-	Use Cloud Data Delivery
fastq	386,250 Kb	AWS	s3://sra-pub-src-13/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_002.fastq.gz	-	Use Cloud Data Delivery
fastq	381,847 Kb	AWS	s3://sra-pub-src-10/SRR1265955/TN1311R4935-1_ACAGTG_L002_R1_001.fastq.gz	-	Use Cloud Data Delivery
fastq	206,927 Kb	AWS	s3://sra-pub-src-14/SRR1265955/TN1311R4935-1_ACAGTG_L002_R2_008.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: 12.01%
Identified reads: 87.99%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Accipitrinae	subfamily	81.5	4,906,802
Eukaryota	Aquila chrysaetos canadensis	subspecies	8.3	502,307
Eukaryota	Haliaeetus	genus	7.6	458,042
Eukaryota	Haliaeetus leucocephalus	species	1.6	96,242
Eukaryota	Passeriformes	order	0.5	31,640
Eukaryota	Nipponia nippon	species	0.5	30,887
Eukaryota	Aptenodytes forsteri	species	0.3	21,035
Eukaryota	Haliaeetus albicilla	species	0.3	17,322
Eukaryota	Phaethon lepturus	species	0.3	16,228

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

The_Cinereous_vulture_transcriptome(SRR1265955)

Abstract:

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