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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR2135042	18.2M	4.6Gbp	3.2G	47.6%	2016-01-01	public

Quality graph (bigger)(smaller)

241

Phred quality score

This run has 2 reads per spot:

L=126, 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
SRX1124982	NCT	Illumina	RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED

Show designHide design

Seeds of Ningjiang3 (the non-cold tolerant cultivar) were sowed in pots in a incubator set to 25℃ and 14h light per day. When treatment started, half of the two-week-old seedlings were transferred to another incubator set to 4℃, other conditions remain unchanged.24 hours later, one well developed leaf was harvested from each seedling.More than 5 seedlings were collected and pooled for each cultivar. These collected leaves were frozen in liquid nitrogen immediately and stored at −80 °C. Total RNA was extracted from the collected leaves using RNAiso Plus (TaKaRa Biotechnology CO., LTD). The quality of RNA was determined by a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc. Waltham, MA, USA). RNA integrity was confirmed by electrophoresis on 1.5 % agarose gel. Approximately 20 μg of total RNA was used for Illumina sequencing at Biomarker technologies (Beijing, China). cDNA library construction was performed via following steps. First, mRNA was purified with biotin-Oligo (dT) magnetic bead and was randomly sheared by Fragmentation Buffer. Then using mRNA as template, First strand cDNA was synthesized with random hexamers, then buffer、dNTPs、RNase H and DNA polymerase I were added to synthesis second-strand cDNA, and the product was purified with AMPure XP beads. Afterwards, purified double-strand cDNA was end-repaired, poly-A tail-added and ligated to Illumina adapter, AMPure XP beads were used to select fragment size. Finally, cDNA library was obtained by PCR enrichment. Sequencing of the purified library was carried out on an Hiseq2500 (Illumina Inc., USA).

Biosample	Sample Description	Organism	Links
SAMN03944580 (SRS1016998)		Vigna unguiculata subsp. sesquipedalis	PRJNA290938

Bioproject	SRA Study	Title
PRJNA290938	SRP061809	Vigna unguiculata subsp. sesquipedalis Transcriptome or Gene expression

Show abstractHide abstract

This project is aimed at identifying differentially expressed genes in two asparagus bean cultivars under cold stress. One of them is cold tolerant, while the other is cold sensitive. Transcriptome analysis of these two will enable us to understand the gene expression patern of asparagus bean under cold treatment and the difference between two cultivars.

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	1,127,967 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR002/135/SRR2135042/SRR2135042.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-5/SRR2135042/SRR2135042.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-107/SRR2135042/SRR2135042.zq.1	gs.us-east1	gcp identity
SRA Normalized	3,108,177 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR2135042/SRR2135042	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	1,939,232 Kb	AWS	s3://sra-pub-src-8/SRR2135042/Bean_I73-NCT-I_good_2.fq.gz	-	Use Cloud Data Delivery
fastq	1,888,546 Kb	AWS	s3://sra-pub-src-4/SRR2135042/Bean_I73-NCT-I_good_1.fq.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: 42.86%
Identified reads: 57.14%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Vigna radiata var. radiata	varietas	39.9	1,827,654
Eukaryota	Phaseolus vulgaris	species	10.8	492,303
Eukaryota	Glycine max	species	3.7	168,442
Eukaryota	Vigna unguiculata	species	1.2	54,468
Eukaryota	Arachis duranensis	species	0.6	26,482
Eukaryota	Capsicum annuum	species	0.1	6,565
Eukaryota	Ziziphus jujuba	species	0.1	6,507
Eukaryota	Gossypium hirsutum	species	0.1	6,140
Eukaryota	Homininae	subfamily	0.1	5,315

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

RNA-seq of the Non-cold tolerant cultivar under cold treatment(SRR2135042)

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