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

Run	Spots	Bases	Size	GC content	Published	Access Type
SRR8996282	8.7M	2.2Gbp	802.4M	50.5%	2019-05-01	public

Quality graph (bigger)(smaller)

237

Phred quality score

This run has 2 reads per spot:

L=125, 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
SRX5775156	68333	Illumina	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED

Show designHide design

To obtain a comprehensive list of transcripts from the bar regions of skin in T. duboisi, we performed library preparation step according to the protocol described by Standard TruSeq Stranded mRNA Sample Prep Kit (Illumina), on the RNA extractions. The samples used all had high RNA integrity (RIN > 7) and an RNA input of 1500ng for each sample was used for the library preparation. Next, we checked the quality of the libraries using D1000 ScreenTapes and reagents (Agilent) on a TapeStation 2200 (Agilent). The libraries were diluted based on an optimal quantity required for sequencing and then pooled equimolar. The sequencing was performed in the NGS Facility at Vienna Biocenter Core Facilities (VBCF, Austria) on one flowcell of an Illumina HiSeq2500, which generated 125bp paired-end reads. The demultiplexing of the raw reads was performed by the sequencing facility based on unique barcodes introduced in each sample during library preparation.

Biosample	Sample Description	Organism	Links
SAMN11552724 (SRS4708644)	T. duboisi Kigoma, ventral part of the bar region of the skin, biological replicate 5	Tropheus duboisi	PRJNA540663

Bioproject	SRA Study	Title
PRJNA540663	SRP194390	Molecular players shaping a dorsally restricted colour pattern in Tropheus duboisi

Show abstractHide abstract

The goal of this study is to profile the expression of genes involved in the formation of a dorsally restricted yellow bar pigmentation in adult Tropheus duboisi Maswa morph from Lake Tanganyika. As a proxy, we used another morph, Tropheus duboisi Kigoma, which displays similar vertical bar formation in on its body skin but without the dorsal bar yellow pigmentation observed in Maswa morph. This allows us to identify genes underlying the yellow bar colouration, as well as genes involved in dorsal bar restriction of the pigment pattern by comparing dorsal versus ventral bar regions in each morph.Our study provides the first transcriptional profile of yellow bar pigmentation in cichlids, and also the first list of xanthophore-related genes in a member of Tropheini cichlid tribe. In addition, the identified list of differentially expressed genes in the bar regions allowed us to hypothesize potential molecular players controlling the dispersal of xanthophores along the dorso-ventral body axis in teleost fish.

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	783,605 Kb	AWS	https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8996282/SRR8996282	worldwide	anonymous
SRA Lite	552,174 Kb	NCBI	https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR008/996/SRR8996282.sralite.1	worldwide	anonymous
		AWS	s3://sra-pub-zq-3/SRR8996282/SRR8996282.sralite.1	s3.us-east-1	aws identity
		GCP	gs://sra-pub-zq-105/SRR8996282/SRR8996282.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	2,582,163 Kb	AWS	s3://sra-pub-src-16/SRR8996282/K-L5_2.fastq	-	Use Cloud Data Delivery
fastq	2,582,163 Kb	AWS	s3://sra-pub-src-17/SRR8996282/K-L5_1.fastq	-	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: 3.39%
Identified reads: 96.61%

View in Krona

Strong signals

SuperKingdom	Organism	Rank	%%	Kbp
Eukaryota	Haplochromini	tribe	96.2	2,096,281
Bacteria	Bacteria	superkingdom	0.3	7,438
Viruses	Escherichia virus phiX174	species	0.0	469
Viruses	Enterobacteria phage S13		0.0	14

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 ventral part of the bar region of the skin of Tropheus duboisi Kigoma(SRR8996282)

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