GTEx RNA-Seq Coverage Track Settings
 
GTEx V8 RNA-Seq Read Coverage by Tissue   (All Expression tracks)

Display mode:       Reset to defaults

Type of graph:
Track height: pixels (range: 8 to 100)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 127)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
All subtracks:
List subtracks: only selected/visible    all    ()  
hide
 Configure
 Adip Subcut  Adipose Subcutaneous   Schema 
hide
 Configure
 Adip Visc Om  Adipose Visceral Omentum - GTEX-14BMU-0626-SM-73KZ6   Schema 
hide
 Configure
 Adren Gland  Adrenal Gland   Schema 
hide
 Configure
 Artery Aorta  Artery Aorta   Schema 
hide
 Configure
 Artery Coron  Artery Coronary   Schema 
hide
 Configure
 Artery Tibia  Artery Tibial   Schema 
hide
 Configure
 Bladder  Bladder   Schema 
hide
 Configure
 Brain Amygd  Brain Amygdala   Schema 
hide
 Configure
 Brain Ant cin cort  Brain Anterior cingulate cortex BA24   Schema 
hide
 Configure
 Brain Caud bas gangl  Brain Caudate basal ganglia   Schema 
hide
 Configure
 Brain Cereb  Brain Cerebellum   Schema 
hide
 Configure
 Brain Cereb Hemisph  Brain Cerebellar Hemisphere   Schema 
hide
 Configure
 Brain Cortex  Brain Cortex   Schema 
hide
 Configure
 Brain Front Cortex  Brain Frontal Cortex BA9   Schema 
hide
 Configure
 Brain Hippocamp  Brain Hippocampus   Schema 
hide
 Configure
 Brain Hypothal  Brain Hypothalamus   Schema 
hide
 Configure
 Brain Nucl acc bas gang  Brain Nucleus accumbens basal ganglia   Schema 
hide
 Configure
 Brain Put bas gang  Brain Putamen basal ganglia   Schema 
hide
 Configure
 Brain Spinal cord cerv  Brain Spinal cord cervical c-1   Schema 
hide
 Configure
 Brain Subst nigr  Brain Substantia nigra   Schema 
hide
 Configure
 Breast Mammary  Breast Mammary Tissue   Schema 
hide
 Configure
 Cells EBV lymphoc  Cells EBV-transformed lymphocytes   Schema 
hide
 Configure
 Cells fibrobl cult  Cells Cultured fibroblasts   Schema 
hide
 Configure
 Cervix Ectocerv  Cervix Ectocervix   Schema 
hide
 Configure
 Cervix Endocerv  Cervix Endocervix   Schema 
hide
 Configure
 Colon Sigmoid  Colon Sigmoid   Schema 
hide
 Configure
 Colon Transverse  Colon Transverse   Schema 
hide
 Configure
 Esoph Gastroes Junc  Esophagus Gastroesophageal Junction   Schema 
hide
 Configure
 Esoph Mucosa  Esophagus Mucosa   Schema 
hide
 Configure
 Esoph Muscularis  Esophagus Muscularis   Schema 
hide
 Configure
 Fallopian Tube  Fallopian Tube   Schema 
hide
 Configure
 Heart Atr Append  Heart Atrial Appendage   Schema 
hide
 Configure
 Heart Left Ventr  Heart Left Ventricle   Schema 
hide
 Configure
 Kidney Cortex  Kidney Cortex   Schema 
hide
 Configure
 Kidney Medulla  Kidney Medulla   Schema 
hide
 Configure
 Liver  Liver   Schema 
hide
 Configure
 Lung  Lung   Schema 
hide
 Configure
 Minor Saliv Gland  Minor Salivary Gland   Schema 
hide
 Configure
 Muscle Skeletal  Muscle Skeletal   Schema 
hide
 Configure
 Nerve Tibial  Nerve Tibial   Schema 
hide
 Configure
 Ovary  Ovary   Schema 
hide
 Configure
 Pancreas  Pancreas   Schema 
hide
 Configure
 Pituitary  Pituitary   Schema 
hide
 Configure
 Prostate  Prostate   Schema 
hide
 Configure
 Skin not sun exp  Skin Not Sun Exposed Suprapubic   Schema 
hide
 Configure
 Skin sun exp  Skin Sun Exposed Lower leg   Schema 
hide
 Configure
 Small Intestine  Small Intestine Terminal Ileum   Schema 
hide
 Configure
 Spleen  Spleen   Schema 
hide
 Configure
 Stomach  Stomach   Schema 
hide
 Configure
 Testis  Testis   Schema 
hide
 Configure
 Thyroid  Thyroid   Schema 
hide
 Configure
 Uterus  Uterus   Schema 
hide
 Configure
 Vagina  Vagina   Schema 
hide
 Configure
 Whole Blood  Whole Blood   Schema 
    

Description

The NIH Genotype-Tissue Expression (GTEx) project determined genetic variation and gene expression in 52 tissues and 2 cell lines using RNA-seq data (V8, August 2019), on 17,382 samples from 948 adults. This track focuses on the gene expression part. It shows read coverage, from one single sample per tissue, selected for high-quality and high read depth. The data is summarized to one number per base pair, the number of sequencing reads that cover this position. The plot allows finding out if a given exon is transcribed primarily in certain tissues and also whether transcription is uniform over the length of a single exon.

Display Conventions

This track follows the display conventions for composite "wiggle" tracks. The subtracks, one per tissue, of this track may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

Tissue colors were assigned to conform to the GTEx Consortium publication conventions.

In Dense mode, the darkness of the grayscale rectangle displayed for the gene reflects the absolute read count.

Methods

For background information about GTEx sample selection, see our GTEx gene expression track. In short, samples were sequenced with the Illumina TrueSeq protocol on unstranded polyA+ librarires to obtain 76-bp paired end reads with HiSeq 2000 and 2500 machines.

Sequence reads were aligned to the hg38/GRCh38 human genome using STAR v2.5.3a and the GENCODE 26 transcriptome. The alignment pipeline is available here. For further method details, see the GTEx Portal Documentation page.

To obtain read coverage, the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC) at the Broad Institute decided to select a single, high-quality representative sample for each tissue type, since aggregated tracks may obscure certain features or even introduce some artifacts (e.g. intronic coverage). For each tissue, the selected sample has the highest RIN value with a high coverage (>80M reads) and exonic rate (>85%). The alignment-to-coverage pipeline is available from Github: Python script, Docker file and Pipeline WDL description.

To show the exact GTEx sample that was used for each tissue, click the "Schema" link on the track configuration page (above), the filename under "bigDataUrl" includes the identifier.

Subject and Sample Characteristics

The scientific goal of the GTEx project required that the donors and their biospecimen present with no evidence of disease. The tissue types collected were chosen based on their clinical significance, logistical feasibility and their relevance to the scientific goal of the project and the research community. Summary plots of GTEx sample characteristics are available at the GTEx Portal Tissue Summary page.

Data Access

The raw data for the GTEx Read Coverage track can be accessed interactively through the Table Browser.

For automated analysis and downloads, the track data files can be downloaded from our downloads server or the JSON API. Individual regions or the whole genome annotation can be accessed as text using our utility bigBedToBed. Instructions for downloading the utility can be found here. That utility can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/gtex/gtexGeneV8.bb -chrom=chr21 -start=0 -end=100000000 stdout

Data can also be obtained directly from GTEx at the following link: https://gtexportal.org/home/datasets

Credits

Statistical analysis and data interpretation was performed by The GTEx Consortium Analysis Working Group. Data was provided by the GTEx LDACC at The Broad Institute of MIT and Harvard.

References

GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. In press.

GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun;45(6):580-5. PMID: 23715323; PMC: PMC4010069

Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, DeLuca DS, Peter-Demchok J, Gelfand ET et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreserv Biobank. 2015 Oct;13(5):311-9. PMID: 26484571; PMC: PMC4675181

Melé M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, Young TR, Goldmann JM, Pervouchine DD, Sullivan TJ et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015 May 8;348(6235):660-5. PMID: 25954002; PMC: PMC4547472

DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012 Jun 1;28(11):1530-2. PMID: 22539670; PMC: PMC3356847