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