Subtracks⇓  Description⇓  Male Donors Male 60-79 Yrs Track Settings
 
GTEx RNA-seq read coverage for male donor samples (60-79 years)

Track collection: GTEx RNA-seq from 371 Male Donors

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 All
Tissue
adiposeSubcut
adiposeVisceral
adrenalGland
arteryAorta
arteryCoronary
arteryTibial
brainAmygdala
brainAnCinCortex
brainCaudate
brainCerebelHemi
brainCerebellum
brainCortex
brainFrontCortex
brainHippocampus
brainHypothalamus
brainNucAccumbens
brainPutamen
brainSpinalcord
brainSubstanNigra
breastMamTissue
xformedlymphocytes
xformedfibroblasts
colonSigmoid
colonTransverse
esophagusJunction
esophagusMucosa
esophagusMuscular
heartAtrialAppend
heartLeftVentricl
kidneyCortex
liver
lung
minorSalivGland
muscleSkeletal
nerveTibial
pancreas
pituitary
prostate
skinNotExposed
skinExposed
smallIntestine
spleen
stomach
testis
thyroid
wholeBlood
Tissue
All 
Donor













































Donor
GTEX-111FC 60 yrs   GTEX-111FC 60 yrs
GTEX-111VG 60 yrs   GTEX-111VG 60 yrs
GTEX-111YS 60 yrs   GTEX-111YS 60 yrs
GTEX-113IC 60 yrs   GTEX-113IC 60 yrs
GTEX-117XS 60 yrs   GTEX-117XS 60 yrs
GTEX-1192W 60 yrs   GTEX-1192W 60 yrs
GTEX-11DXY 60 yrs   GTEX-11DXY 60 yrs
GTEX-11DYG 60 yrs   GTEX-11DYG 60 yrs
GTEX-11EI6 60 yrs   GTEX-11EI6 60 yrs
GTEX-11EQ8 60 yrs   GTEX-11EQ8 60 yrs
GTEX-11GS4 60 yrs   GTEX-11GS4 60 yrs
GTEX-11GSO 60 yrs   GTEX-11GSO 60 yrs
GTEX-11NV4 60 yrs   GTEX-11NV4 60 yrs
GTEX-11OC5 60 yrs   GTEX-11OC5 60 yrs
GTEX-11OF3 60 yrs   GTEX-11OF3 60 yrs
GTEX-11ONC 60 yrs   GTEX-11ONC 60 yrs
GTEX-11TUW 60 yrs   GTEX-11TUW 60 yrs
GTEX-11WQC 60 yrs   GTEX-11WQC 60 yrs
GTEX-11ZU8 60 yrs   GTEX-11ZU8 60 yrs
GTEX-1212Z 60 yrs   GTEX-1212Z 60 yrs
GTEX-12696 60 yrs   GTEX-12696 60 yrs
GTEX-12BJ1 60 yrs   GTEX-12BJ1 60 yrs
GTEX-12WSA 60 yrs   GTEX-12WSA 60 yrs
GTEX-12WSF 70 yrs   GTEX-12WSF 70 yrs
GTEX-12WSM 60 yrs   GTEX-12WSM 60 yrs
GTEX-12ZZY 60 yrs   GTEX-12ZZY 60 yrs
GTEX-12ZZZ 60 yrs   GTEX-12ZZZ 60 yrs
GTEX-131XF 60 yrs   GTEX-131XF 60 yrs
GTEX-132NY 60 yrs   GTEX-132NY 60 yrs
GTEX-132Q8 60 yrs   GTEX-132Q8 60 yrs
GTEX-132QS 60 yrs   GTEX-132QS 60 yrs
GTEX-1399T 60 yrs   GTEX-1399T 60 yrs
GTEX-139T8 60 yrs   GTEX-139T8 60 yrs
GTEX-139TS 60 yrs   GTEX-139TS 60 yrs
GTEX-139TT 60 yrs   GTEX-139TT 60 yrs
GTEX-139TU 60 yrs   GTEX-139TU 60 yrs
GTEX-139UC 60 yrs   GTEX-139UC 60 yrs
GTEX-139UW 60 yrs   GTEX-139UW 60 yrs
GTEX-13CF2 60 yrs   GTEX-13CF2 60 yrs
GTEX-13CZV 60 yrs   GTEX-13CZV 60 yrs
GTEX-13FHO 60 yrs   GTEX-13FHO 60 yrs
GTEX-13FTZ 60 yrs   GTEX-13FTZ 60 yrs
GTEX-13G51 60 yrs   GTEX-13G51 60 yrs
GTEX-13IVO 70 yrs   GTEX-13IVO 70 yrs
GTEX-13JVG 60 yrs   GTEX-13JVG 60 yrs
GTEX-13N1W 70 yrs   GTEX-13N1W 70 yrs
GTEX-13N2G 60 yrs   GTEX-13N2G 60 yrs
GTEX-13NYC 60 yrs   GTEX-13NYC 60 yrs
GTEX-13NYS 60 yrs   GTEX-13NYS 60 yrs
GTEX-13NZA 60 yrs   GTEX-13NZA 60 yrs
GTEX-13O1R 60 yrs   GTEX-13O1R 60 yrs
GTEX-13O61 60 yrs   GTEX-13O61 60 yrs
GTEX-13OVG 60 yrs   GTEX-13OVG 60 yrs
GTEX-13OVH 70 yrs   GTEX-13OVH 70 yrs
GTEX-13OW5 60 yrs   GTEX-13OW5 60 yrs
GTEX-13OW8 60 yrs   GTEX-13OW8 60 yrs
GTEX-13PDP 60 yrs   GTEX-13PDP 60 yrs
GTEX-13RTJ 60 yrs   GTEX-13RTJ 60 yrs
GTEX-13SLW 70 yrs   GTEX-13SLW 70 yrs
GTEX-13X6I 60 yrs   GTEX-13X6I 60 yrs
GTEX-13YAN 60 yrs   GTEX-13YAN 60 yrs
GTEX-1445S 60 yrs   GTEX-1445S 60 yrs
GTEX-144GO 60 yrs   GTEX-144GO 60 yrs
GTEX-145MO 60 yrs   GTEX-145MO 60 yrs
GTEX-14753 60 yrs   GTEX-14753 60 yrs
GTEX-1477Z 60 yrs   GTEX-1477Z 60 yrs
GTEX-147GR 60 yrs   GTEX-147GR 60 yrs
GTEX-147JS 60 yrs   GTEX-147JS 60 yrs
GTEX-148VJ 70 yrs   GTEX-148VJ 70 yrs
GTEX-1497J 60 yrs   GTEX-1497J 60 yrs
GTEX-14A5H 60 yrs   GTEX-14A5H 60 yrs
GTEX-14ASI 60 yrs   GTEX-14ASI 60 yrs
GTEX-14C5O 60 yrs   GTEX-14C5O 60 yrs
GTEX-14E7W 70 yrs   GTEX-14E7W 70 yrs
GTEX-N7MS 60 yrs   GTEX-N7MS 60 yrs
GTEX-NL3H 60 yrs   GTEX-NL3H 60 yrs
GTEX-O5YU 60 yrs   GTEX-O5YU 60 yrs
GTEX-OHPJ 60 yrs   GTEX-OHPJ 60 yrs
GTEX-OOBJ 60 yrs   GTEX-OOBJ 60 yrs
GTEX-P4PQ 60 yrs   GTEX-P4PQ 60 yrs
GTEX-P4QR 60 yrs   GTEX-P4QR 60 yrs
GTEX-P4QS 60 yrs   GTEX-P4QS 60 yrs
GTEX-POYW 60 yrs   GTEX-POYW 60 yrs
GTEX-QLQ7 60 yrs   GTEX-QLQ7 60 yrs
GTEX-REY6 60 yrs   GTEX-REY6 60 yrs
GTEX-RVPV 60 yrs   GTEX-RVPV 60 yrs
GTEX-S4Z8 60 yrs   GTEX-S4Z8 60 yrs
GTEX-S7PM 60 yrs   GTEX-S7PM 60 yrs
GTEX-S95S 60 yrs   GTEX-S95S 60 yrs
GTEX-SJXC 60 yrs   GTEX-SJXC 60 yrs
GTEX-SSA3 60 yrs   GTEX-SSA3 60 yrs
GTEX-SUCS 70 yrs   GTEX-SUCS 70 yrs
GTEX-TMZS 60 yrs   GTEX-TMZS 60 yrs
GTEX-U412 60 yrs   GTEX-U412 60 yrs
GTEX-U8T8 60 yrs   GTEX-U8T8 60 yrs
GTEX-UTHO 60 yrs   GTEX-UTHO 60 yrs
GTEX-V955 60 yrs   GTEX-V955 60 yrs
GTEX-VJYA 60 yrs   GTEX-VJYA 60 yrs
GTEX-WOFL 60 yrs   GTEX-WOFL 60 yrs
GTEX-WQUQ 60 yrs   GTEX-WQUQ 60 yrs
GTEX-X4XX 60 yrs   GTEX-X4XX 60 yrs
GTEX-X4XY 60 yrs   GTEX-X4XY 60 yrs
GTEX-XBED 60 yrs   GTEX-XBED 60 yrs
GTEX-XLM4 60 yrs   GTEX-XLM4 60 yrs
GTEX-XMD1 60 yrs   GTEX-XMD1 60 yrs
GTEX-Y5V6 60 yrs   GTEX-Y5V6 60 yrs
GTEX-Y8DK 60 yrs   GTEX-Y8DK 60 yrs
GTEX-Y8E5 60 yrs   GTEX-Y8E5 60 yrs
GTEX-YECK 60 yrs   GTEX-YECK 60 yrs
GTEX-YJ89 60 yrs   GTEX-YJ89 60 yrs
GTEX-ZAKK 70 yrs   GTEX-ZAKK 70 yrs
GTEX-ZDTS 60 yrs   GTEX-ZDTS 60 yrs
GTEX-ZDTT 60 yrs   GTEX-ZDTT 60 yrs
GTEX-ZDXO 60 yrs   GTEX-ZDXO 60 yrs
GTEX-ZE9C 60 yrs   GTEX-ZE9C 60 yrs
GTEX-ZF28 60 yrs   GTEX-ZF28 60 yrs
GTEX-ZXG5 60 yrs   GTEX-ZXG5 60 yrs
GTEX-ZYW4 60 yrs   GTEX-ZYW4 60 yrs
Donor













































Donor
 All
Tissue
adiposeSubcut
adiposeVisceral
adrenalGland
arteryAorta
arteryCoronary
arteryTibial
brainAmygdala
brainAnCinCortex
brainCaudate
brainCerebelHemi
brainCerebellum
brainCortex
brainFrontCortex
brainHippocampus
brainHypothalamus
brainNucAccumbens
brainPutamen
brainSpinalcord
brainSubstanNigra
breastMamTissue
xformedlymphocytes
xformedfibroblasts
colonSigmoid
colonTransverse
esophagusJunction
esophagusMucosa
esophagusMuscular
heartAtrialAppend
heartLeftVentricl
kidneyCortex
liver
lung
minorSalivGland
muscleSkeletal
nerveTibial
pancreas
pituitary
prostate
skinNotExposed
skinExposed
smallIntestine
spleen
stomach
testis
thyroid
wholeBlood
Tissue
All 
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List subtracks: only selected/visible    all    (24 of 1568 selected)  Top⇑
  Tissue↓1 ↓2 Age↓3 Donor↓4   Track Name↓5  
 
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 Configure 		 adiposeSubcut      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Adipose - Subcutaneous (GTEX-13OW8-1226-SM-5K7XD)    Data format 
 
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 Configure 		 adiposeVisceral      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Adipose - Visceral (Omentum) (GTEX-13OW8-0326-SM-5L3FB)    Data format 
 
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 Configure 		 arteryAorta      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Artery - Aorta (GTEX-13OW8-1826-SM-5L3H1)    Data format 
 
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 Configure 		 arteryTibial      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Artery - Tibial (GTEX-13OW8-1626-SM-5L3HW)    Data format 
 
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 Configure 		 brainAnCinCortex      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Anterior cingulate cortex (BA24) (GTEX-13OW8-0011-R3a-SM-5L3I4)    Data format 
 
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 Configure 		 brainCerebelHemi      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Cerebellar Hemisphere (GTEX-13OW8-0011-R11a-SM-5L3GT)    Data format 
 
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 Configure 		 brainCerebellum      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Cerebellum (GTEX-13OW8-2926-SM-5L3FV)    Data format 
 
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 Configure 		 brainFrontCortex      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Frontal Cortex (BA9) (GTEX-13OW8-0011-R10a-SM-5L3H6)    Data format 
 
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 Configure 		 brainHippocampus      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Hippocampus (GTEX-13OW8-0011-R1a-SM-5L3HI)    Data format 
 
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 Configure 		 brainHypothalamus      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Hypothalamus (GTEX-13OW8-0011-R8a-SM-5L3G5)    Data format 
 
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 Configure 		 brainNucAccumbens      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Nucleus accumbens (basal ganglia) (GTEX-13OW8-0011-R6b-SM-5L3I3)    Data format 
 
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 Configure 		 brainPutamen      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Brain - Putamen (basal ganglia) (GTEX-13OW8-0011-R7a-SM-5L3FP)    Data format 
 
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 Configure 		 breastMamTissue      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Breast - Mammary Tissue (GTEX-13OW8-0226-SM-5K7UP)    Data format 
 
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 Configure 		 colonSigmoid      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Colon - Sigmoid (GTEX-13OW8-2726-SM-5L3FZ)    Data format 
 
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 Configure 		 esophagusJunction      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Esophagus - Gastroesophageal Junction (GTEX-13OW8-2426-SM-5L3ID)    Data format 
 
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 Configure 		 esophagusMucosa      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Esophagus - Mucosa (GTEX-13OW8-2326-SM-5L3I9)    Data format 
 
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 Configure 		 esophagusMuscular      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Esophagus - Muscularis (GTEX-13OW8-2226-SM-5K7Z4)    Data format 
 
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 Configure 		 lung      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Lung (GTEX-13OW8-1726-SM-5L3GO)    Data format 
 
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 Configure 		 muscleSkeletal      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Muscle - Skeletal (GTEX-13OW8-1426-SM-5IJDT)    Data format 
 
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 Configure 		 nerveTibial      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Nerve - Tibial (GTEX-13OW8-1526-SM-5K7V2)    Data format 
 
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 Configure 		 prostate      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Prostate (GTEX-13OW8-0426-SM-5J2NR)    Data format 
 
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 Configure 		 skinExposed      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Skin - Sun Exposed (Lower leg) (GTEX-13OW8-1326-SM-5J1OW)    Data format 
 
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 Configure 		 skinNotExposed      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Skin - Not Sun Exposed (Suprapubic) (GTEX-13OW8-1026-SM-5J1NQ)    Data format 
 
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 Configure 		 thyroid      60-69  GTEX-13OW8 60 yrs  GTEx RNA signal from male Thyroid (GTEX-13OW8-0126-SM-5IJE5)    Data format 
    24 of 1568 selected
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

The NIH Genotype-Tissue Expression (GTEX) project was created to establish a sample and data resource for studies on the relationship between genetic variation and gene expression in multiple human tissues. This track hub shows RNA-seq read coverage signal graphs of GTEx samples in the GTEx midpoint milestone data release (V6, October 2015). A total of 7572 tracks representing samples from 570 adult post-mortem individuals are included.

Display Conventions

The individual sample tracks are organized by gender (Female Donors, Male Donors) and age, in 6 tracks, where samples can be selected from a donor vs. tissue matrix.

  • Female 20-49 yrs
  • Female 50-59 yrs
  • Female 60-69 yrs
  • Male 20-49 yrs
  • Male 50-59 yrs
  • Male 60-69 yrs
An alternative organization is provided by the 'By Tissues' supertrack set, which consists of a track containing all samples for each of the 53 tissues, with a selection matrix of donor gender and age.

Methods

Tissue samples were obtained using the GTEx standard operating procedures for informed consent and tissue collection, in conjunction with the National Cancer Institute Biorepositories and Biospecimen. All tissue specimens were reviewed by pathologists to characterize and verify organ source. Images from stained tissue samples can be viewed via the NCI histopathology viewer. The Qiagen PAXgene non-formalin tissue preservation product was used to stabilize tissue specimens without cross-linking biomolecules.

The Illumina TruSeq protocol was used to create an unstranded polyA+ library sequenced on the Illumina HiSeq 2000 platform to produce 76-bp paired end reads at a depth averaging 50M aligned reads per sample.

Sequence reads for this track were aligned to the hg38/GRCh38 human genome using STAR2 assisted by the GENCODE v24 transcriptome definition. The read coverage signal graphs were produced using the --outWig option of STAR2. Read mapping was performed at UCSC by the Computational Genomics lab, using the Toil pipeline. The resulting bedGraph files were converted to bigWig format for display. The bedGraph files were coordinate converted to the hg19/GRCh37 assembly via the UCSC liftOver tool.

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. Postmortem samples were collected from non-diseased donors with ages ranging from 20 to 79. 34.4% of donors were female and 65.6% male.

Additional summary plots of GTEx sample characteristics are available at the GTEx Portal Tissue Summary page.

Credits

Samples were collected by the GTEx Consortium. RNA-seq was performed by the GTEx Laboratory, Data Analysis and Coordinating Center (LDACC) at the Broad Institute. John Vivian, Melissa Cline, and Benedict Paten of the UCSC Computational Genomics lab were responsible for the sequence read mapping and signal file generation used to produce this hub. Kate Rosenbloom and Parisa Nejad of the UCSC Genome Browser group were responsible for data file post-processing and track hub configuration.

Contacts

For questions about the GTEx data, contact the GTEx LDACC at the Broad Institute. For questions about this track hub, contact the UCSC Genome Browser mailing list.

References

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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