Female Donors Female 20-49 Yrs Track Settings
 
GTEx RNA-seq read coverage for female donor samples (20-49 years)

Track collection: GTEx RNA-seq from 199 Female Donors

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+  All tracks in this collection (3)

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


















































Donor
GTEX-11EM3 20 yrs   GTEX-11EM3 20 yrs
GTEX-11ILO 40 yrs   GTEX-11ILO 40 yrs
GTEX-11P81 30 yrs   GTEX-11P81 30 yrs
GTEX-11UD1 40 yrs   GTEX-11UD1 40 yrs
GTEX-11VI4 40 yrs   GTEX-11VI4 40 yrs
GTEX-11XUK 40 yrs   GTEX-11XUK 40 yrs
GTEX-12WSJ 40 yrs   GTEX-12WSJ 40 yrs
GTEX-12WSK 40 yrs   GTEX-12WSK 40 yrs
GTEX-12ZZX 40 yrs   GTEX-12ZZX 40 yrs
GTEX-133LE 20 yrs   GTEX-133LE 20 yrs
GTEX-1399S 30 yrs   GTEX-1399S 30 yrs
GTEX-139D8 30 yrs   GTEX-139D8 30 yrs
GTEX-13FTX 20 yrs   GTEX-13FTX 20 yrs
GTEX-13FTY 40 yrs   GTEX-13FTY 40 yrs
GTEX-13JUV 40 yrs   GTEX-13JUV 40 yrs
GTEX-13PL6 40 yrs   GTEX-13PL6 40 yrs
GTEX-13QBU 40 yrs   GTEX-13QBU 40 yrs
GTEX-13U4I 40 yrs   GTEX-13U4I 40 yrs
GTEX-13VXT 20 yrs   GTEX-13VXT 20 yrs
GTEX-145ME 40 yrs   GTEX-145ME 40 yrs
GTEX-14AS3 40 yrs   GTEX-14AS3 40 yrs
GTEX-14BMU 20 yrs   GTEX-14BMU 20 yrs
GTEX-14H4A 40 yrs   GTEX-14H4A 40 yrs
GTEX-P4PP 30 yrs   GTEX-P4PP 30 yrs
GTEX-P78B 40 yrs   GTEX-P78B 40 yrs
GTEX-POMQ 20 yrs   GTEX-POMQ 20 yrs
GTEX-PWCY 20 yrs   GTEX-PWCY 20 yrs
GTEX-PWN1 40 yrs   GTEX-PWN1 40 yrs
GTEX-PWOO 40 yrs   GTEX-PWOO 40 yrs
GTEX-PX3G 20 yrs   GTEX-PX3G 20 yrs
GTEX-Q2AG 40 yrs   GTEX-Q2AG 40 yrs
GTEX-Q734 40 yrs   GTEX-Q734 40 yrs
GTEX-QDT8 30 yrs   GTEX-QDT8 30 yrs
GTEX-R3RS 40 yrs   GTEX-R3RS 40 yrs
GTEX-R55G 40 yrs   GTEX-R55G 40 yrs
GTEX-RU1J 20 yrs   GTEX-RU1J 20 yrs
GTEX-S341 40 yrs   GTEX-S341 40 yrs
GTEX-S4UY 40 yrs   GTEX-S4UY 40 yrs
GTEX-S7SF 20 yrs   GTEX-S7SF 20 yrs
GTEX-SE5C 40 yrs   GTEX-SE5C 40 yrs
GTEX-T2IS 20 yrs   GTEX-T2IS 20 yrs
GTEX-T5JW 20 yrs   GTEX-T5JW 20 yrs
GTEX-T6MO 40 yrs   GTEX-T6MO 40 yrs
GTEX-TML8 40 yrs   GTEX-TML8 40 yrs
GTEX-TMMY 40 yrs   GTEX-TMMY 40 yrs
GTEX-U3ZN 30 yrs   GTEX-U3ZN 30 yrs
GTEX-UPIC 20 yrs   GTEX-UPIC 20 yrs
GTEX-W5X1 40 yrs   GTEX-W5X1 40 yrs
GTEX-WEY5 40 yrs   GTEX-WEY5 40 yrs
GTEX-WI4N 40 yrs   GTEX-WI4N 40 yrs
GTEX-WRHK 20 yrs   GTEX-WRHK 20 yrs
GTEX-WYVS 40 yrs   GTEX-WYVS 40 yrs
GTEX-XUZC 30 yrs   GTEX-XUZC 30 yrs
GTEX-XV7Q 40 yrs   GTEX-XV7Q 40 yrs
GTEX-Y5LM 40 yrs   GTEX-Y5LM 40 yrs
GTEX-YB5K 40 yrs   GTEX-YB5K 40 yrs
GTEX-YFC4 40 yrs   GTEX-YFC4 40 yrs
GTEX-YJ8O 40 yrs   GTEX-YJ8O 40 yrs
GTEX-ZC5H 40 yrs   GTEX-ZC5H 40 yrs
GTEX-ZGAY 40 yrs   GTEX-ZGAY 40 yrs
GTEX-ZP4G 20 yrs   GTEX-ZP4G 20 yrs
GTEX-ZPIC 40 yrs   GTEX-ZPIC 40 yrs
GTEX-ZTPG 20 yrs   GTEX-ZTPG 20 yrs
GTEX-ZV6S 40 yrs   GTEX-ZV6S 40 yrs
GTEX-ZXES 30 yrs   GTEX-ZXES 30 yrs
GTEX-ZYWO 40 yrs   GTEX-ZYWO 40 yrs
Donor


















































Donor
 All
Tissue
adiposeSubcut
adiposeVisceral
adrenalGland
arteryAorta
arteryCoronary
arteryTibial
bladder
brainAmygdala
brainAnCinCortex
brainCaudate
brainCerebelHemi
brainCerebellum
brainCortex
brainFrontCortex
brainHippocampus
brainHypothalamus
brainNucAccumbens
brainPutamen
brainSpinalcord
brainSubstanNigra
breastMamTissue
xformedlymphocytes
xformedfibroblasts
ectocervix
endocervix
colonSigmoid
colonTransverse
esophagusJunction
esophagusMucosa
esophagusMuscular
fallopianTube
heartAtrialAppend
heartLeftVentricl
kidneyCortex
liver
lung
minorSalivGland
muscleSkeletal
nerveTibial
ovary
pancreas
pituitary
skinNotExposed
skinExposed
smallIntestine
spleen
stomach
thyroid
uterus
vagina
wholeBlood
Tissue
All 
Select subtracks further by: (select multiple categories and items - Help)
Age:

List subtracks: only selected/visible    all    ()
  Tissue↓1 ↓2 Age↓3 Donor↓4   Track Name↓5  
 
hide
 Configure 		 adiposeSubcut      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Adipose - Subcutaneous (GTEX-YFC4-0226-SM-57WD2)    Data format 
 
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 Configure 		 arteryTibial      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Artery - Tibial (GTEX-YFC4-0926-SM-5S2U7)    Data format 
 
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 Configure 		 brainAmygdala      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Amygdala (GTEX-YFC4-0011-R4a-SM-4RGLQ)    Data format 
 
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 Configure 		 brainCaudate      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Caudate (basal ganglia) (GTEX-YFC4-0011-R5a-SM-4RGLR)    Data format 
 
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 Configure 		 brainCerebelHemi      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Cerebellar Hemisphere (GTEX-YFC4-0011-R11a-SM-4SOK6)    Data format 
 
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 Configure 		 brainCerebellum      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Cerebellum (GTEX-YFC4-3026-SM-5IFJK)    Data format 
 
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 Configure 		 brainFrontCortex      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Frontal Cortex (BA9) (GTEX-YFC4-0011-R10a-SM-4SOK5)    Data format 
 
hide
 Configure 		 brainHippocampus      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Hippocampus (GTEX-YFC4-0011-R1a-SM-4V6EH)    Data format 
 
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 Configure 		 brainNucAccumbens      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Nucleus accumbens (basal ganglia) (GTEX-YFC4-0011-R6b-SM-4V6E1)    Data format 
 
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 Configure 		 brainSpinalcord      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Spinal cord (cervical c-1) (GTEX-YFC4-0011-R9a-SM-4SOK4)    Data format 
 
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 Configure 		 brainSubstanNigra      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Brain - Substantia nigra (GTEX-YFC4-0011-R2a-SM-4V6DZ)    Data format 
 
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 Configure 		 breastMamTissue      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Breast - Mammary Tissue (GTEX-YFC4-1426-SM-5IFJG)    Data format 
 
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 Configure 		 esophagusMucosa      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Esophagus - Mucosa (GTEX-YFC4-1226-SM-5LU9R)    Data format 
 
hide
 Configure 		 liver      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Liver (GTEX-YFC4-1526-SM-5IFJS)    Data format 
 
hide
 Configure 		 lung      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Lung (GTEX-YFC4-1126-SM-5RQJN)    Data format 
 
hide
 Configure 		 muscleSkeletal      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Muscle - Skeletal (GTEX-YFC4-1026-SM-5RQJM)    Data format 
 
hide
 Configure 		 nerveTibial      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Nerve - Tibial (GTEX-YFC4-0826-SM-5CVM1)    Data format 
 
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 Configure 		 ovary      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Ovary (GTEX-YFC4-2726-SM-5IFJW)    Data format 
 
hide
 Configure 		 pituitary      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Pituitary (GTEX-YFC4-3226-SM-5CVM2)    Data format 
 
hide
 Configure 		 skinExposed      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Skin - Sun Exposed (Lower leg) (GTEX-YFC4-0126-101855-SM-5CVLZ)   Data format 
 
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 Configure 		 skinExposed      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Skin - Sun Exposed (Lower leg) (GTEX-YFC4-0126-SM-5CVLY)    Data format 
 
hide
 Configure 		 thyroid      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Thyroid (GTEX-YFC4-2626-SM-5P9FQ)   Data format 
 
hide
 Configure 		 uterus      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Uterus (GTEX-YFC4-2826-SM-5P9FR)    Data format 
 
hide
 Configure 		 vagina      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Vagina (GTEX-YFC4-2926-SM-5IFJ8)    Data format 
 
hide
 Configure 		 wholeBlood      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Whole Blood (GTEX-YFC4-0006-SM-4RGLV)    Data format 
 
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 Configure 		 xformedfibroblasts      40-49  GTEX-YFC4 40 yrs  GTEx RNA signal from female Cells - Transformed fibroblasts (GTEX-YFC4-0008-SM-4RGM3)    Data format 
    
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