Female Donors Female 50-59 Yrs Track Settings
 
GTEx RNA-seq read coverage for female donor samples (50-59 yrs)

Track collection: GTEx RNA-seq from 199 Female Donors

+  Description
+  All tracks in this collection (3)

Display mode:       Reset to defaults   

Type of graph:
Track height: pixels (range: 8 to 64)
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
Select subtracks by tissue and donor: (help)
 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-113JC 50 yrs   GTEX-113JC 50 yrs
GTEX-11I78 50 yrs   GTEX-11I78 50 yrs
GTEX-11ZVC 50 yrs   GTEX-11ZVC 50 yrs
GTEX-12WS9 50 yrs   GTEX-12WS9 50 yrs
GTEX-12WSG 50 yrs   GTEX-12WSG 50 yrs
GTEX-1313W 50 yrs   GTEX-1313W 50 yrs
GTEX-131XG 50 yrs   GTEX-131XG 50 yrs
GTEX-131XW 50 yrs   GTEX-131XW 50 yrs
GTEX-132AR 50 yrs   GTEX-132AR 50 yrs
GTEX-1399U 50 yrs   GTEX-1399U 50 yrs
GTEX-139T4 50 yrs   GTEX-139T4 50 yrs
GTEX-13D11 50 yrs   GTEX-13D11 50 yrs
GTEX-13FH7 50 yrs   GTEX-13FH7 50 yrs
GTEX-13N11 50 yrs   GTEX-13N11 50 yrs
GTEX-13OVJ 50 yrs   GTEX-13OVJ 50 yrs
GTEX-13SLX 50 yrs   GTEX-13SLX 50 yrs
GTEX-13X6H 50 yrs   GTEX-13X6H 50 yrs
GTEX-146FH 50 yrs   GTEX-146FH 50 yrs
GTEX-147F3 50 yrs   GTEX-147F3 50 yrs
GTEX-14A5I 50 yrs   GTEX-14A5I 50 yrs
GTEX-14BIN 50 yrs   GTEX-14BIN 50 yrs
GTEX-OHPK 50 yrs   GTEX-OHPK 50 yrs
GTEX-OXRK 50 yrs   GTEX-OXRK 50 yrs
GTEX-P4QT 50 yrs   GTEX-P4QT 50 yrs
GTEX-PLZ4 50 yrs   GTEX-PLZ4 50 yrs
GTEX-QCQG 50 yrs   GTEX-QCQG 50 yrs
GTEX-R53T 50 yrs   GTEX-R53T 50 yrs
GTEX-RNOR 50 yrs   GTEX-RNOR 50 yrs
GTEX-RU72 50 yrs   GTEX-RU72 50 yrs
GTEX-S32W 50 yrs   GTEX-S32W 50 yrs
GTEX-S4P3 50 yrs   GTEX-S4P3 50 yrs
GTEX-SN8G 50 yrs   GTEX-SN8G 50 yrs
GTEX-UJHI 50 yrs   GTEX-UJHI 50 yrs
GTEX-VJWN 50 yrs   GTEX-VJWN 50 yrs
GTEX-W5WG 50 yrs   GTEX-W5WG 50 yrs
GTEX-WRHU 50 yrs   GTEX-WRHU 50 yrs
GTEX-WWYW 50 yrs   GTEX-WWYW 50 yrs
GTEX-WXYG 50 yrs   GTEX-WXYG 50 yrs
GTEX-X15G 50 yrs   GTEX-X15G 50 yrs
GTEX-X8HC 50 yrs   GTEX-X8HC 50 yrs
GTEX-XMD3 50 yrs   GTEX-XMD3 50 yrs
GTEX-XUW1 50 yrs   GTEX-XUW1 50 yrs
GTEX-Y114 50 yrs   GTEX-Y114 50 yrs
GTEX-Y3IK 50 yrs   GTEX-Y3IK 50 yrs
GTEX-Y8LW 50 yrs   GTEX-Y8LW 50 yrs
GTEX-YBZK 50 yrs   GTEX-YBZK 50 yrs
GTEX-ZAJG 50 yrs   GTEX-ZAJG 50 yrs
GTEX-ZAK1 50 yrs   GTEX-ZAK1 50 yrs
GTEX-ZE7O 50 yrs   GTEX-ZE7O 50 yrs
GTEX-ZF2S 50 yrs   GTEX-ZF2S 50 yrs
GTEX-ZF3C 50 yrs   GTEX-ZF3C 50 yrs
GTEX-ZLWG 50 yrs   GTEX-ZLWG 50 yrs
GTEX-ZV68 50 yrs   GTEX-ZV68 50 yrs
GTEX-ZVE1 50 yrs   GTEX-ZVE1 50 yrs
GTEX-ZVT2 50 yrs   GTEX-ZVT2 50 yrs
GTEX-ZVT4 50 yrs   GTEX-ZVT4 50 yrs
GTEX-ZYVF 50 yrs   GTEX-ZYVF 50 yrs
GTEX-ZZPU 50 yrs   GTEX-ZZPU 50 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      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Adipose - Subcutaneous (GTEX-13OVJ-0326-SM-5L3GL)    Data format 
 
hide
 Configure 		 adiposeVisceral      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Adipose - Visceral (Omentum) (GTEX-13OVJ-0926-SM-5K7U1)    Data format 
 
hide
 Configure 		 brainAnCinCortex      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Anterior cingulate cortex (BA24) (GTEX-13OVJ-0011-R3b-SM-5P9H6)   Data format 
 
hide
 Configure 		 brainCaudate      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Caudate (basal ganglia) (GTEX-13OVJ-0011-R5a-SM-5P9H7)    Data format 
 
hide
 Configure 		 brainCerebelHemi      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Cerebellar Hemisphere (GTEX-13OVJ-0011-R11a-SM-5P9H8)    Data format 
 
hide
 Configure 		 brainCerebellum      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Cerebellum (GTEX-13OVJ-2726-SM-5IJG6)    Data format 
 
hide
 Configure 		 brainCortex      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Cortex (GTEX-13OVJ-2826-SM-5L3GW)    Data format 
 
hide
 Configure 		 brainFrontCortex      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Frontal Cortex (BA9) (GTEX-13OVJ-0011-R10b-SM-5L3HT)    Data format 
 
hide
 Configure 		 brainHippocampus      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Hippocampus (GTEX-13OVJ-0011-R1b-SM-5L3I6)    Data format 
 
hide
 Configure 		 brainHypothalamus      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Hypothalamus (GTEX-13OVJ-0011-R8b-SM-5L3FS)    Data format 
 
hide
 Configure 		 brainNucAccumbens      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Nucleus accumbens (basal ganglia) (GTEX-13OVJ-0011-R6b-SM-5L3GH)    Data format 
 
hide
 Configure 		 brainPutamen      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Putamen (basal ganglia) (GTEX-13OVJ-0011-R7a-SM-5L3G1)    Data format 
 
hide
 Configure 		 brainSpinalcord      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Spinal cord (cervical c-1) (GTEX-13OVJ-0011-R9b-SM-5L3GD)    Data format 
 
hide
 Configure 		 brainSubstanNigra      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Brain - Substantia nigra (GTEX-13OVJ-0011-R2b-SM-5L3GP)    Data format 
 
hide
 Configure 		 colonSigmoid      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Colon - Sigmoid (GTEX-13OVJ-1826-SM-5KM2D)    Data format 
 
hide
 Configure 		 esophagusJunction      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Esophagus - Gastroesophageal Junction (GTEX-13OVJ-1426-SM-5K7Z2)    Data format 
 
hide
 Configure 		 esophagusMucosa      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Esophagus - Mucosa (GTEX-13OVJ-1226-SM-5L3HA)    Data format 
 
hide
 Configure 		 esophagusMuscular      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Esophagus - Muscularis (GTEX-13OVJ-1326-SM-5K7Z9)    Data format 
 
hide
 Configure 		 liver      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Liver (GTEX-13OVJ-1026-SM-5IFGI)   Data format 
 
hide
 Configure 		 lung      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Lung (GTEX-13OVJ-0726-SM-5KM1W)    Data format 
 
hide
 Configure 		 muscleSkeletal      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Muscle - Skeletal (GTEX-13OVJ-0226-SM-5L3GK)    Data format 
 
hide
 Configure 		 nerveTibial      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Nerve - Tibial (GTEX-13OVJ-0426-SM-5L3GX)    Data format 
 
hide
 Configure 		 ovary      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Ovary (GTEX-13OVJ-2426-SM-5KM3I)    Data format 
 
hide
 Configure 		 pituitary      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Pituitary (GTEX-13OVJ-2626-SM-5IJFT)    Data format 
 
hide
 Configure 		 skinExposed      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Skin - Sun Exposed (Lower leg) (GTEX-13OVJ-0126-SM-5KM36)    Data format 
 
hide
 Configure 		 skinNotExposed      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Skin - Not Sun Exposed (Suprapubic) (GTEX-13OVJ-0826-SM-5J1OK)    Data format 
 
hide
 Configure 		 uterus      50-59  GTEX-13OVJ 50 yrs  GTEx RNA signal from female Uterus (GTEX-13OVJ-2326-SM-5IJGA)    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