GTEx v9

 

v9 was released in October 2022. 

Hong Qin tried to download it, but found the old request "expired". So, he submitted a new request. 

GTEX data sets

 

https://www.gtexportal.org/home/faq#sampleIdFormat

What does the sample ID for an RNA-seq or genotype sample stand for, such as GTEX-14753-1626-SM-5NQ9L?

The format of the sample ID is GTEX-[donor ID]-[tissue site ID]-SM-[aliquot ID].

The donor ID (e.g. GTEX-14753) should be used to link between the various RNA-seq and genotype samples that come from the same donor.

The tissue site ID (e.g. 1626) mostly refers to the tissue site. BUT we do not recommend using it for tissue site designation. Sometimes, sample mix-ups occur, and will be corrected, however this part of the ID will not change when that happens. The accurate tissue site info for all samples can be obtained from the "Tissue Site Detail field" (encoded as "SMTSD") in the Sample Attribute file, available on the Download page.

The aliquot ID (e.g. SM-5NQ9L) is the RNA or DNA aliquot ID used for sequencing.

GTEx factorization tissue specific regulation

 

sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02129-6

gtex aspera command line, ts117

reference: 

https://www.ibm.com/support/pages/downloading-data-ncbi-command-line 

conda create --name aspera

conda active aspera

-bash-4.2$ wget https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz

--2021-06-24 12:32:34--  https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz

Resolving d3gcli72yxqn2z.cloudfront.net (d3gcli72yxqn2z.cloudfront.net)... 13.249.125.124, 13.249.125.227, 13.249.125.202, ...

Connecting to d3gcli72yxqn2z.cloudfront.net (d3gcli72yxqn2z.cloudfront.net)|13.249.125.124|:443... connected.

HTTP request sent, awaiting response... 200 OK

Length: 38715569 (37M) [application/gzip]

Saving to: ‘ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz’

100%[===========================================================================================================================>] 38,715,569  80.1MB/s   in 0.5s   

2021-06-24 12:32:35 (80.1 MB/s) - ‘ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz’ saved [38715569/38715569]

-bash-4.2$ ll

(aspera) -bash-4.2$ sh ibm-aspera-connect-3.11.2.63-linux-g2.12-64.sh 

Installing IBM Aspera Connect

Deploying IBM Aspera Connect (/home/hqin/.aspera/connect) for the current user only.

Install complete.

(aspera) -bash-4.2$ cd /scr/hqin/gtex/

(aspera) -bash-4.2$ ls

(aspera) -bash-4.2$ /home/hqin/.aspera/connect/bin/ascp  -QTr -l 300M -k 1 -i /home/hqin/.aspera/connect/etc/asperaweb_id_dsa.openssh -W private-key-here dbtest@gap-upload.ncbi.nlm.nih.gov:data/instant/hongqin/82927 .

Release_Notes.phs000424.GTEx.v8.p2.MULTI.pdf.                                                                                      100%  432KB  5.0Mb/s    00:00    

Study_Report.phs000424.GTEx.v8.p2.MULTI.pdf.n                                                                                      100%   94KB  5.0Mb/s    00:00    

manifest_phs000424.GTEx.v8.p2.c1.GRU.pdf.ncbi                                                                                      100%   43KB  5.0Mb/s    00:00    

phs000424.v8.pht002740.v8.GTEx_Subject.data_d                                                                                      100% 1200    5.0Mb/s    00:00    

phs000424.v8.pht002740.v8.p2.GTEx_Subject.MUL                                                                                      100% 6000    5.0Mb/s    00:00    

phs000424.v8.pht002740.v8.p2.GTEx_Subject.var                                                                                      100% 3264    5.0Mb/s    00:00    

phs000424.v8.pht002741.v8.GTEx_Sample.data_di                                                                                      100%  992    5.0Mb/s    00:00    

phs000424.v8.pht002741.v8.p2.GTEx_Sample.MULT                                                                                      100%  271KB  5.0Mb/s    00:01    

phs000424.v8.pht002741.v8.p2.GTEx_Sample.var_                                                                                      100% 2032    5.0Mb/s    00:01    

phs000424.v8.pht002742.v8.GTEx_Subject_Phenot                                                                                      100%   89KB  5.0Mb/s    00:01    

phs000424.v8.pht002742.v8.p2.GTEx_Subject_Phe                                                                                      100%  293KB 11.2Mb/s    00:01    

phs000424.v8.pht002742.v8.p2.c1.GTEx_Subject_                                                                                      100%  197KB 11.2Mb/s    00:01    

phs000424.v8.pht002743.v8.GTEx_Sample_Attribu                                                                                      100%   26KB 11.2Mb/s    00:01    

phs000424.v8.pht002743.v8.p2.GTEx_Sample_Attr                                                                                      100%  124KB 11.2Mb/s    00:01    

phs000424.v8.pht002743.v8.p2.c1.GTEx_Sample_A                                                                                      100% 3617KB 23.6Mb/s    00:02    

phg000219.v4.GTEx_Pilot_Illumina5M.genotype-c                                                                                      100%  698MB  292Mb/s    00:24    

phg000219.v4.GTEx_Pilot_Illumina5M.genotype-o                                                                                       14% 5337MB  290Mb/s    15:44 ETAc

......

(aspera) -bash-4.2$ Completed: 1448373288K bytes transferred in 40722 seconds

 (291366K bits/sec), in 59 files, 7 directories; 16 files skipped or empty.

gtex

 

Your request #29078: "Develop a multi-view knowledge-based neural network model to integrate heterogeneous genomics data and detect conserved mechanisms for cellular lifespan regulation" for access to NCBI dbGaP Program datasets has been authorized by your institutional Signing Official (Meredith Perry) and forwarded to the responsible Data Access Committee(s) (DAC) for review.

The result of DAC review will be communicated by email. If access is approved, that communication also will contain instructions for access to the datasets.

The DAC(s) responsible for reviewing your request can be contacted by email to

• Genotype-Tissue Expression (GTEx): nhgridac@mail.nih.gov

GTEx phenotypes

 

Here is a sample phenotype data that I found from the public site of GTEx. The example file provide attributes of

Sample_id, age, sex, blood test results, postmortem information, sequence entries. 

 

This file is from 

https://storage.googleapis.com/gtex_external_datasets/eyegex_data/annotations/EyeGEx_meta_combined_inferior_retina_summary_deidentified_geo_ids.csv

 

I would expect the unreleased files may contain similar but more disease-related attribute based on GTEx-based publications. 

 

More on phenotypes: 

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/dataset.cgi?study_id=phs000424.v8.p2&phv=169091&phd=3910&pha=&pht=2742&phvf=&phdf=&phaf=&phtf=&dssp=1&consent=&temp=1

The "Phenotype Datasets" describes 189 variables in the table for v8. 

GTEx data portals

 

DBGAP

https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=pi_requests&filter=wlid&wlid=29078

ANVIL

https://anvil.terra.bio/#profile

https://app.terra.bio/#workspaces

GTEx protected data

 the GTEx portal,  "who can apply":

Extramural Investigators must be permanent employees of their institution at a level equivalent to a tenure-track professor or senior scientist with responsibilities that most likely include laboratory administration and oversight. Laboratory staff and trainees such as graduate students and postdoctoral fellows are not permitted to submit project requests.

Here is a link that walks through the application process: 

https://www.gtexportal.org/home/protectedDataAccess

Here is the "request access" page on the first step:

https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login

From there, you can click on the "How does one apply" link and it will walk though all the steps.

Tips: 

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetPdf.cgi?document_name=GeneralAAInstructions.pdf

dbGAP project PI: 

Research Use Statement. The approval of project requests depends primarily on a carefully written Research Use Statement (2,200 characters max). The statement should include the following components: • Objectives of the proposed research; • Study design; • Analysis plan, including the phenotypic characteristics that will be evaluated in association with genetic variants; • Explanation of how the proposed research is consistent with the data use limitations for the requested dataset(s); and • Brief description of any planned collaboration with researchers at other institutions, including the name of the collaborator(s) and their institution(s).

From T Day: 

I’ve been doing some digging to try and find the GTEx policy on data limitation. I found this document (attached) which highlights that they follow the NIH Genome Data Sharing GDS policy (found here: 

https://osp.od.nih.gov/scientific-sharing/genomic-data-sharing/ ) with slight variations. These variations are noted in the attached document which I was able to locate in the documentations section of the GTEx portal. 

GTEx Data Release and Publication Policy version 5-8-15

https://storage.googleapis.com/gtex-public-data/GTEx_Data_Release_and_Publication_Policy_v05-08-15.docx 

It is the intent of the NIH to promote the dissemination of research findings from NIH genomic dataset(s) as widely as possible through scientific publication or other appropriate public dissemination mechanisms. The Genotype-Tissue Expression (GTEx) project will follow the 8-27-14 Genomic Data Sharing (GDS) policy (gds.nih.gov/index.html) with the following exceptions:

1. Pilot data set (phs000424.v3.p1) - acceptance of the “Ft. Lauderdale” principles of rapid, pre-publication data release (see Sharing Data from Large-Scale Biological Research Projects: A System of Tripartite Responsibility, 2003). The continued success of rapid pre-publication data release relies on the scientific community to respect the data producer’s interest to publish a full analysis of their data first. Secondary users are asked to refrain from submitting manuscripts describing comprehensive analyses until the Consortium has published their analysis. 

May 8, 2015 - No restrictions - main manuscript published.

2. phs000424.v4.p1 - the dataset is subject to 9 months publication restriction starting from the date of the release; no restrictions after Jan 4, 2015. 

All datasets from phs00424.v5.p1 forward will follow the NIH GDS policy.  This means that once released through dbGaP, there are no restrictions on use or publication.  This document and an accompanying table of dataset releases can be found at http://www.gtexportal.org/home/documentationPage.

Overall, users of GTEx data are strongly encouraged to publish their results in peer-reviewed journals and to present research findings at scientific meetings, etc. Investigators planning to conduct analyses similar to those described at http://www.gtexportal.org/home/documentationPage may contact Consortium members or the NIH program staff at nhgrigtex@mail.nih.gov to discuss collaborations, if so desired