{"__v":51,"_id":"564672ffc454ee0d00cbe476","category":{"project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","_id":"58458b4fba4f1c0f009692bb","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"parentDoc":null,"project":"55faf11ba62ba1170021a9a7","user":"5613e4f8fdd08f2b00437620","version":{"__v":35,"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2015-11-13T23:32:15.121Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":2,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [Introduction](#section-introduction)\\n* [Can I access the data I need in the CGC right away?](#section-can-i-access-the-data-i-need-on-the-cgc-right-away-)\\n  * [Do I need Controlled Data for your research?](#section-1-do-i-need-tcga-controlled-data-for-my-research-)\\n  * [How do I check if I am approved to access TCGA Controlled Data in dbGaP?](#section-2-how-do-i-check-if-i-am-approved-to-access-tcga-controlled-data-in-dbgap-)\\n  * [How do I set up a new eRA Commons account?](#section-3-how-do-i-set-up-a-new-era-commons-account-)\\n  * [How do I request approval for TCGA Controlled Data in dbGaP as a PI?](#section-4-how-do-i-request-approval-for-tcga-controlled-data-in-dbgap-as-a-pi-)\\n  * [How do I check if my PI has approval for TCGA Controlled Data?](#section-5-how-do-i-check-if-my-pi-has-approval-for-tcga-controlled-data-)\\n  * [How do I check if my institutional affiliation is in eRA Commons?](#section-6-how-do-i-check-if-my-institutional-affiliation-is-in-era-commons-)\\n  * [How do I update a researcher’s institutional affiliation in eRA Commons?](#section-7-how-do-i-update-a-researcher-s-institutional-affiliation-in-era-commons-)\\n  * [How do I sign into dbGaP?](#section-8-how-do-i-sign-into-dbgap-)\\n  * [How do I set a member of my lab as an approved ‘downloader’ in dbGaP?](#section-9-how-do-i-set-a-member-of-my-lab-as-an-approved-downloader-in-dbgap-)\\n* [How can I link my eRA Commons account to my CGC account after sign-up?](#section-how-can-i-link-my-era-commons-account-to-my-cgc-account-after-sign-up-)\"\n}\n[/block]\n##Introduction\n\nThe Cancer Genomics Cloud (CGC) hosts the complete The Cancer Genome Atlas (TCGA) dataset including both Open and Controlled Data.\n\nWhile all data in TCGA is stripped of direct identifiers, DNA information is inherently unique to an individual. Two types of data access ‘tiers’ have been put in place to balance the desire to make the data as widely available as possible while ensuring that the rights of study participants are well protected.\n\n<a name=\"open-data\"></a>\n**Open Data **includes information which is not unique to an individual.  This includes information such as:\n\n  * De-identified clinical and demographic data\n  * Gene expression data\n  * Copy number alterations in regions of the genome\n  * Epigenetic data\n  * Summaries of data across individuals\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"Upon login, you'll be able to access TCGA Open Data right away as long as you agree to the data-use restrictions and requirements outlined in the <a href=\\\"http://cancergenome.nih.gov/publications/publicationguidelines\\\" target=\\\"blank\\\">TCGA publication guidelines</a>.\",\n  \"title\": \"Access TCGA Open Data\"\n}\n[/block]\n<a name=\"controlled-data\"></a>\n**Controlled Data** includes information which is unique to an individual.  This includes most raw data files and some processed data such as:\n\n  * Primary sequencing data (BAM and FASTQ files) from DNA, RNA, miRNA or bisulfite sequencing studies\n  * Raw and processed SNP6 array data\n  * Raw and processed Exon array data\n  * Somatic and germline mutation calls for an individual (VCF and MAF files)\n\nResearchers requiring access to Controlled Data for their studies are required to obtain an approved Data Access Request through the <a href=\"https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login\" target=\"blank\">Database of Genotypes and Phenotypes (dbGaP)</a> and agree to the <a href=\"http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014\" target=\"blank\">TCGA Data Use Certifications</a>  as well as the <a href=\"http://cancergenome.nih.gov/publications/publicationguidelines\" target=\"blank\">TCGA publication guidelines</a>.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"To access TCGA Controlled Data on the CGC, you need to be either a PI or a downloader in an approved dbGaP application.\",\n  \"title\": \"Access TCGA Controlled Data\"\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n##Can I access the data I need on the CGC right away?\n\nWe'd like to help you find out if you'll be able to access TCGA data required by your research on the CGC.\n\nTo facilitate this, we have prepared a flowchart. Please follow it and refer to the numbered explanations when necessary. Please find the relevant information below the flowchart by checking the numbered title.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/92362e6-Screen_Shot_2017-02-06_at_11.07.04_AM.png\",\n        \"Screen Shot 2017-02-06 at 11.07.04 AM.png\",\n        538,\n        692,\n        \"#c3c5c2\"\n      ]\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###1. Do I need TCGA Controlled Data for my research?\n\nPlease see the [introduction](#section-introduction).\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###2. How do I check if I am approved to access TCGA Controlled Data in dbGaP?\n\n1. Log in to the Authorized Access system on <a href=\"https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login\" target=\"blank\">dbGaP</a>. Read more about [signing into dbGaP](#section-8-how-do-i-sign-into-dbgap-).  \n\n2. Click the **My Requests **tab.\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"My Requests tab on dbGaP\",\n      \"image\": [\n        \"https://files.readme.io/02It6uCwRFqD88tlk3pd_*46.png\",\n        \"*46.png\",\n        \"1511\",\n        \"503\",\n        \"#366a9e\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n3. Verify that **TCGA - The Cancer Genome Atlas (phs000178.v9.p8)** is listed with a status of **GRANTED**.\n\n  * **PIs** will see the title and project number of their access request. As a PI, you also have the option to revise your project from this page. Also note that the expiration date of your data access is shown.\n  * **Approved downloaders** will see the PI and the project that their approval is associated with.  \n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"Verify TCGA status\",\n      \"image\": [\n        \"https://files.readme.io/kgqrEIXAQ86EE4x83WGq_*47.png\",\n        \"*47.png\",\n        \"1295\",\n        \"450\",\n        \"\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###3. How do I set up a new eRA Commons account?\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"These steps must be performed by an individual designated as an [eRA Commons](http://docs.cancergenomicscloud.org/v1.0/docs/glossary#section--era-commons-) Signing Official (SO) or Accounts Administrator (AA). Typically these individuals are in the grants or business office of your institution.\",\n  \"title\": \"Who can do this?\"\n}\n[/block]\n\nBefore setting up an eRA Commons account for an individual, your institution must be registered in the eRA Commons system, and at least one individual must be designated as a ‘Signing Official’. See <a href=\"http://www.ncbi.nlm.nih.gov/books/NBK99225/#DArequest.i_don_t_think_my_institution_h\" target=\"blank\">here</a> for further directions.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"title\": \"Intramural users\",\n  \"body\": \"If you are an intramural (NIH employee), you will use your NIH credentials to sign into the systems and will not need an eRA Commons account.\"\n}\n[/block]\nTo set up a new eRA Commons account:\n\n1. Sign in to <a href=\"https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f\" target=\"blank\">eRA Commons</a>.\n2. Select **Admin** from the top navigation bar.\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"Sign into eRA Commons\",\n      \"image\": [\n        \"https://files.readme.io/umREUGM8RzyOJpzIM5jv_*48.png\",\n        \"*48.png\",\n        \"1319\",\n        \"236\",\n        \"#5787c7\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n3. Select **Accounts** and then **Manage Accounts**.\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"eRA Commons Accounts\",\n      \"image\": [\n        \"https://files.readme.io/70M5YsNtS8ub5kpUoXIc_*49.png\",\n        \"*49.png\",\n        \"1364\",\n        \"436\",\n        \"#244b76\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n4. Search for the researcher who requires the eRA Commons account by ID, email, or name.\n[block:image]\n{\n  \"images\": [\n    {\n      \"image\": [\n        \"https://files.readme.io/F7vFPOTUTzKlhb4g0W5C_*50.png\",\n        \"*50.png\",\n        \"1273\",\n        \"580\",\n        \"#386592\",\n        \"\"\n      ],\n      \"caption\": \"Search for researcher in eRA Commons\"\n    }\n  ]\n}\n[/block]\n5. Select **search outside institution** to verify that an account has not been previously created for the researcher.\n6. If no account exists, select **Create Account**.\n7. Complete the contact information for the researcher.\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"Create an Account on eRA Commons\",\n      \"image\": [\n        \"https://files.readme.io/oaO1xnIpSi2UCSqZ3Bxr_*51.png\",\n        \"*51.png\",\n        \"1291\",\n        \"662\",\n        \"#315378\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"You’ll need to create the **USER ID** for the researcher. Pick something that will be easy for them to remember!\",\n  \"title\": \"Create a User ID\"\n}\n[/block]\n8. Click the magnifying glass under **Role** and select the appropriate role for the researcher on the new screen that opens. You can find out more about eRA Commons roles and the permissions associated with each role <a href=\"https://era.nih.gov/files/eRA_Commons_Roles.pdf\" target=\"blank\">here</a>.\n9. The role and organization will be populated on the demographic screen.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"If you are an AA or SO for multiple organizations, use the magnifying glass to select the correct organization to affiliate the individual.\",\n  \"title\": \"Selecting an organization\"\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###4. How do I request approval for TCGA Controlled Data in dbGaP as a PI?\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"These steps must be performed by an individual designated as a PI in eRA Commons.\",\n  \"title\": \"Note:\"\n}\n[/block]\nSee the video tutorial <a href=\"https://www.youtube.com/watch?annotation_id=annotation_2856830007&feature=iv&src_vid=ekFlMgLFZDE&v=-3tUBeKbP5c\" target=\"blank\">here</a>.\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n ###5. How do I check if my PI has approval for TCGA Controlled Data?\n\nThe full list of PIs approved to use TCGA Controlled Data is available on the <a href=\"http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178.v1.p1\" target=\"blank\">TCGA dbGaP page</a> in the Authorized Data Access Requests section.\n[block:callout]\n{\n  \"type\": \"success\",\n  \"body\": \"Requests are listed alphabetically by last name. The affiliation of the requestor and the current status of the request is also provided.\",\n  \"title\": \"Tip:\"\n}\n[/block]\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"List of PIs with Controlled Access to TCGA data\",\n      \"image\": [\n        \"https://files.readme.io/i0z5M04KThSISYEv49rq_*52.png\",\n        \"*52.png\",\n        \"1085\",\n        \"433\",\n        \"#6474f4\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###6. How do I check if my institutional affiliation is in eRA Commons?\n1. Log in to <a href=\"https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f\" target=\"blank\">eRA Commons</a>.\n2. Your account affiliation is shown under your name and account ID.\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"eRA Commons by Institution\",\n      \"image\": [\n        \"https://files.readme.io/32MMfUtsTdGzOYlGEHL2_*53.png\",\n        \"*53.png\",\n        \"1321\",\n        \"675\",\n        \"\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"body\": \"It is possible to be affiliated with more than one institution.  To see other institutions you are affiliated, click the hyperlinked name of your default institution.\",\n  \"title\": \"Institutional affiliation\"\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###7. How do I update a researcher’s institutional affiliation in eRA Commons?\n[block:callout]\n{\n  \"type\": \"info\",\n  \"title\": \"Who should I ask?\",\n  \"body\": \"These steps must be performed by an individual designated as an eRA Commons Signing Official (SO) or Accounts Administrator (AA). Typically these individuals are in the grants or business office of your institution.\"\n}\n[/block]\n1. Sign into <a href=\"https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f\" target=\"blank\">eRA Commons</a>.\n2. Select the **Admin** tab and then **Manage Accounts** as described in [Setting up a new eRA Commons account](#section-3-how-do-i-set-up-a-new-era-commons-account-).\n3. Search for an individual based on their eRA Commons account or last name. \n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Remember:\",\n  \"body\": \"Be sure to select **Search outside of your institution**.\"\n}\n[/block]\n4. Once you identify the correct individual, click **Create Affiliation** and add the role and organization of the individual.\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###8. How do I sign into dbGaP?\n1. Log in to the <a href=\"https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login\" target=\"blank\">Authorized Access system</a> on dbGaP.\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"Sign into dbGaP\",\n      \"image\": [\n        \"https://files.readme.io/inolCNotSASnsgij4wdA_*54.png\",\n        \"*54.png\",\n        \"1169\",\n        \"298\",\n        \"#3971a1\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n2. Your browser will redirect to the NIH Secure identity provider **iTrust**. \n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"Sign into iTrust\",\n      \"image\": [\n        \"https://files.readme.io/NduWBuKSsOazNvkcYPCA_*55.png\",\n        \"*55.png\",\n        \"1182\",\n        \"375\",\n        \"#4880b8\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n3. Enter your **User name **and **Password**.\n\n**Extramural (non-NIH) researchers:** Use your eRA Commons ID and Password.  \n[block:callout]\n{\n  \"type\": \"warning\",\n  \"body\": \"If your eRA Commons password has expired, you will receive an error message ‘Authentication failed’.  If this occurs, go to <a href=\\\"https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f\\\" target=\\\"blank\\\">eRA Commons</a> and set a new password. Make sure you can successfully login to eRA Commons with your username and password before proceeding.\",\n  \"title\": \"Expired password?\"\n}\n[/block]\n**Intramural (NIH) researchers: **Use your NIH cit login credentials (the same login credential as your NIH email account). See the dbGaP authorized access system login <a href=\"http://www.ncbi.nlm.nih.gov/books/NBK63573/#DArequest.when_trying_to_access_the_dbga\" target=\"blank\">FAQ</a> for more information and troubleshooting tips for logging into dbGaP.\n\nIf this is a first time you have logged into the system, a new dbGaP account will be created for you using the provided credentials.  Additional information for intramural researchers creating a dbGaP account for the first time can be found <a href=\"http://www.ncbi.nlm.nih.gov/books/NBK99225/#DArequest.i_am_an_investigator_of_nih_wh\" target=\"blank\">here</a>.\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"body\": \"If your eRA Commons account was recently created or updated, it may require 24 - 48 hours before these changes are reflected in the dbGaP databases.  If you have trouble logging into dbGaP but can access your eRA account, wait 48 hours before contacting [dbgap-help](mailto:dbgap-help:::at:::ncbi.nlm.nih.gov).\",\n  \"title\": \"Trouble logging in?\"\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n###9. How do I set a member of my lab as an approved ‘downloader’ in dbGaP?\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"My Projects on dbGaP\",\n      \"image\": [\n        \"https://files.readme.io/CvEHZIGqSl4B7Ko1X7XE_*56.png\",\n        \"*56.png\",\n        \"1439\",\n        \"501\",\n        \"#376c9b\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n1. After signing into dbGaP click the **Downloaders** tab.\n2. Enter the first and/or last name of the individual to be set as an approved downloader.\n3. Select the correct individual from the list of returned results\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"Remember:\",\n  \"body\": \"The individual must be affiliated with your institution.\"\n}\n[/block]\n\n[block:image]\n{\n  \"images\": [\n    {\n      \"caption\": \"Add Downloaders to dbGaP\",\n      \"image\": [\n        \"https://files.readme.io/FofPUnTTleuo0Emem5WQ_*57.png\",\n        \"*57.png\",\n        \"1440\",\n        \"375\",\n        \"#3972a3\",\n        \"\"\n      ]\n    }\n  ]\n}\n[/block]\n4. Confirm that the selected individual’s email and phone number appears correct and select **Set Downloader**. If you have multiple Open Data access approvals, you can choose to provide access to either **all** or a subset of projects.\n\nThe list of current downloaders will be updated to reflect the addition. You can return to this page to change access permissions at any time.\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Because of the way the dbGaP system was set up, it can take up to 24 hours before access rights are updated in other systems such as cgHub or the CGC.  Don’t be worried if you are not immediately able to log into these systems after being set up as a Downloader.\",\n  \"title\": \"Don't worry\"\n}\n[/block]\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>\n\n##How can I link my eRA Commons account to my CGC account after sign-up?\n\nYou can link your eRA Commons account to your CGC account at any time. Doing so will associate your dbGaP access permissions with your CGC account. Learn how to [link your eRA Commons account to your CGC account](account-settings-and-billing#section-link-your-era-commons-account-to-your-cgc-account).\n\n<div align=\"right\"><a href=\"#&nbsp;\">top</a></div>","excerpt":"<a name=\"&nbsp;\"></a><a href=\"about-datasets\" style=\"color:#132c56\">ABOUT DATASETS</a> > <a href=\"tcga-data\" style=\"color:#132c56\">TCGA data</a> > TCGA data access","slug":"tcga-data-access","type":"basic","title":"↳ TCGA data access"}

↳ TCGA data access

<a name="&nbsp;"></a><a href="about-datasets" style="color:#132c56">ABOUT DATASETS</a> > <a href="tcga-data" style="color:#132c56">TCGA data</a> > TCGA data access

[block:callout] { "type": "warning", "title": "On this page:", "body": "* [Introduction](#section-introduction)\n* [Can I access the data I need in the CGC right away?](#section-can-i-access-the-data-i-need-on-the-cgc-right-away-)\n * [Do I need Controlled Data for your research?](#section-1-do-i-need-tcga-controlled-data-for-my-research-)\n * [How do I check if I am approved to access TCGA Controlled Data in dbGaP?](#section-2-how-do-i-check-if-i-am-approved-to-access-tcga-controlled-data-in-dbgap-)\n * [How do I set up a new eRA Commons account?](#section-3-how-do-i-set-up-a-new-era-commons-account-)\n * [How do I request approval for TCGA Controlled Data in dbGaP as a PI?](#section-4-how-do-i-request-approval-for-tcga-controlled-data-in-dbgap-as-a-pi-)\n * [How do I check if my PI has approval for TCGA Controlled Data?](#section-5-how-do-i-check-if-my-pi-has-approval-for-tcga-controlled-data-)\n * [How do I check if my institutional affiliation is in eRA Commons?](#section-6-how-do-i-check-if-my-institutional-affiliation-is-in-era-commons-)\n * [How do I update a researcher’s institutional affiliation in eRA Commons?](#section-7-how-do-i-update-a-researcher-s-institutional-affiliation-in-era-commons-)\n * [How do I sign into dbGaP?](#section-8-how-do-i-sign-into-dbgap-)\n * [How do I set a member of my lab as an approved ‘downloader’ in dbGaP?](#section-9-how-do-i-set-a-member-of-my-lab-as-an-approved-downloader-in-dbgap-)\n* [How can I link my eRA Commons account to my CGC account after sign-up?](#section-how-can-i-link-my-era-commons-account-to-my-cgc-account-after-sign-up-)" } [/block] ##Introduction The Cancer Genomics Cloud (CGC) hosts the complete The Cancer Genome Atlas (TCGA) dataset including both Open and Controlled Data. While all data in TCGA is stripped of direct identifiers, DNA information is inherently unique to an individual. Two types of data access ‘tiers’ have been put in place to balance the desire to make the data as widely available as possible while ensuring that the rights of study participants are well protected. <a name="open-data"></a> **Open Data **includes information which is not unique to an individual. This includes information such as: * De-identified clinical and demographic data * Gene expression data * Copy number alterations in regions of the genome * Epigenetic data * Summaries of data across individuals [block:callout] { "type": "success", "body": "Upon login, you'll be able to access TCGA Open Data right away as long as you agree to the data-use restrictions and requirements outlined in the <a href=\"http://cancergenome.nih.gov/publications/publicationguidelines\" target=\"blank\">TCGA publication guidelines</a>.", "title": "Access TCGA Open Data" } [/block] <a name="controlled-data"></a> **Controlled Data** includes information which is unique to an individual. This includes most raw data files and some processed data such as: * Primary sequencing data (BAM and FASTQ files) from DNA, RNA, miRNA or bisulfite sequencing studies * Raw and processed SNP6 array data * Raw and processed Exon array data * Somatic and germline mutation calls for an individual (VCF and MAF files) Researchers requiring access to Controlled Data for their studies are required to obtain an approved Data Access Request through the <a href="https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login" target="blank">Database of Genotypes and Phenotypes (dbGaP)</a> and agree to the <a href="http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014" target="blank">TCGA Data Use Certifications</a> as well as the <a href="http://cancergenome.nih.gov/publications/publicationguidelines" target="blank">TCGA publication guidelines</a>. [block:callout] { "type": "success", "body": "To access TCGA Controlled Data on the CGC, you need to be either a PI or a downloader in an approved dbGaP application.", "title": "Access TCGA Controlled Data" } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ##Can I access the data I need on the CGC right away? We'd like to help you find out if you'll be able to access TCGA data required by your research on the CGC. To facilitate this, we have prepared a flowchart. Please follow it and refer to the numbered explanations when necessary. Please find the relevant information below the flowchart by checking the numbered title. [block:image] { "images": [ { "image": [ "https://files.readme.io/92362e6-Screen_Shot_2017-02-06_at_11.07.04_AM.png", "Screen Shot 2017-02-06 at 11.07.04 AM.png", 538, 692, "#c3c5c2" ] } ] } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ###1. Do I need TCGA Controlled Data for my research? Please see the [introduction](#section-introduction). <div align="right"><a href="#&nbsp;">top</a></div> ###2. How do I check if I am approved to access TCGA Controlled Data in dbGaP? 1. Log in to the Authorized Access system on <a href="https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login" target="blank">dbGaP</a>. Read more about [signing into dbGaP](#section-8-how-do-i-sign-into-dbgap-). 2. Click the **My Requests **tab. [block:image] { "images": [ { "caption": "My Requests tab on dbGaP", "image": [ "https://files.readme.io/02It6uCwRFqD88tlk3pd_*46.png", "*46.png", "1511", "503", "#366a9e", "" ] } ] } [/block] 3. Verify that **TCGA - The Cancer Genome Atlas (phs000178.v9.p8)** is listed with a status of **GRANTED**. * **PIs** will see the title and project number of their access request. As a PI, you also have the option to revise your project from this page. Also note that the expiration date of your data access is shown. * **Approved downloaders** will see the PI and the project that their approval is associated with. [block:image] { "images": [ { "caption": "Verify TCGA status", "image": [ "https://files.readme.io/kgqrEIXAQ86EE4x83WGq_*47.png", "*47.png", "1295", "450", "", "" ] } ] } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ###3. How do I set up a new eRA Commons account? [block:callout] { "type": "info", "body": "These steps must be performed by an individual designated as an [eRA Commons](http://docs.cancergenomicscloud.org/v1.0/docs/glossary#section--era-commons-) Signing Official (SO) or Accounts Administrator (AA). Typically these individuals are in the grants or business office of your institution.", "title": "Who can do this?" } [/block] Before setting up an eRA Commons account for an individual, your institution must be registered in the eRA Commons system, and at least one individual must be designated as a ‘Signing Official’. See <a href="http://www.ncbi.nlm.nih.gov/books/NBK99225/#DArequest.i_don_t_think_my_institution_h" target="blank">here</a> for further directions. [block:callout] { "type": "success", "title": "Intramural users", "body": "If you are an intramural (NIH employee), you will use your NIH credentials to sign into the systems and will not need an eRA Commons account." } [/block] To set up a new eRA Commons account: 1. Sign in to <a href="https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f" target="blank">eRA Commons</a>. 2. Select **Admin** from the top navigation bar. [block:image] { "images": [ { "caption": "Sign into eRA Commons", "image": [ "https://files.readme.io/umREUGM8RzyOJpzIM5jv_*48.png", "*48.png", "1319", "236", "#5787c7", "" ] } ] } [/block] 3. Select **Accounts** and then **Manage Accounts**. [block:image] { "images": [ { "caption": "eRA Commons Accounts", "image": [ "https://files.readme.io/70M5YsNtS8ub5kpUoXIc_*49.png", "*49.png", "1364", "436", "#244b76", "" ] } ] } [/block] 4. Search for the researcher who requires the eRA Commons account by ID, email, or name. [block:image] { "images": [ { "image": [ "https://files.readme.io/F7vFPOTUTzKlhb4g0W5C_*50.png", "*50.png", "1273", "580", "#386592", "" ], "caption": "Search for researcher in eRA Commons" } ] } [/block] 5. Select **search outside institution** to verify that an account has not been previously created for the researcher. 6. If no account exists, select **Create Account**. 7. Complete the contact information for the researcher. [block:image] { "images": [ { "caption": "Create an Account on eRA Commons", "image": [ "https://files.readme.io/oaO1xnIpSi2UCSqZ3Bxr_*51.png", "*51.png", "1291", "662", "#315378", "" ] } ] } [/block] [block:callout] { "type": "success", "body": "You’ll need to create the **USER ID** for the researcher. Pick something that will be easy for them to remember!", "title": "Create a User ID" } [/block] 8. Click the magnifying glass under **Role** and select the appropriate role for the researcher on the new screen that opens. You can find out more about eRA Commons roles and the permissions associated with each role <a href="https://era.nih.gov/files/eRA_Commons_Roles.pdf" target="blank">here</a>. 9. The role and organization will be populated on the demographic screen. [block:callout] { "type": "success", "body": "If you are an AA or SO for multiple organizations, use the magnifying glass to select the correct organization to affiliate the individual.", "title": "Selecting an organization" } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ###4. How do I request approval for TCGA Controlled Data in dbGaP as a PI? [block:callout] { "type": "info", "body": "These steps must be performed by an individual designated as a PI in eRA Commons.", "title": "Note:" } [/block] See the video tutorial <a href="https://www.youtube.com/watch?annotation_id=annotation_2856830007&feature=iv&src_vid=ekFlMgLFZDE&v=-3tUBeKbP5c" target="blank">here</a>. <div align="right"><a href="#&nbsp;">top</a></div> ###5. How do I check if my PI has approval for TCGA Controlled Data? The full list of PIs approved to use TCGA Controlled Data is available on the <a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000178.v1.p1" target="blank">TCGA dbGaP page</a> in the Authorized Data Access Requests section. [block:callout] { "type": "success", "body": "Requests are listed alphabetically by last name. The affiliation of the requestor and the current status of the request is also provided.", "title": "Tip:" } [/block] [block:image] { "images": [ { "caption": "List of PIs with Controlled Access to TCGA data", "image": [ "https://files.readme.io/i0z5M04KThSISYEv49rq_*52.png", "*52.png", "1085", "433", "#6474f4", "" ] } ] } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ###6. How do I check if my institutional affiliation is in eRA Commons? 1. Log in to <a href="https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f" target="blank">eRA Commons</a>. 2. Your account affiliation is shown under your name and account ID. [block:image] { "images": [ { "caption": "eRA Commons by Institution", "image": [ "https://files.readme.io/32MMfUtsTdGzOYlGEHL2_*53.png", "*53.png", "1321", "675", "", "" ] } ] } [/block] [block:callout] { "type": "warning", "body": "It is possible to be affiliated with more than one institution. To see other institutions you are affiliated, click the hyperlinked name of your default institution.", "title": "Institutional affiliation" } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ###7. How do I update a researcher’s institutional affiliation in eRA Commons? [block:callout] { "type": "info", "title": "Who should I ask?", "body": "These steps must be performed by an individual designated as an eRA Commons Signing Official (SO) or Accounts Administrator (AA). Typically these individuals are in the grants or business office of your institution." } [/block] 1. Sign into <a href="https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f" target="blank">eRA Commons</a>. 2. Select the **Admin** tab and then **Manage Accounts** as described in [Setting up a new eRA Commons account](#section-3-how-do-i-set-up-a-new-era-commons-account-). 3. Search for an individual based on their eRA Commons account or last name. [block:callout] { "type": "warning", "title": "Remember:", "body": "Be sure to select **Search outside of your institution**." } [/block] 4. Once you identify the correct individual, click **Create Affiliation** and add the role and organization of the individual. <div align="right"><a href="#&nbsp;">top</a></div> ###8. How do I sign into dbGaP? 1. Log in to the <a href="https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login" target="blank">Authorized Access system</a> on dbGaP. [block:image] { "images": [ { "caption": "Sign into dbGaP", "image": [ "https://files.readme.io/inolCNotSASnsgij4wdA_*54.png", "*54.png", "1169", "298", "#3971a1", "" ] } ] } [/block] 2. Your browser will redirect to the NIH Secure identity provider **iTrust**. [block:image] { "images": [ { "caption": "Sign into iTrust", "image": [ "https://files.readme.io/NduWBuKSsOazNvkcYPCA_*55.png", "*55.png", "1182", "375", "#4880b8", "" ] } ] } [/block] 3. Enter your **User name **and **Password**. **Extramural (non-NIH) researchers:** Use your eRA Commons ID and Password. [block:callout] { "type": "warning", "body": "If your eRA Commons password has expired, you will receive an error message ‘Authentication failed’. If this occurs, go to <a href=\"https://public.era.nih.gov/commons/public/login.do?TYPE=33554433&REALMOID=06-1edb031f-46c7-44b3-b803-60b537de74d2&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-938PYmoLVb4VrDeXo04LZUDVDvc%2b3899ByInEAjuSUvWNIGfB2zRpWiCivYGCogG&TARGET=-SM-http%3a%2f%2fpublic%2eera%2enih%2egov%2f\" target=\"blank\">eRA Commons</a> and set a new password. Make sure you can successfully login to eRA Commons with your username and password before proceeding.", "title": "Expired password?" } [/block] **Intramural (NIH) researchers: **Use your NIH cit login credentials (the same login credential as your NIH email account). See the dbGaP authorized access system login <a href="http://www.ncbi.nlm.nih.gov/books/NBK63573/#DArequest.when_trying_to_access_the_dbga" target="blank">FAQ</a> for more information and troubleshooting tips for logging into dbGaP. If this is a first time you have logged into the system, a new dbGaP account will be created for you using the provided credentials. Additional information for intramural researchers creating a dbGaP account for the first time can be found <a href="http://www.ncbi.nlm.nih.gov/books/NBK99225/#DArequest.i_am_an_investigator_of_nih_wh" target="blank">here</a>. [block:callout] { "type": "warning", "body": "If your eRA Commons account was recently created or updated, it may require 24 - 48 hours before these changes are reflected in the dbGaP databases. If you have trouble logging into dbGaP but can access your eRA account, wait 48 hours before contacting [dbgap-help](mailto:dbgap-help@ncbi.nlm.nih.gov).", "title": "Trouble logging in?" } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ###9. How do I set a member of my lab as an approved ‘downloader’ in dbGaP? [block:image] { "images": [ { "caption": "My Projects on dbGaP", "image": [ "https://files.readme.io/CvEHZIGqSl4B7Ko1X7XE_*56.png", "*56.png", "1439", "501", "#376c9b", "" ] } ] } [/block] 1. After signing into dbGaP click the **Downloaders** tab. 2. Enter the first and/or last name of the individual to be set as an approved downloader. 3. Select the correct individual from the list of returned results [block:callout] { "type": "warning", "title": "Remember:", "body": "The individual must be affiliated with your institution." } [/block] [block:image] { "images": [ { "caption": "Add Downloaders to dbGaP", "image": [ "https://files.readme.io/FofPUnTTleuo0Emem5WQ_*57.png", "*57.png", "1440", "375", "#3972a3", "" ] } ] } [/block] 4. Confirm that the selected individual’s email and phone number appears correct and select **Set Downloader**. If you have multiple Open Data access approvals, you can choose to provide access to either **all** or a subset of projects. The list of current downloaders will be updated to reflect the addition. You can return to this page to change access permissions at any time. [block:callout] { "type": "info", "body": "Because of the way the dbGaP system was set up, it can take up to 24 hours before access rights are updated in other systems such as cgHub or the CGC. Don’t be worried if you are not immediately able to log into these systems after being set up as a Downloader.", "title": "Don't worry" } [/block] <div align="right"><a href="#&nbsp;">top</a></div> ##How can I link my eRA Commons account to my CGC account after sign-up? You can link your eRA Commons account to your CGC account at any time. Doing so will associate your dbGaP access permissions with your CGC account. Learn how to [link your eRA Commons account to your CGC account](account-settings-and-billing#section-link-your-era-commons-account-to-your-cgc-account). <div align="right"><a href="#&nbsp;">top</a></div>