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<html lang="en" data-reactroot=""><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>ENCBS435HZC – ENCODE</title><link rel="canonical" href="/biosamples/ENCBS435HZC/"/><link rel="stylesheet" href="/static/build/cssFile"/><link href="https://fonts.googleapis.com/css2?family=Mada:wght@200;400;500;600;700&family=Oswald:wght@200;300;400;500&family=Quicksand:wght@300;400;600&display=swap" rel="stylesheet"/><script async="" src="//www.google-analytics.com/analytics.js"></script><script async="" src="https://cdn.walkme.com/users/8c7ff9322d01408798869806f9f5a132/test/walkme_8c7ff9322d01408798869806f9f5a132_https.js"></script></head><body><script data-prop-name="context" type="application/json">
{"accession":"ENCBS435HZC","aliases":["richard-myers:HEK293-lot70036272-batch2021-J-20210728"],"schema_version":"26","status":"released","lab":{"fax":"256-327-0978","institute_label":"HAIB","address1":"601 Genome Way","state":"AL","institute_name":"HudsonAlpha Institute for Biotechnology","awards":["/awards/U54HG006998/","/awards/U54HG004576/","/awards/UM1HG009411/"],"title":"Richard Myers, HAIB","phone1":"256-327-5220","phone2":"","schema_version":"5","pi":"/users/a62cfec5-57a0-45ab-b943-8ca0e0057bb6/","postal_code":"35806","name":"richard-myers","city":"Huntsville","country":"USA","status":"current","@id":"/labs/richard-myers/","@type":["Lab","Item"],"uuid":"c0a3540e-8ef0-4d4d-a449-ae47c2475838"},"award":{"status":"current","url":"https://projectreporter.nih.gov/project_info_description.cfm?aid=9247485\u0026icde=32921409\u0026ddparam=\u0026ddvalue=\u0026ddsub=\u0026cr=1\u0026csb=default\u0026cs=ASC\u0026pball=","schema_version":"11","title":"AN ENCODE CHIP-SEQ PIPELINE USING ENDOGENOUSLY TAGGED HUMAN DNA-ASSOCIATED PROTEINS","name":"UM1HG009411","description":"Almost a tenth of human genes code for proteins that interact with chromosomes in the nucleus. Most of these DNA-associated proteins (referred to as DAPs) are involved in regulating the expression of genes, by serving as part of the basic transcriptional machinery, as transcription factors that regulate the spatial and temporal levels of transcription, or as chromatin state regulators. These proteins are key components in biology, as transcriptional regulation underlies fundamental biological processes in organismal development, in determining cell states during differentiation, and in directing physiological responses to the internal and external environment. Thus, comprehensive and detailed assessment of the molecular actions of DAPs, that is, where they interact throughout the human genome, is a fundamental long-term goal of both basic and clinical research. In response to RFA-HG-16-002, “Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Mouse (UM1)”, this application proposes to use a recently-established \"shovel ready\" pipeline for mapping DAPs in human cell lines that overcomes the very high failure rates of traditional ChIP-seq, a widely- used approach that requires specific antibodies for each factor. The new approach, called CETCh-seq, involves adding an epitope tag at the endogenous locus encoding each protein, and using chromatin immunoprecipitation with a universal antibody against the epitope followed by high-throughput sequencing (ChIP-seq) to identify DAP-DNA associations genome-wide. This production pipeline will be applied to each of 1,244 DAPs that are expressed in a set of human cell lines and have not yet been mapped by ENCODE. During the four-year project, this pipeline will be used to test each of these factors in one human cell line, and for 100 of the DAPs, in four human cell lines, allowing characterization of cell-type differences. The project will also tag and assay multiple allelic versions of a small number of DAPs in which pathogenic or potentially pathogenic mutations have been identified. The project will produce genome-wide DAP maps and identify motifs for hundreds of human regulatory proteins, providing an important component for the next phase of the ENCODE Project. All data, as well as useful materials in the form of gene editing plasmids and tagged human cell lines, will be made freely available to the research community.","start_date":"2017-02-01","end_date":"2021-01-31","pi":{"@id":"/users/a62cfec5-57a0-45ab-b943-8ca0e0057bb6/","@type":["User","Item"],"uuid":"a62cfec5-57a0-45ab-b943-8ca0e0057bb6","lab":{"fax":"256-327-0978","institute_label":"HAIB","address1":"601 Genome Way","state":"AL","institute_name":"HudsonAlpha Institute for Biotechnology","awards":["/awards/U54HG006998/","/awards/U54HG004576/","/awards/UM1HG009411/"],"title":"Richard Myers, HAIB","phone1":"256-327-5220","phone2":"","schema_version":"5","pi":"/users/a62cfec5-57a0-45ab-b943-8ca0e0057bb6/","postal_code":"35806","name":"richard-myers","city":"Huntsville","country":"USA","status":"current","@id":"/labs/richard-myers/","@type":["Lab","Item"],"uuid":"c0a3540e-8ef0-4d4d-a449-ae47c2475838"},"title":"Richard Myers","submits_for":["/labs/richard-myers/","/labs/barbara-wold/","/labs/ali-mortazavi/","/labs/ross-hardison/","/labs/tim-reddy/","/labs/greg-cooper/"]},"rfa":"ENCODE4","project":"ENCODE","viewing_group":"ENCODE4","component":"mapping","@id":"/awards/UM1HG009411/","@type":["Award","Item"],"uuid":"48a4972b-fdff-4f73-b5bb-d15d6424b44c"},"date_created":"2022-08-23T16:25:01.175390+00:00","submitted_by":{"@id":"/users/5e189705-c6ca-4849-ab5c-e6d679dc96ae/","@type":["User","Item"],"uuid":"5e189705-c6ca-4849-ab5c-e6d679dc96ae","lab":"/labs/richard-myers/","title":"Scott Newberry","submits_for":["/labs/richard-myers/"]},"documents":[],"references":[],"source":{"title":"Richard Myers","aliases":[],"description":"Richard Myers at the HudsonAlpha Institute for Biotechnology","schema_version":"6","name":"richard-myers","status":"released","@id":"/sources/richard-myers/","@type":["Source","Item"],"uuid":"db12505e-fd2b-40bc-9dad-bd9a09707647"},"biosample_ontology":{"status":"released","schema_version":"1","classification":"cell line","term_name":"HEK293","references":[],"dbxrefs":["Cellosaurus:CVCL_0045"],"aliases":[],"term_id":"EFO:0001182","@id":"/biosample-types/cell_line_EFO_0001182/","@type":["BiosampleType","Item"],"uuid":"014c9be0-20d4-4df5-b816-b0dca4cfee9d","name":"cell_line_EFO_0001182","organ_slims":["kidney","epithelium"],"cell_slims":["epithelial cell"],"developmental_slims":["mesoderm"],"system_slims":["excretory system"],"synonyms":["human embryonic kidney cell"]},"genetic_modifications":[],"alternate_accessions":[],"treatments":[],"dbxrefs":[],"donor":{"schema_version":"13","accession":"ENCDO000ABF","aliases":["encode:donor of HEK293","encode:donor of HEK293T"],"status":"released","lab":"/labs/encode-consortium/","award":"/awards/U41HG006992/","date_created":"2013-12-06T21:06:24.449752+00:00","submitted_by":"/users/3787a0ac-f13a-40fc-a524-69628b04cd59/","notes":"Donor of HEK293. Embryonic kidney, cells contain Adenovirus 5 DNA (PMID: 11967234); hypotriploid, XXX","documents":[],"references":[{"documents":[],"status":"released","lab":"/labs/encode-consortium/","award":"/awards/U41HG006992/","date_created":"2015-11-18T19:34:21.440133+00:00","submitted_by":"/users/85978cd9-131e-48e2-a389-f752ab05b0a6/","schema_version":"9","title":"Preferential transformation of human neuronal cells by human adenoviruses and the origin of HEK 293 cells.","abstract":"The 293 cell line was derived by transformation of primary cultures of human embryonic kidney (HEK) cells with sheared adenovirus (Ad)5 DNA. A combination of immunostaining, immunoblot, and microarray analysis showed that 293 cells express the neurofilament (NF) subunits NF-L, NF-M, NF-H, and a-internexin as well as many other proteins typically found in neurons. Three other independently derived HEK lines, two transformed by Ad5 and one by Ad12, also expressed NFs, as did one human embryonic retinal cell line transformed with Ad5. Two rodent kidney lines transformed with Ad12 were also found to express NF proteins, although several rodent kidney cell lines transformed by Ad5 DNA and three HEK cell lines transformed by the SV40 early region did not express NFs. These results suggest that human Ads preferentially transform human neuronal lineage cells. We also demonstrate that the widely used HEK293 cells have an unexpected relationship to neurons, a finding that may require reinterpretation of many previous studies in which it was assumed that HEK293 cells resembled more typical kidney epithelial cells.","authors":"Shaw G, Morse S, Ararat M, Graham FL","date_published":"2002 Jun","issue":"8","page":"869-71","volume":"16","journal":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","identifiers":["doi:10.1096/fj.01-0995fje","PMID:11967234"],"supplementary_data":[],"categories":[],"published_by":["historical reference"],"@id":"/publications/b42243ab-26d8-4ff6-b801-d368df994167/","@type":["Publication","Item"],"uuid":"b42243ab-26d8-4ff6-b801-d368df994167","publication_year":2002}],"external_ids":[],"alternate_accessions":[],"organism":{"schema_version":"6","scientific_name":"Homo sapiens","name":"human","status":"released","taxon_id":"9606","@id":"/organisms/human/","@type":["Organism","Item"],"uuid":"7745b647-ff15-4ff3-9ced-b897d4e2983c"},"sex":"female","life_stage":"embryonic","age":"unknown","health_status":"unknown","parents":[],"siblings":[],"dbxrefs":["GEO:SAMN06122596"],"@id":"/human-donors/ENCDO000ABF/","@type":["HumanDonor","Donor","Item"],"uuid":"28fbb880-be14-44c9-9104-c2a93b59a249","characterizations":[],"children":[],"superseded_by":[]},"organism":{"schema_version":"6","scientific_name":"Homo sapiens","name":"human","status":"released","taxon_id":"9606","@id":"/organisms/human/","@type":["Organism","Item"],"uuid":"7745b647-ff15-4ff3-9ced-b897d4e2983c"},"internal_tags":[],"nih_institutional_certification":"NIC00003","@id":"/biosamples/ENCBS435HZC/","@type":["Biosample","Item"],"uuid":"db298d03-82d4-4a6f-92f6-133a1f1fd11e","sex":"female","age":"unknown","health_status":"unknown","life_stage":"embryonic","applied_modifications":[],"characterizations":[],"parent_of":[],"origin_batch":"/biosamples/ENCBS435HZC/","perturbed":false,"simple_summary":"","summary":"Homo sapiens HEK293 cell line","@context":"/terms/","audit":{}}
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disabled=""><svg version="1.1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512" class="svg-icon svg-icon-user"><path d="M224,256c70.7,0,128-57.3,128-128S294.7,0,224,0S96,57.3,96,128S153.3,256,224,256z M134.4,288C85,297,0,348.2,0,422.4V464 c0,26.5,0,48,48,48h352c48,0,48-21.5,48-48v-41.6c0-74.2-92.8-125.4-134.4-134.4S183.8,279,134.4,288z"></path></svg></a></li><a href="https://twitter.com/EncodeDCC" class="navbar-twitter" target="_blank" rel="noopener noreferrer" aria-label="ENCODE Twitter feed"><svg version="1.1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" class="svg-icon svg-icon-twitter"><path d="M24,4.6c-0.9,0.4-1.8,0.7-2.8,0.8c1-0.6,1.8-1.6,2.2-2.7c-1,0.6-2,1-3.1,1.2c-0.9-1-2.2-1.6-3.6-1.6c-3.2,0-5.5,3-4.8,6 C7.7,8.1,4.1,6.1,1.7,3.1C0.4,5.4,1,8.3,3.2,9.7C2.4,9.7,1.6,9.5,1,9.1c-0.1,2.3,1.6,4.4,3.9,4.9c-0.7,0.2-1.5,0.2-2.2,0.1 c0.6,2,2.4,3.4,4.6,3.4c-2.1,1.6-4.7,2.3-7.3,2c2.2,1.4,4.8,2.2,7.5,2.2c9.1,0,14.3-7.7,14-14.6C22.5,6.4,23.3,5.5,24,4.6z"></path></svg></a></ul></div></div></nav><div class="test-warning"><div class="container test-warning__content"><div class="test-warning__text">The data displayed on this page is not official and only for testing purposes.</div><button type="button" class="test-warning__close"><i class="icon icon-times-circle-o"></i><span class="sr-only">Close test warning banner</span></button></div></div></div><div id="content" class="container Biosample Item"><div class="view-item type-Biosample type-Item"><header><div class="top-accessories"><ol class="breadcrumb"><li><span>Biosamples</span></li><li><a href="/search/?type=Biosample&biosample_ontology.classification=cell line&status=released" title="Search for cell line in released Biosamples">cell line</a></li><li><a href="/search/?type=Biosample&biosample_ontology.classification=cell line&organism.scientific_name=Homo sapiens&status=released" title="Search for cell line and Homo sapiens in released Biosamples"><i>Homo sapiens</i></a></li><li><a href="/search/?type=Biosample&biosample_ontology.classification=cell line&organism.scientific_name=Homo sapiens&biosample_ontology.term_name=HEK293&status=released" title="Search for cell line and Homo sapiens and HEK293 in released Biosamples">HEK293</a></li></ol></div><h1>ENCBS435HZC<!-- --> / <span class="sentence-case">cell line</span></h1><div class="replacement-accessions"></div><div class="item-accessories"><div class="item-accessories--left"></div><div class="item-accessories--right"><button type="button" class="btn btn-info btn-sm" title="Convert page to JSON-formatted data" aria-label="Convert page to JSON-formatted data">{ ; }</button></div></div></header><div class="panel panel-default"><div class="panel-body panel__split"><div class="panel__split-element"><div class="panel__split-heading panel__split-heading--biosample"><h4>Summary</h4></div><dl class="key-value"><div data-test="status"><dt>Status</dt><dd><div class="status--inline"><div class="status status--standard status--released"><div class="status__icon status__icon--spacer"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16"><circle cx="8" cy="8" r="8"></circle></svg></div><div class="status__label">released</div></div></div></dd></div><div data-test="term-name"><dt>Term name</dt><dd>HEK293</dd></div><div data-test="term-id"><dt>Term ID</dt><dd><a href="http://www.ebi.ac.uk/efo/EFO_0001182">EFO:0001182</a></dd></div><div data-test="summary"><dt>Summary</dt><dd><div> <i>Homo sapiens</i> HEK293 cell line<!-- --> </div></dd></div></dl></div><div class="panel__split-element"><div class="panel__split-heading panel__split-heading--biosample"><h4>Attribution</h4><div class="badge-encode4 badge-heading"><span class="sr-only">ENCODE4 project</span></div></div><dl class="key-value"><div data-test="lab"><dt>Lab</dt><dd>Richard Myers, HAIB</dd></div><div data-test="awardpi"><dt>Award PI</dt><dd>Richard Myers, HAIB</dd></div><div data-test="submittedby"><dt>Submitted by</dt><dd>Scott Newberry</dd></div><div data-test="sourcetitle"><dt>Source</dt><dd><span>Richard Myers</span></dd></div><div data-test="project"><dt>Project</dt><dd>ENCODE</dd></div><div data-test="externalresources"><dt>External resources</dt><dd><ul class=""><li><a href="https://web.expasy.org/cellosaurus/CVCL_0045">Cellosaurus:CVCL_0045</a></li></ul></dd></div><div data-test="aliases"><dt>Aliases</dt><dd>richard-myers:HEK293-lot70036272-batch2021-J-20210728</dd></div></dl></div></div></div><div><div><div class="panel panel-default"><div class="panel-heading"><h4>Donor information</h4></div><div class="panel-body"><dl class="key-value"><div data-test="status"><dt>Status</dt><dd><div class="status--inline"><div class="status status--standard status--released"><div class="status__icon status__icon--spacer"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16"><circle cx="8" cy="8" r="8"></circle></svg></div><div class="status__label">released</div></div></div></dd></div><div data-test="accession"><dt>Accession</dt><dd><a href="/human-donors/ENCDO000ABF/">ENCDO000ABF</a></dd></div><div data-test="aliases"><dt>Aliases</dt><dd>encode:donor of HEK293, encode:donor of HEK293T</dd></div><div data-test="species"><dt>Species</dt><dd class="sentence-case"><em>Homo sapiens</em></dd></div><div data-test="life-stage"><dt>Life stage</dt><dd class="sentence-case">embryonic</dd></div><div data-test="age"><dt>Age</dt><dd class="sentence-case">Unknown</dd></div><div data-test="sex"><dt>Sex</dt><dd class="sentence-case">female</dd></div><div data-test="health-status"><dt>Health status</dt><dd class="sentence-case">unknown</dd></div><div data-test="external-resources"><dt>External resources</dt><dd><ul class=""><li><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN06122596">GEO:SAMN06122596</a></li></ul></dd></div><div data-test="references"><dt>References</dt><dd><ul><li><a href="/publications/b42243ab-26d8-4ff6-b801-d368df994167/">doi:10.1096/fj.01-0995fje</a></li><li><a href="/publications/b42243ab-26d8-4ff6-b801-d368df994167/">PMID:11967234</a></li></ul></dd></div></dl></div></div></div></div><div class="communicating"><div class="loading-spinner"></div></div><div class="communicating"><div class="loading-spinner"></div></div><div class="communicating"><div class="loading-spinner"></div></div><div class="communicating"><div class="loading-spinner"></div></div></div></div><div id="layout-footer"></div></div><footer><div class="container"><div class="app-version"></div></div><div class="page-footer"><div class="container"><div class="footer-sections"><div class="footer-links-section"><ul class="footer-links"><li><a href="/help/citing-encode">Citing ENCODE</a></li><li><a href="https://www.stanford.edu/site/privacy/">Privacy</a></li><li><a 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