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Epigenomic profiling of neuroblastoma cell lines

Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic...

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Autores principales: Upton, Kristen, Modi, Apexa, Patel, Khushbu, Kendsersky, Nathan M., Conkrite, Karina L., Sussman, Robyn T., Way, Gregory P., Adams, Rebecca N., Sacks, Gregory I., Fortina, Paolo, Diskin, Sharon J., Maris, John M., Rokita, Jo Lynne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156688/
https://www.ncbi.nlm.nih.gov/pubmed/32286315
http://dx.doi.org/10.1038/s41597-020-0458-y
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author Upton, Kristen
Modi, Apexa
Patel, Khushbu
Kendsersky, Nathan M.
Conkrite, Karina L.
Sussman, Robyn T.
Way, Gregory P.
Adams, Rebecca N.
Sacks, Gregory I.
Fortina, Paolo
Diskin, Sharon J.
Maris, John M.
Rokita, Jo Lynne
author_facet Upton, Kristen
Modi, Apexa
Patel, Khushbu
Kendsersky, Nathan M.
Conkrite, Karina L.
Sussman, Robyn T.
Way, Gregory P.
Adams, Rebecca N.
Sacks, Gregory I.
Fortina, Paolo
Diskin, Sharon J.
Maris, John M.
Rokita, Jo Lynne
author_sort Upton, Kristen
collection PubMed
description Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.
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spelling pubmed-71566882020-04-24 Epigenomic profiling of neuroblastoma cell lines Upton, Kristen Modi, Apexa Patel, Khushbu Kendsersky, Nathan M. Conkrite, Karina L. Sussman, Robyn T. Way, Gregory P. Adams, Rebecca N. Sacks, Gregory I. Fortina, Paolo Diskin, Sharon J. Maris, John M. Rokita, Jo Lynne Sci Data Data Descriptor Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma. Nature Publishing Group UK 2020-04-14 /pmc/articles/PMC7156688/ /pubmed/32286315 http://dx.doi.org/10.1038/s41597-020-0458-y Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.
spellingShingle Data Descriptor
Upton, Kristen
Modi, Apexa
Patel, Khushbu
Kendsersky, Nathan M.
Conkrite, Karina L.
Sussman, Robyn T.
Way, Gregory P.
Adams, Rebecca N.
Sacks, Gregory I.
Fortina, Paolo
Diskin, Sharon J.
Maris, John M.
Rokita, Jo Lynne
Epigenomic profiling of neuroblastoma cell lines
title Epigenomic profiling of neuroblastoma cell lines
title_full Epigenomic profiling of neuroblastoma cell lines
title_fullStr Epigenomic profiling of neuroblastoma cell lines
title_full_unstemmed Epigenomic profiling of neuroblastoma cell lines
title_short Epigenomic profiling of neuroblastoma cell lines
title_sort epigenomic profiling of neuroblastoma cell lines
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156688/
https://www.ncbi.nlm.nih.gov/pubmed/32286315
http://dx.doi.org/10.1038/s41597-020-0458-y
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