Chromatin landscape of medulloblastoma reveals context dependent driver

In this study, we defined subgroup specific chromatin landscape (H3K27ac, H3K27me3, RNA-Seq, 27ac hichip, WGS) of medulloblastoma to identify pathogenic epigenetic alterations that regulate expression of a context dependent driver gene.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001009709	We profiled 111 patient medulloblastoma primary tumor samples by bulk RNA-seq (19 samples), 27ac (98 samples) / 27me3 (61 samples) ChIP-Seq, WGS (4 samples) and 27ac hichip (8 samples). Submitted data consists of data generated from previously unpublished tumors as well as complementary data for data sets already published for identical medulloblastoma tumors (ex: 27me3 ChIP-Seq and RNA-Seq data submitted for a tumor with publicly available WGS data). The raw fastqs and hg19 aligned RNA-Seq bams are provided.	HiSeq X Ten Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina NovaSeq 6000	111

Publications	Citations
ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip. Lee JJY, Tao R, You Z, Haldipur P, Erickson AW, Farooq H, Hendriske LD, Abeysundara N, Richman CM, Wang EY, Das Gupta N, Hadley J, Batts M, Mount CW, Wu X, Rasnitsyn A, Bailey S, Cavalli FMG, Morrissy S, Garzia L, Michealraj KA, Visvanathan A, Fong V, Palotta J, Suarez R, Livingston BG, Liu M, Luu B, Daniels C, Loukides J, Bendel A, French PJ, Kros JM, Korshunov A, Kool M, Chico Ponce de León F, Perezpeña-Diazconti M, Lach B, Singh SK, Leary SES, Cho BK, Kim SK, Wang KC, Lee JY, Tominaga T, Weiss WA, Phillips JJ, Dai S, Zadeh G, Saad AG, Bognár L, Klekner A, Pollack IF, Hamilton RL, Ra YS, Grajkowska WA, Perek-Polnik M, Thompson RC, Kenney AM, Cooper MK, Mack SC, Jabado N, Lupien M, Gallo M, Ramaswamy V, Suva ML, Suzuki H, Millen KJ, Huang LF, Northcott PA, Taylor MD. Nat Genet 57: 2025 88-102	0

Publications

Citations

ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip.
Lee JJY, Tao R, You Z, Haldipur P, Erickson AW, Farooq H, Hendriske LD, Abeysundara N, Richman CM, Wang EY, Das Gupta N, Hadley J, Batts M, Mount CW, Wu X, Rasnitsyn A, Bailey S, Cavalli FMG, Morrissy S, Garzia L, Michealraj KA, Visvanathan A, Fong V, Palotta J, Suarez R, Livingston BG, Liu M, Luu B, Daniels C, Loukides J, Bendel A, French PJ, Kros JM, Korshunov A, Kool M, Chico Ponce de León F, Perezpeña-Diazconti M, Lach B, Singh SK, Leary SES, Cho BK, Kim SK, Wang KC, Lee JY, Tominaga T, Weiss WA, Phillips JJ, Dai S, Zadeh G, Saad AG, Bognár L, Klekner A, Pollack IF, Hamilton RL, Ra YS, Grajkowska WA, Perek-Polnik M, Thompson RC, Kenney AM, Cooper MK, Mack SC, Jabado N, Lupien M, Gallo M, Ramaswamy V, Suva ML, Suzuki H, Millen KJ, Huang LF, Northcott PA, Taylor MD. Nat Genet 57: 2025 88-102