Integrative sequencing reveals alterations in untreated and castration resistant prostate cancer

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Dataset ID	Description	Technology	Samples
EGAD00001000609	Whole transcriptome sequencing of 28 untreated prostate cancers, 13 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.	Illumina HiSeq 2000	53
EGAD00001000610	Methylated DNA immunoprecipitation sequencing of 28 untreated prostate cancers, 11 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.	Illumina HiSeq 2000	51
EGAD00001000611	Small RNA sequencing of 28 untreated prostate cancers, 12 castration resistant prostate cancers, and 3 benign prostatic hyperplasias.	Illumina HiSeq 2000	43
EGAD00001000612	Low coverage whole genome sequencing of 27 untreated prostate cancers, 9 castration resistant prostate cancers, and 4 benign prostatic hyperplasias.	Illumina HiSeq 2000	40
EGAD00001007921	Two sections of cryopreserved prostate cancer tissue from one untreated prostate cancer patient were profiled for spatial transcriptomics using the Visium Spatial library preparation protocol from 10x Genomics. The GRCh38 aligned sequencing reads from the two prostate cancer tissue sections are provided as BAM files.	Illumina NovaSeq 6000	2

Publications	Citations
Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer. Annala M, Kivinummi K, Tuominen J, Karakurt S, Granberg K, Latonen L, Ylipää A, Sjöblom L, Ruusuvuori P, Saramäki O, Kaukoniemi KM, Yli-Harja O, Vessella RL, Tammela TL, Zhang W, Visakorpi T, Nykter M. Oncotarget 6: 2015 6235-6250	18
Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi KK, Tammela TTL, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T. Nat Commun 9: 2018 1176	85
Gene Regulation Network Analysis on Human Prostate Orthografts Highlights a Potential Role for the JMJD6 Regulon in Clinical Prostate Cancer. Cangiano M, Grudniewska M, Salji MJ, Nykter M, Jenster G, Urbanucci A, Granchi Z, Janssen B, Hamilton G, Leung HY, Beumer IJ. Cancers (Basel) 13: 2021 2094	5
Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TLJ, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Nat Commun 12: 2021 5307	56
Spatial transcriptomics technology in cancer research. Yu Q, Jiang M, Wu L. Front Oncol 12: 2022 1019111	21
Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases. Sattari M, Kohvakka A, Moradi E, Rauhala H, Urhonen H, Isaacs WB, Nykter M, Murtola TJ, Tammela TLJ, Latonen L, Bova GS, Kesseli J, Visakorpi T. Endocr Relat Cancer 30: 2023 e220247	2