Uterine leiomyoma: DNA methylation, chromatin activity and gene expression

In this study, we observed the effects of different uterine leiomyoma driver mutations to tumor DNA methylation, chromatin activity and gene expression, to form a comprehensive view on the epigenetic consequences of the mutations.

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

10 Datasets 2 Publications

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
EGAD00001006278	HiChIP experiments with two sequencing libraries each. Illumina HiSeq 4000/2500.	Illumina HiSeq 4000	10
EGAD00001006279	ChIP-seq experiments: fastq files; both ChIP and Input for each sample. Illumina HiSeq 2500. ChIP-seq alignment files for trimmed, mapping q20 and nonredundant reads; both ChIP and Input for each sample. Software: Trim Galore v0.3.7; Bowtie 2 v2.1.0; samtools v1.7	Illumina HiSeq 2500	76
EGAD00010001923	ChIP-seq narrowPeaks. Software: MACS2 v2.1.2	Illumina HiSeq 2500	23
EGAD00010001924	Gene expression gene-level count values from Stringtie processing including alignment to GRCh37 or GRCh38 genome version. Software: HISAT2 v2.1.0;StringTie v1.3.4d.	Illumina HiSeq 2500/NovaSeq 6000	438
EGAD00010001925	CpG methylation. Software: minimap2 v2.16;Nanopolish.	Oxford Nanopore	202
EGAD00010001926	Allelic imbalance (AI) region calls: start and end positions and the measured mBAF and LRR mean of each region after the BAF segmentation algorithm. Software: Illumina GenomeStudio;PennCNV v. 1.0.4;BAF segmentation v1.2.0.	Illumina Infinium HumanCore-24/HumanOmni2.5-8	2186
EGAD00010001927	Haplotype expression counts. Software: phASER v1.1.1.	Illumina HiSeq 2500/NovaSeq 6000	438
EGAD00010001928	ATAC-seq non-overlapping fixed width peaks with score normalization. Software: MACS2 v2.1.2	Illumina HiSeq 4000	31
EGAD00010002051	Second batch of ChIP-seq narrowPeaks. Software: MACS2 v2.1.2	Illumina HiSeq 2500	48
EGAD00010002155	Third batch of ChIP-seq narrowPeaks. Software: MACS2 v2.1.2	Illumina HiSeq 2500	5

Publications	Citations
Molecular subclass of uterine fibroids predicts tumor shrinkage in response to ulipristal acetate. Kolterud Å, Välimäki N, Kuisma H, Patomo J, Ilves ST, Mäkinen N, Kaukomaa J, Palin K, Kaasinen E, Karhu A, Pasanen A, Bützow R, Heikinheimo O, Kopp Kallner H, Aaltonen LA. Hum Mol Genet 32: 2023 1063-1071	2
Inherited mutations affecting the SRCAP complex are central in moderate-penetrance predisposition to uterine leiomyomas. Välimäki N, Jokinen V, Cajuso T, Kuisma H, Taira A, Dagnaud O, Ilves S, Kaukomaa J, Pasanen A, Palin K, Heikinheimo O, Bützow R, Aaltonen LA, Karhu A. Am J Hum Genet 110: 2023 460-474	4