Study
Uterine leiomyoma: DNA methylation, chromatin activity and gene expression
| Study ID | Alternative Stable ID | Type |
|---|---|---|
| EGAS00001004499 | Other |
Study Description
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.
Study Datasets 10 datasets.
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 |
Who archives the data?
