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Finland Myoma Study

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Mika Frederiksen
dac-finlandmyomastudy@helsinki.fi

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This DAC controls 10 datasets

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	1
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