Dataset

ChIP-sequencing fragment coverage

Dataset ID Technology Samples
EGAD00010001671 Illumina HiSeq 2500 5

Dataset Description

Raw sequencing reads from H3K27ac ChIP and input DNA from lymphoblastoid cells of three TET2 mutation carriers and two wild-type family members were quality and adapter trimmed with cutadapt version 1.16 in Trim Galore version 0.3.7 using default parameters. Trimmed reads were aligned to hs37d5 reference genome using Bowtie2 (version 2.1.0). Duplicate reads were removed with samtools rmdup (v1.7). Fragment coverage of paired-end reads was calculated from bam files with BEDtools genomecov (v2.26.0).

Who controls access to this dataset

For each dataset that requires controlled access, there is a corresponding Data Access Committee (DAC) who determine access permissions. Access to actual data files is not managed by the EGA. If you need to request access to this data set, please contact:

Germline TET2 and DNMT3A committee
Contact person: Janne Ravantti
Email: janne [dot] ravantti [at] helsinki [dot] fi
More details: EGAC00001001130

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