About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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Buffy coat dataset 1

Single-cell DNA methylation profiling (sciMET) of buffy coat nuclei from eight healthy adult donors (3 male, 5 female; seven European and one Asian ancestry), to characterize the effects of donor genetic diversity in pooled single-cell DNA methylation experiments. Nuclei were fixed, nucleosome-depleted and tagmented with the Single-cell DNA Methylation Kit (v1.1, Scale Biosciences/10x Genomics), with two modifications: HEPES resuspension buffer was used instead of the kit’s Met Wash buffer, and centrifugation steps during nuclei preparation and tagmentation were kept at 300 × g. Each donor was kept separate on the tagmentation plates (45 wells per donor, 5,000 nuclei per well) and received a donor-specific set of tagmentation indices, so donor identity could be assigned from the barcodes. Nuclei were stained with DRAQ5 and singlets were sorted by FACS. Libraries were prepared with the v1.1 kit. This dataset (4,240 nuclei) provided ground-truth donor identities for pseudobulk genotype calling (Revelio double-masking, then FreeBayes), and those genotypes were used downstream to demultiplex the pooled datasets.

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Data policy of Data Access Committee of UZ Leuven

The procedure described below always applies to re-use transfer of genomic or genetic data that are in an external database. This external database can be the European Genome-phenome Archive (EGA). When a researcher receives requests for reuse of data, or when the database requires an intervention of a data access committee, the DAC will assess these requests for reuse and transfer of genomic or genetic data by third parties. Patient consent to research participation (ICF) and compatibility with new data processing should be checked. An application should be submitted at dac@uzleuven.be. So applications for re-use of genomic/genomic data go through the DAC. In the first place, DAC performs a front desk function here. An application form should be completed by the applicant. To begin with, the DAC employee then checks the ICF and its compatibility with further use. The DAC employee also ensures that a check is made with the competent services to ensure that there are no legal impediments. If i) there are possible commercial interests (commercial use of the data by the recipient or the requesting party is a commercial party), ii) the researcher does not agree, or iii) there is some ambiguity about potential risks of the data transfer (e.g. violation (GDPR) legislation, identity of recipient party, use of the data), the question is referred to the DAC advisory board.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000002212 Epigenetics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50001069996 fastq.gz 348.7 MB
EGAF50001069997 fastq.gz 629.9 MB
EGAF50001069998 fastq.gz 5.7 GB
EGAF50001069999 fastq.gz 8.1 GB
EGAF50001070000 fastq.gz 867.9 MB
EGAF50001070001 fastq.gz 5.6 GB
EGAF50001070002 fastq.gz 725.5 MB
EGAF50001070003 fastq.gz 8.7 GB
EGAF50001070004 fastq.gz 427.3 MB
EGAF50001070005 fastq.gz 385.0 MB
EGAF50001070006 fastq.gz 7.1 GB
EGAF50001070007 fastq.gz 6.5 GB
EGAF50001070008 fastq.gz 5.2 GB
EGAF50001070009 fastq.gz 638.6 MB
EGAF50001070010 fastq.gz 540.4 MB
EGAF50001070011 fastq.gz 5.4 GB
EGAF50001070012 fastq.gz 7.0 GB
EGAF50001070013 fastq.gz 3.5 GB
EGAF50001070014 fastq.gz 529.0 MB
EGAF50001070015 fastq.gz 216.7 MB
EGAF50001070016 fastq.gz 551.5 MB
EGAF50001070017 fastq.gz 590.3 MB
EGAF50001070018 fastq.gz 3.9 GB
EGAF50001070019 fastq.gz 10.1 GB
EGAF50001070020 fastq.gz 582.5 MB
EGAF50001070021 fastq.gz 440.8 MB
EGAF50001070022 fastq.gz 5.2 GB
EGAF50001070023 fastq.gz 6.9 GB
EGAF50001070024 fastq.gz 330.9 MB
EGAF50001070025 fastq.gz 501.4 MB
EGAF50001070026 fastq.gz 4.6 GB
EGAF50001070027 fastq.gz 3.2 GB
EGAF50001070028 fastq.gz 3.0 GB
EGAF50001070029 fastq.gz 508.2 MB
EGAF50001070030 fastq.gz 468.2 MB
EGAF50001070031 fastq.gz 5.0 GB
EGAF50001070032 fastq.gz 815.3 MB
EGAF50001070033 fastq.gz 288.7 MB
EGAF50001070034 fastq.gz 7.4 GB
EGAF50001070035 fastq.gz 4.5 GB
EGAF50001070036 fastq.gz 3.9 GB
EGAF50001070037 fastq.gz 513.6 MB
EGAF50001070038 fastq.gz 262.9 MB
EGAF50001070039 fastq.gz 4.8 GB
EGAF50001070040 fastq.gz 650.4 MB
EGAF50001070041 fastq.gz 2.6 GB
EGAF50001070042 fastq.gz 619.0 MB
EGAF50001070043 fastq.gz 6.7 GB
EGAF50001070168 vcf.gz 1.1 GB
49 Files (148.2 GB)