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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4 - transcriptome (.bam) files, 2 -called somatic mutations (.vcf) files and 2 coverage (.csv) files

The dataset contains 4 .bam whole transcriptome files that were generated from 2 tumor samples (one .bam file per sample was created using exome-capture (hybrid capture) and the other .bam file was created using ribo-repletion (inverse mRNA selection) library preparation technology). The dataset also contains 2 somatic mutations (.vcf - sample) files (one per sample) which serve as input for Vardetector package (vardetector/vardetector at main · julijselb/vardetector) to produce somatic coverage over those mutations from the .bam file. Therefore, the dataset also contains 4- .csv files (number of reads per somatic mutation that contain the somatic mutation variant and the ones that do not contain the somatic mutation variant) that serve as outputs of the Vardetector package.

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DUO:0000006
version: 2021-02-23

health or medical or biomedical research

This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.

DUO:0000018
version: 2021-02-23

not for profit, non commercial use only

This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.

DUO:0000021
version: 2021-02-23

ethics approval required

This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval.

DUO:0000024
version: 2021-02-23

publication moratorium

This data use modifier indicates that requestor agrees not to publish results of studies until a specific date.

DUO:0000028
version: 2021-02-23

institution specific restriction

This data use modifier indicates that use is limited to use within an approved institution.

UCG Institutional approval policy

To obtain the data, the Golnik University Clinic Institutional Review Board must approve the request, regarding the potential data usage and the compliance of usage with ethics guidelines

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
EGAS50000001419 Transcriptome Analysis

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
EGAF50000499895 csv 274.6 kB
EGAF50000499896 bam 3.5 GB
EGAF50000499897 csv 355.4 kB
EGAF50000499898 bam 4.7 GB
EGAF50000499899 vcf 6.8 MB
EGAF50000499900 csv 237.3 kB
EGAF50000499901 bam 3.1 GB
EGAF50000499902 csv 407.8 kB
EGAF50000499903 bam 5.2 GB
EGAF50000499904 vcf 8.2 MB
10 Files (16.5 GB)