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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scRNAseq of single cell outgrowths of HCC organoid

FASTQ files were processed using the TrailmakerTM pipeline module (v1.5.0, Parse Biosciences). Unfiltered count matrices were uploaded to Trailmaker, and background was removed by setting a minimum transcripts per cell threshold on a per sample basis (threshold range: 998 to 1799). Dead or dying cells were removed by filtering barcodes with high mitochondrial content on a per sample basis (threshold range: 12.62% to 21.1%). Outliers in the distribution of number of genes vs number of transcripts were removed by fitting a spline regression model (p-values between 0.000003 and 0.000264). Cells with a high probability of being doublets were filtered out using the scDblFinder method on a per sample basis (threshold range: 0.72763 to 0.80853). Read counts were normalized by log1p. Output files are normalized counts.

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Data Access Policy – Basel Liver Biopsy Biobank (University Hospital Basel / University of Basel)

Data Access Policy – Basel Liver Biopsy Biobank (University Hospital Basel / University of Basel) Access is granted only to qualified researchers affiliated with a bona fide research institution, for a clearly described research project, and subject to review and approval by the Data Access Committee "Basel Liver Biopsy Biobank". Application requirements: A completed and signed Data Access Request and Agreement, a brief project description, and the applicant’s CV (and/or relevant track record) must be provided. Permitted use: Data may be used only for the approved research project and for the approved duration. Any new purpose requires a new request and approval. Privacy and confidentiality: Data are pseudonymised. Applicants must not attempt to re-identify individuals and must protect confidentiality at all times. Data security: Data must be handled within an institutional IT environment with appropriate access controls, malware protection, and secure backup procedures. No onward transfer: Data must not be shared or transferred outside the recipient institution or to external collaborators without prior written approval; external collaborators may require a separate agreement. Publication and acknowledgement: Publications and presentations resulting from use of the data must acknowledge the data controllers as specified in the agreement. Incident reporting: Any security breach leading to disclosure must be reported without undue delay and at the latest within 72 hours. Governing law: Switzerland (Basel-City jurisdiction), as specified in the agreement.

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
EGAS50000002198 RNASeq

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
EGAF50001049108 fastq.gz 15.8 GB
EGAF50001049109 fastq.gz 16.0 GB
EGAF50001049110 fastq.gz 19.6 GB
EGAF50001049111 fastq.gz 20.0 GB
EGAF50001049112 fastq.gz 17.6 GB
EGAF50001049113 fastq.gz 18.0 GB
EGAF50001049114 fastq.gz 16.3 GB
EGAF50001049115 fastq.gz 16.6 GB
EGAF50001049116 fastq.gz 15.3 GB
EGAF50001049117 fastq.gz 15.4 GB
EGAF50001049118 fastq.gz 17.0 GB
EGAF50001049119 fastq.gz 17.3 GB
EGAF50001049120 fastq.gz 16.7 GB
EGAF50001049121 fastq.gz 16.9 GB
EGAF50001049122 fastq.gz 13.9 GB
EGAF50001049123 fastq.gz 14.2 GB
EGAF50001049124 csv.gz 311.2 MB
EGAF50001049125 csv.gz 190.7 MB
EGAF50001049126 csv.gz 523.6 MB
EGAF50001049127 csv.gz 260.1 MB
EGAF50001049128 csv.gz 314.6 MB
EGAF50001049129 csv.gz 90.8 MB
EGAF50001049130 csv.gz 130.8 MB
EGAF50001049131 csv.gz 112.6 MB
EGAF50001049132 csv.gz 290.6 MB
EGAF50001049133 csv.gz 233.2 MB
26 Files (269.0 GB)