Biopsy and resection samples of HCC and non-tumor tissue
A total of 16 patients with primary liver cancer, who first underwent diagnostic biopsy and then surgical resection shortly afterwards (median 27 days) were included. Tumor and non-tumor biopsy and resection tissue were analyzed by RNA sequencing. Total RNA from frozen tumor- and non-tumor tissue from biopsy and resection specimens was extracted using the ZR-Duet DNA and RNA MiniPrep Plus kit (Zymo Research) according to the manufacturer’s instructions. Prior to extraction, frozen tissues were crushed in liquid nitrogen to facilitate lysis. Extracted RNA was quantified using the Qubit Fluorometer (Thermo Fisher Scientific). 200 ng total RNA was used for RNAseq library prep with the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) according to the manufacturer’s specifications. Paired-End sequencing was performed on a Novaseq 6000 (Illumina) with 51 cycles at the Genomics Facility Basel according to the manufacturer’s guidelines.
- 04/08/2026
- 60 samples
- DAC: EGAC50000000917
- Technology: Illumina NovaSeq 6000
- Archive: European Genome-phenome Archive (EGA)
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 |
|---|---|---|
| EGAS50000001602 | 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
|
|---|---|---|---|---|
| EGAF50000581729 | bam | 5.5 GB |
|
|
| EGAF50000581730 | bam | 3.6 GB |
|
|
| EGAF50000581731 | bam | 4.4 GB |
|
|
| EGAF50000581732 | bam | 2.8 GB |
|
|
| EGAF50000581733 | bam | 7.3 GB |
|
|
| EGAF50000581734 | bam | 3.7 GB |
|
|
| EGAF50000581735 | bam | 2.7 GB |
|
|
| EGAF50000581736 | bam | 4.7 GB |
|
|
| EGAF50000581737 | bam | 2.4 GB |
|
|
| EGAF50000581738 | bam | 1.8 GB |
|
|
| EGAF50000581739 | bam | 1.6 GB |
|
|
| EGAF50000581740 | bam | 2.1 GB |
|
|
| EGAF50000581741 | bam | 2.1 GB |
|
|
| EGAF50000581742 | bam | 1.2 GB |
|
|
| EGAF50000581743 | bam | 1.2 GB |
|
|
| EGAF50000581744 | bam | 1.4 GB |
|
|
| EGAF50000581745 | bam | 1.3 GB |
|
|
| EGAF50000581746 | bam | 1.3 GB |
|
|
| EGAF50000581747 | bam | 1.3 GB |
|
|
| EGAF50000581748 | bam | 1.3 GB |
|
|
| EGAF50000581749 | bam | 1.2 GB |
|
|
| EGAF50000581750 | bam | 1.4 GB |
|
|
| EGAF50000581751 | bam | 1.3 GB |
|
|
| EGAF50000581752 | bam | 1.2 GB |
|
|
| EGAF50000581753 | bam | 1.4 GB |
|
|
| EGAF50000581754 | bam | 1.1 GB |
|
|
| EGAF50000581755 | bam | 1.7 GB |
|
|
| EGAF50000581756 | bam | 2.3 GB |
|
|
| EGAF50000581757 | bam | 3.0 GB |
|
|
| EGAF50000581758 | bam | 2.6 GB |
|
|
| EGAF50000581759 | bam | 3.2 GB |
|
|
| EGAF50000581760 | bam | 2.6 GB |
|
|
| EGAF50000581761 | bam | 2.2 GB |
|
|
| EGAF50000581762 | bam | 2.3 GB |
|
|
| EGAF50000581763 | bam | 2.3 GB |
|
|
| EGAF50000581764 | bam | 5.5 GB |
|
|
| EGAF50000581765 | bam | 2.9 GB |
|
|
| EGAF50000581766 | bam | 4.0 GB |
|
|
| EGAF50000581767 | bam | 4.4 GB |
|
|
| EGAF50000581768 | bam | 3.4 GB |
|
|
| EGAF50000581769 | bam | 8.1 GB |
|
|
| EGAF50000581770 | bam | 4.7 GB |
|
|
| EGAF50000581771 | bam | 2.3 GB |
|
|
| EGAF50000581772 | bam | 2.5 GB |
|
|
| EGAF50000581773 | bam | 2.9 GB |
|
|
| EGAF50000581774 | bam | 3.3 GB |
|
|
| EGAF50000581775 | bam | 2.5 GB |
|
|
| EGAF50000581776 | bam | 2.8 GB |
|
|
| EGAF50000581777 | bam | 5.4 GB |
|
|
| EGAF50000581778 | bam | 1.8 GB |
|
|
| EGAF50000581779 | bam | 90.6 MB |
|
|
| EGAF50000581780 | bam | 3.0 GB |
|
|
| EGAF50000581781 | bam | 8.2 GB |
|
|
| EGAF50000581782 | bam | 13.3 GB |
|
|
| EGAF50000581783 | bam | 3.6 GB |
|
|
| EGAF50000581784 | bam | 5.1 GB |
|
|
| EGAF50000581785 | bam | 4.0 GB |
|
|
| EGAF50000581786 | bam | 5.5 GB |
|
|
| EGAF50000581787 | bam | 3.6 GB |
|
|
| EGAF50000581788 | bam | 3.5 GB |
|
|
| EGAF50000581789 | out | 51.9 MB |
|
|
| 61 Files (190.0 GB) | ||||