Omics · dataset · 2025
Transcriptomes From Hepatocellular Carcinoma and Normal Liver Tissues
Listed in Riga Stradins University dataverse
This dataset describes a specific study group.
Description
Nine patients were included in the study group, all with clinical diagnosis of hepatocellular carcinoma (HCC). The study group consisted of seven male patients and two female patients of age from 45 to 80.
Patients had a single liver tumor and indications for surgery were set according to the Barcelona Clinic Liver Cancer (BCLC) staging system. All patients were evaluated according to BCLC criteria and belong to 0-A stage. The diagnosis of HCC before the operation was confirmed by radiology examinations and/or histopathological findings.
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None of the patients received any other specific treatment before the surgery. HCC patients underwent radical liver surgery, and according to subsequent histology results – three patients were Stage I, two patients Stage II, three Stage III and one Stage IV HCC. During operation, no dissemination of tumor was found, and all resected specimens were with R0 resection margins.
RNA isolation from tissues and transcriptome sequencing and primary data analysis was performed by Personal Genomics (Italy). After RNA quality control, mRNA-seq library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit (NEB) (neb.com/en/products/e7760-nebnext-ultra-ii-directional-rna-library-prep-kit-for-illumina) and libraries were sequenced on an Illumina NovaSeq 6000 (illumina.com/systems/sequencing-platforms/novaseq.html) using 150 nt paired-end reads.
The mRNA-sequencing generated an average of 72 Million paired-end fragments/sample. The average alignment rate was of 97.80%.
Links
Where it is published
- Dataverse dataset page dataverse.rsu.lv/dataset.xhtml?persistentId=doi%3A10.48510%2FFK2%2F00NG93 ↗
landing page · from dataverse rsu lv
- DOI doi.org/10.48510/fk2/00ng93 ↗
DOI / persistent id · from dataverse rsu lv
Catalogue records · 1
- Dataverse API dataverse.rsu.lv/api/datasets/:persistentId/?persistentId=doi%3A10.48510%2FFK2%… ↗
metadata API · from dataverse rsu lv
Topics
- Stated by source
- Medicine, Health and Life Sciences
- From keywords
- Life Sciences · Medicine & Health · Sequencing
- Inferred from text
- Cancer 75% · Medical biochemistry and metabolomics 72% · RNA sequencing 65%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Riga Stradins University dataverse | doi:10.48510/FK2/00NG93 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[disease].local:disease:cancer | enrichment · dataverse rsu lv | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].anzsrc:group:3205 | enrichment · dataverse rsu lv | taxonomy-embedding@1.1.0 | title+keywords+description (72%) |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /subjects |
| concepts[modality].local:modality:rna-seq | enrichment · dataverse rsu lv | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:sequencing | mapping · dataverse rsu lv | vocabulary-mapper@1.0.0 | keywords['NGS'] |
| created_date | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | |
| description | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /description |
| publication_date | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | |
| title | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | /name |
| updated_date | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 | |
| version_label | source · dataverse rsu lv | connector:dataverse_rsu_lv@1.0.0 |