Subject | Immunology and Microbiology: Virology |
Specific subject area | Human Endogenous Retroviruses and Oncology |
Type of data | Tables Figures Additional Data- text file (FASTA) of genomic sequences |
How data were acquired | Bioinformatic analysis of HERV-K elements in RNA-seq data (Salmon, HISAT2, DESeq2) |
Data format | Raw and Analysed |
Parameters for data collection | 91 HERV-K proviral sequences contained in the NCBI Data Repository (GenBank ID JN675007-JN675097) were concatenated into a single FASTA file. The HERV-K FASTA file was used to analyze a publically available RNA-seq dataset of Hepatoblastoma and Normal Liver Controls. |
Description of data collection | HERV-K FASTA file was used to perform a standard differential gene expression analysis across conditions with ensuing gene enrichment analysis (GO & KEGG) as well as a positional alignment analysis of RNA-seq reads across individual proviruses. |
Data source location | University of Virginia School of Medicine Charlottesville, Virginia United States |
Data accessibility | With the article |
Related research article | David F Grabski, Aakrosh Ratan, Laurie R Gray, Stefan Bekiranov, David Rekosh, Marie-Louise Hammarskjold, Sara K Rasmussen; Upregulation of Human Endogenous Retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers; Jounral of Pediatric Surgery; Submitted. |