Immune profiling reveals enrichment of distinct immune signatures in oral epithelial dysplasia
The dataset contains transcriptomic information of 36 oral potentially malignant disorders (OPMD), 14 fibroepithelial polyps (FEP), and 6 early stage oral squamous cell carcinoma (OSCC) from the Asian population. Total RNA was extracted from formalin-fixed paraffin embedded (FFPE) tissue sections. RNA libraries were prepared using the NEB NextUltra RNA kit with Illumina Ribo-Zero rRNA removal as per manufacturer’s instructions. RNA sequencing was performed on the HiSeq2500 platform to generate paired-end 150 nucleotides reads and with a coverage of 50 million reads per sample. Uploaded bam files have been mapped to the GRCh38 human genome using TopHat2. Clinical and demographic data for these patients are available from the associated publications or by request.
- 10 samples
- DAC: EGAC00001002249
- Technology: Illumina HiSeq 2500
Access to controlled data will follow the guidelines provided by the European Genotype Archive (EGA), and requires the review of the Data Access Committee (DAC) before access is permitted, to protect patient privacy. Given that all patients in the cohort are Malaysian, data access is further subjected to the Malaysian Personal Data Protection Act (PDPA) and its various prohibitions.
Access to controlled Data must adhere to the guidelines and regulations indicated by the European Genotype Archive (EGA) Data Access Committee (DAC) and the terms and conditions by Cancer Research Malaysia as follow: 1. Provision of data. Access to Data will be determined by the DAC. The Principal Investigator will be required to fill out the Data Access Agreement and complete the description of the Research Project. User will submit a completed Data Access Agreement for each research project for which Data are requested. The Data required to be transmitted between the parties will be uploaded to a secure server with the EGA. Each party will store and analyze Data electronically in a password protected database. 2. Non-transferability. The Data Access Agreement is not transferable. User agrees that substantive changes made to the Research Project and/or appointment by of another Principal Investigator to complete the Research Project, require execution of a new Data Access Agreement in which the new Principal Investigator and/or new Research Project are designated. 3. Control of Data. The parties agree that despite disclosure of Data to the user, the Data remains solely in Cancer Research Malaysia’s control for the purposes of the Personal Data Protection Act (PDPA) or equivalent. 4. Use of Data. The user agrees as follows: (a) the Data must be used only for the Research Purpose and no other use or commercial purpose; (b) all works must be written and presented in a way that ensures no individuals are or can be directly or indirectly identified. 5. Non-Identification. User agrees not to attempt to identify and /or contact any individual human research participants included in the Data. 6. No Distribution. User agrees to retain control over Data, and further agrees not to transfer Data, with or without charge, to any other entity or any individual. 7. Acknowledgments. User agrees to acknowledge in all oral or written presentations, disclosures, or publications the specific dataset(s) or applicable accession number(s) and the data repositories resulting from any and all analyses of Data.
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 |
|---|---|---|
| EGAS00001005520 | Other |
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.