Single-nuclei RNA sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations
10x genomics single-nuclei RNA sequencing of 9 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. snRNA-seq was performed using the ‘Frankenstein’ protocol (dx.doi.org/10.17504/protocols.io.bqxymxpw). Briefly, nuclei were extracted from frozen tissues and subjected to fluorescence-activated nuclei sorting (FANS) using 4′,6-diamidino-2-phenylindole (DAPI). Sorting was performed using a BD FACSaria 2 instrument, sorting between 3000 and 10,000 nuclei per sample, capturing both diploid and tetraploid populations. FAN-sorted nuclei were immediately processed using either the 10x Chromium Single Cell 5’ (PN-1000006, 4 samples) or 3’ (PN-1000075, 4 samples) Library & Gel Bead Kit (10x Genomics, USA). Once processed, snRNA-seq libraries were sequenced on the Illumina Nova-Seq 6000 (Illumina, USA) using 150bp paired-end sequencing. This dataset contains raw sequencing reads in FASTQ format.
- 23/07/2024
- 9 samples
- DAC: EGAC00001002442
- Technology: Illumina NovaSeq 6000
University of Melbourne Cancer Research Centre (UMCCR) Data Access Committee (DAC) request form
University of Melbourne Cancer Research Centre (UMCCR) Data Access Committee (DAC) request form Email the completed form to: UMCCR-DAC@unimelb.edu.au The following form is to be used to submit an expression of interest to access data under the purview of the UMCCR-DAC and does not represent a binding data access agreement. REQUESTOR INFORMATION Graduate research student requestors must include their supervisor or a senior researcher as the Principal Investigator. Please use institutional email addresses only. Requestor Name: Job Title/Position: Department and Institution: Telephone: Email: Postal Address: Principal Investigator (if different to the Requestor) Name: Job Title/Position: Department and Institution: Telephone: Email: Postal Address: Authorised Institutional Representative Name: Job Title/Position: Institution: Telephone: Email: Postal Address: DATA REQUESTED Data description Include the EGA study and dataset accession number(s), other data identifier(s) and/or the name of the publication describing the data. Data type Is the requested data identifiable? (Whole-genome sequencing data is not considered identifiable.) ☐ Yes ☐ No PROJECT DETAILS Project description Describe the project in which the data will be used (500 words maximum). This should include specific details of the aims and what you plan to do with the data. Members of the project team requiring access to the data. Include the following information: Name Job title/position Institution Email Supervisor Feasibility Describe previous experience in this field of research and/or in similar projects by the requestor, principal investigator and other members of the project team. ETHICS APPROVAL Does this project require approval from a Human Research Ethics Committee (HREC) or comparable committee? ☐ Yes ☐ No If yes, name the HREC from which approval has been requested or obtained and attach relevant documentation (ethics application and/or approval documentation). If no, please explain why ethics approval is not required.
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 |
|---|---|---|
| EGAS50000000346 | Cancer Genomics |
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.