Epithelial, fibroblast, myeloid, T cell, primary prostate cancer
The collection and use of tissue for this study had Melbourne Health institutional review board approval and patients provided written informed consent (Melbourne Health Local Project Number: 2016.087). Following the prostatectomy of 13 patients, ranging from 52 to 78 years of age and from CAPRA-S risk score of 0 (attributed to benign tissue samples, harvested from a site far from a low grade, low volume cancer) to 7 (Supplementary file 2), a four millimeter tissue core was collected from the prostate tumour site, conditional to histopathological verification66,67. If not otherwise specified, all procedures were carried out at 4 °C. Tissue blocks were washed in Phosphate-buffered saline (PBS) solution for 2 minutes and minced for 2 minutes with a scalpel. Homogenised tissue was added to a solution (total volume of 7 ml) composed by of 1 mg/ml collagenase IV (Worthington Biochemical Corp, USA), 0.02 mg/ml DNase 1 (New England Biolabs, USA), 0.2 mg/ml dispase (Merck, USA). The tissue homogenised was serially digested at 37 °C at 180 rpm, through three steps of 5, 10 and 10 minutes of duration, with the final 3 minutes dedicated to sedimentation at 0 rpm. After each digestion step, the supernatant was aspirated and filtered through a 70 μm strainer into a pre-chilled tube, diluting the solution with 15 ml of 2% bovine serum PBS to quench the enzymatic reaction. The resulting cumulative solution was then centrifuged at 1500 rpm for five minutes, with the supernatant collected and the cell pellet resuspended into 1 ml 2% PBS-serum prior to labelling (Fig. S1).
- 52 samples
- DAC: EGAC00001000661
- Technology: NextSeq 500
Management of Research Data and Records Policy (MPF1242)
SCOPE This policy applies to research undertaken by University of Melbourne students, staff and honorary staff. POLICY 1. Management of research data and records 1.1. The University will ensure that research data and records created by University students, staff and honorary staff are: accurate, complete, authentic and reliable identifiable, retrievable and available when needed secure compliant with legal obligations and the rules of funding bodies. 1.2. The University will retain research data and records for a minimum of five years after publication or public release of the work of research. Refer to pp. 485-517 of the Records Retention and Disposal Authority for full details of obligations. 2. Researchers 2.1. Researchers will: develop appropriate processes for the collection, storage, use, re-use, access and retention of research data and records associated with their research program, including confidential research data and records incorporate this information into their research data management plan register this information in a local department register, or in the Central Research Data Registry if a department register is not established. 2.2. Researchers will establish and document clear procedures for the collection, ownership and storage of research data and records when involved in a joint research project, collaborative research or research undertaken in accordance with a contractual agreement, noting that: when a research project is undertaken under a contractual agreement the principal investigator has overall responsibility for the management of data and records in the case of multi-institutional projects the institution of the principal investigator is ultimately responsible. 2.3. Researchers will: ensure that the integrity and security of their research data and records is maintained, and that this material is stored in a retrievable way be aware of confidentiality restrictions, any relevant agreements that affect access to or disclosure of information and report any breach of confidentiality to the head of department plan for the ongoing custodial responsibilities for the research data and records at the conclusion of the research project or on departure from the University, including information about access and potential re-use of the data and future deposit into open access research databases where such action complies with all legal, ethical and confidentiality agreements on the data, including copyright, privacy and intellectual property negotiate with their head of department for the relocation of data and records within the University make recommendations to the head of department for destruction of research data and records in accordance with all of the relevant requirements and legislation ensure that research students under their supervision are fully informed about this policy and take joint responsibility with students for the fulfilment of these responsibilities, including the registration of data at the conclusion of the project as outlined in section 4.4. 3. Heads of departments 3.1. Heads of departments will: authorise the procedures adopted by researchers and student researchers (following consultation with their supervisor) for the storage of their research data and records authorise the destruction of research data and records on the recommendation of the chief investigator and record details in a local department register, or in the Central Research Data Registry if a department register is not established authorise the destruction of student researchers’ data and records and record details in a local department register, or in the Central Research Data Registry if a department register is not established establish and implement departmental processes for the storage and retention of research data and records, including recording of information about research data generated in a local department register, or in the Central Research Data Registry if a department register is not established ensure that researchers who leave the University have adequately planned for the ongoing custodial responsibilities for the research data and records in compliance with the policy as per section 2.3, and that these plans are recorded in a local department register, or in the Central Research Data Registry if a department register is not established ensure that University and departmental policy and procedures are adequately disseminated to researchers negotiate with researchers for the relocation of research data and records within the University and record details in a local department register, or in the Central Research Data Registry if a department register is not established ensure that staff and students conducting research involving human participants are aware of their responsibilities and related special compliance issues of research data and records collected in the course of their research ensure that staff are aware of the need to report any breach of confidentiality to the head of department secure and/or provide suitable physical and electronic (or virtual) storage space for research data and records. 3.2. Heads of departments will ensure the provision of expert advice on the creation, storage and retention of electronic data, including advice on technological obsolescence and migration requirements; ensuring systems reliability and continuing operation; and facilitating access to electronic data of continuing value over time. Where this expert advice is not available within the division, researchers should seek assistance from Central IT Services. 4. Research students 4.1. Research students will be jointly responsible with their supervisor, for the collection, storage, security and use of research data and records including confidential research data and records, in accordance with University and department procedures. 4.2. Research students will establish collection and storage procedures for their research data and records that are acceptable to their supervisor. This information must be placed in a research data management plan. 4.3. Research students will negotiate appropriate arrangements with their supervisor for the security of research data and records involving human participants. These arrangements must be outlined in their application for ethics clearance. 4.4. Research students will deposit research data and records associated with their thesis within their department immediately following thesis submission (to ensure it is managed appropriately over time). Students will also provide their supervisor with full details of the location of research data and records.
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 |
|---|---|---|
| EGAS00001003579 | 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.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF00002442642 | fastq.gz | 3.0 GB | ||
| EGAF00002442643 | fastq.gz | 3.0 GB | ||
| EGAF00002442644 | fastq.gz | 1.8 GB | ||
| EGAF00002442645 | fastq.gz | 1.8 GB | ||
| EGAF00002442646 | fastq.gz | 1.3 GB | ||
| EGAF00002442647 | fastq.gz | 1.3 GB | ||
| EGAF00002442648 | fastq.gz | 2.5 GB | ||
| EGAF00002442649 | fastq.gz | 2.5 GB | ||
| EGAF00002442650 | fastq.gz | 1.6 GB | ||
| EGAF00002442651 | fastq.gz | 1.6 GB | ||
| EGAF00002442652 | fastq.gz | 1.7 GB | ||
| EGAF00002442653 | fastq.gz | 1.7 GB | ||
| EGAF00002442654 | fastq.gz | 886.6 MB | ||
| EGAF00002442655 | fastq.gz | 904.9 MB | ||
| EGAF00002442656 | fastq.gz | 1.4 GB | ||
| EGAF00002442657 | fastq.gz | 1.4 GB | ||
| EGAF00002442658 | fastq.gz | 843.6 MB | ||
| EGAF00002442659 | fastq.gz | 859.2 MB | ||
| EGAF00002442660 | fastq.gz | 1.1 GB | ||
| EGAF00002442661 | fastq.gz | 1.1 GB | ||
| EGAF00002442662 | fastq.gz | 2.8 GB | ||
| EGAF00002442663 | fastq.gz | 2.9 GB | ||
| EGAF00002442664 | fastq.gz | 1.8 GB | ||
| EGAF00002442665 | fastq.gz | 1.8 GB | ||
| EGAF00002442666 | fastq.gz | 1.7 GB | ||
| EGAF00002442667 | fastq.gz | 1.7 GB | ||
| EGAF00002442668 | fastq.gz | 872.7 MB | ||
| EGAF00002442669 | fastq.gz | 885.2 MB | ||
| EGAF00002442670 | fastq.gz | 2.9 GB | ||
| EGAF00002442671 | fastq.gz | 3.0 GB | ||
| EGAF00002442672 | fastq.gz | 3.7 GB | ||
| EGAF00002442673 | fastq.gz | 3.7 GB | ||
| EGAF00002442674 | fastq.gz | 1.8 GB | ||
| EGAF00002442675 | fastq.gz | 1.8 GB | ||
| EGAF00002442676 | fastq.gz | 1.3 GB | ||
| EGAF00002442677 | fastq.gz | 1.3 GB | ||
| EGAF00002442678 | fastq.gz | 1.3 GB | ||
| EGAF00002442679 | fastq.gz | 1.3 GB | ||
| EGAF00002442680 | fastq.gz | 1.5 GB | ||
| EGAF00002442681 | fastq.gz | 1.5 GB | ||
| EGAF00002442682 | fastq.gz | 609.1 MB | ||
| EGAF00002442683 | fastq.gz | 621.3 MB | ||
| EGAF00002442684 | fastq.gz | 1.0 GB | ||
| EGAF00002442685 | fastq.gz | 1.0 GB | ||
| EGAF00002442686 | fastq.gz | 1.4 GB | ||
| EGAF00002442687 | fastq.gz | 1.5 GB | ||
| EGAF00002442688 | fastq.gz | 1.3 GB | ||
| EGAF00002442689 | fastq.gz | 1.3 GB | ||
| EGAF00002442690 | fastq.gz | 795.7 MB | ||
| EGAF00002442691 | fastq.gz | 812.7 MB | ||
| EGAF00002442692 | fastq.gz | 1.1 GB | ||
| EGAF00002442693 | fastq.gz | 1.1 GB | ||
| EGAF00002442694 | fastq.gz | 1.2 GB | ||
| EGAF00002442695 | fastq.gz | 1.2 GB | ||
| EGAF00002442696 | fastq.gz | 959.4 MB | ||
| EGAF00002442697 | fastq.gz | 970.9 MB | ||
| EGAF00002442698 | fastq.gz | 755.2 MB | ||
| EGAF00002442699 | fastq.gz | 770.5 MB | ||
| EGAF00002442700 | fastq.gz | 1.2 GB | ||
| EGAF00002442701 | fastq.gz | 1.2 GB | ||
| EGAF00002442702 | fastq.gz | 591.4 MB | ||
| EGAF00002442703 | fastq.gz | 599.4 MB | ||
| EGAF00002442704 | fastq.gz | 963.5 MB | ||
| EGAF00002442705 | fastq.gz | 979.9 MB | ||
| EGAF00002442706 | fastq.gz | 1.4 GB | ||
| EGAF00002442707 | fastq.gz | 1.5 GB | ||
| EGAF00002442708 | fastq.gz | 1.9 GB | ||
| EGAF00002442709 | fastq.gz | 1.9 GB | ||
| EGAF00002442710 | fastq.gz | 3.1 GB | ||
| EGAF00002442711 | fastq.gz | 3.2 GB | ||
| EGAF00002442712 | fastq.gz | 884.4 MB | ||
| EGAF00002442713 | fastq.gz | 905.2 MB | ||
| EGAF00002442714 | fastq.gz | 1.5 GB | ||
| EGAF00002442715 | fastq.gz | 1.5 GB | ||
| EGAF00002442716 | fastq.gz | 1.2 GB | ||
| EGAF00002442717 | fastq.gz | 1.3 GB | ||
| EGAF00002442718 | fastq.gz | 1.2 GB | ||
| EGAF00002442719 | fastq.gz | 1.2 GB | ||
| EGAF00002442720 | fastq.gz | 1.1 GB | ||
| EGAF00002442721 | fastq.gz | 1.1 GB | ||
| EGAF00002442722 | fastq.gz | 1.3 GB | ||
| EGAF00002442723 | fastq.gz | 1.3 GB | ||
| EGAF00002442724 | fastq.gz | 1.9 GB | ||
| EGAF00002442725 | fastq.gz | 1.9 GB | ||
| EGAF00002442726 | fastq.gz | 2.4 GB | ||
| EGAF00002442727 | fastq.gz | 2.4 GB | ||
| EGAF00002442728 | fastq.gz | 1.4 GB | ||
| EGAF00002442729 | fastq.gz | 1.4 GB | ||
| EGAF00002442730 | fastq.gz | 1.2 GB | ||
| EGAF00002442731 | fastq.gz | 1.2 GB | ||
| EGAF00002442732 | fastq.gz | 1.4 GB | ||
| EGAF00002442733 | fastq.gz | 1.5 GB | ||
| EGAF00002442734 | fastq.gz | 1.7 GB | ||
| EGAF00002442735 | fastq.gz | 1.7 GB | ||
| EGAF00002442736 | fastq.gz | 1.5 GB | ||
| EGAF00002442737 | fastq.gz | 1.5 GB | ||
| EGAF00002442738 | fastq.gz | 1.8 GB | ||
| EGAF00002442739 | fastq.gz | 1.8 GB | ||
| EGAF00002442740 | fastq.gz | 1.5 GB | ||
| EGAF00002442741 | fastq.gz | 1.5 GB | ||
| EGAF00002442742 | fastq.gz | 1.6 GB | ||
| EGAF00002442743 | fastq.gz | 1.7 GB | ||
| EGAF00002442744 | fastq.gz | 2.0 GB | ||
| EGAF00002442745 | fastq.gz | 2.1 GB | ||
| 104 Files (161.0 GB) | ||||