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SAPCS 20 Blood RNA-seq from Prostate cancer patients.

Raw RNA-seq reads (FASTQ format) and Mapped sequencing reads (BAM format) of 20 Prostate cancer patients in Southern African Prostate Cancer Study (SAPCS). Each patient exhibit different pathogenic variations. The Illumina RNA-sequencing is performed from Blood extraction (from QIAamp RNA Blood Mini Kit). rRNA was removed prior using SortMeRNA. STAR aligner program was used for mapping to human genome GRCh38.p14, resulting in an average genome coverage of 9x.

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Genomic data of SAPCS

SAPCS Data Access Committee The SAPCS Data Access Committee (DAC) consists of eight members, including clinicians, pathologists, researchers, local community and consumer representatives. The SAPCS-DAC is under management of a manager. Members will meet monthly (by zoom, when required) to consider requests. Quorum for decision-making will be a minimum of five members and include at least two of the SAPCS Directors. Decisions will be made by consensus. Application Procedures The SAPCS-DAC will consider requests for published data from all researchers. Data will only be released to researchers who can provide a statement of ethics approval from the IRB I Human Research Ethics Committee (HREC) of their host institution to safeguard patient rights. Before submitting a request, applicants are encouraged to confer with the main contact Prof. Hayes to discuss the appropriateness of the data for the proposed study and the feasibility of the request. The following information will be requested in applications for Data access: (i) The applicant's name, institution, email address, (ii) The research question/hypotheses to be tested, (iii) List of data required, (iv) Statistical justification for the number and types of cases required (where applicable), (v) Brief description of the technical approach, (vi) Evidence of the proposed technical approach's prior successful use (where applicable), (vi) IRB/HREC approval number (and copy of approval if requested) to conduct proposed research (external applicants). Decision-making As all data has been generated through peer-reviewed funding mechanisms, research projects may well be underway to address relevant questions, as such, priority will need to be given to already funded SAPCS research efforts. The SAPCS-DAC will make decisions on approval of access to data using the following criteria: (i) The track record of the applicants in the technical approach and likelihood of significant outcomes from the research proposed. (ii) Non-overlap with projects being undertaken by the SAPCS team (except with compelling justification). (iii) Alignment of the research purpose with patient’s informed consent and ethics approval (e.g., restrictions as to commercial research, or other requirements needing additional approval). (iv) Any other restrictions or conditions that may apply to the use or disclosure of the relevant data. The SAPCS-DAC can impose certain restrictions on all approvals, and/or specific restrictions on approvals, as follows: (i) No transfer to third parties allowed (all). (ii) Acknowledgment of the SAPCS in publications/presentations (all). (iii) A report of the results of the research to be provided to DAC after completion (or when requested). (iv) Researchers cannot utilize the data for commercial purposes (all). (v) Approval will not be given that excludes other researchers from accessing data (all). (vi) Approval might be time-limited exclusive rights for a particular research development (particular). After approval by the DAC, the Database Manager will organize for the data to be sent de-identified to the researchers or allow access through an established database. Responsibilities It is the responsibility of the applicants to: (i) Provide a research proposal that justifies the request for data (adequate preliminary data); (ii) consult with a SAPCS Director prior to making an application; (iii) submit an email request to SAPCS-DAC Manager; (iv) obtain appropriate IRB/HREC approval for the use of the data; (v) appropriately acknowledge SAPCS in publications using relevant data. It is the responsibility of Data Access Committee to: (i) Review applications and approve the release of data based on the scientific value of the research proposal that is not in conflict with current SAPCS approved/funded studies; (ii) coordinate data release, (iii) review the completed data and publication.

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
EGAS50000000702 RNASeq
  • Dataset Released
  • Added new data - Raw RNA-sequencing data (In FASTQ format) for 20 Blood.

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
EGAF50000237788 bam 14.4 GB
EGAF50000237789 bam 11.3 GB
EGAF50000237790 bam 12.4 GB
EGAF50000237791 bam 17.4 GB
EGAF50000237792 bam 12.9 GB
EGAF50000237793 bam 22.9 GB
EGAF50000237794 bam 16.1 GB
EGAF50000237795 bam 9.7 GB
EGAF50000237796 bam 19.8 GB
EGAF50000237797 bam 10.8 GB
EGAF50000237798 bam 16.6 GB
EGAF50000237799 bam 12.8 GB
EGAF50000237800 bam 13.0 GB
EGAF50000237801 bam 15.8 GB
EGAF50000237802 bam 15.8 GB
EGAF50000237803 bam 19.3 GB
EGAF50000237804 bam 11.0 GB
EGAF50000237805 bam 14.0 GB
EGAF50000237806 bam 14.1 GB
EGAF50000237807 bam 14.1 GB
EGAF50000319930 fastq.gz 3.3 GB
EGAF50000319931 fastq.gz 3.3 GB
EGAF50000319932 fastq.gz 3.4 GB
EGAF50000319933 fastq.gz 3.4 GB
EGAF50000319934 fastq.gz 4.5 GB
EGAF50000319935 fastq.gz 4.6 GB
EGAF50000319936 fastq.gz 4.6 GB
EGAF50000319937 fastq.gz 4.7 GB
EGAF50000319938 fastq.gz 1.8 GB
EGAF50000319939 fastq.gz 1.8 GB
EGAF50000319940 fastq.gz 1.9 GB
EGAF50000319941 fastq.gz 1.9 GB
EGAF50000319942 fastq.gz 2.3 GB
EGAF50000319943 fastq.gz 2.4 GB
EGAF50000319944 fastq.gz 2.4 GB
EGAF50000319945 fastq.gz 2.4 GB
EGAF50000319946 fastq.gz 3.8 GB
EGAF50000319947 fastq.gz 3.9 GB
EGAF50000319948 fastq.gz 2.6 GB
EGAF50000319949 fastq.gz 2.7 GB
EGAF50000319950 fastq.gz 3.9 GB
EGAF50000319951 fastq.gz 2.5 GB
EGAF50000319952 fastq.gz 4.0 GB
EGAF50000319953 fastq.gz 2.7 GB
EGAF50000319954 fastq.gz 3.0 GB
EGAF50000319955 fastq.gz 3.1 GB
EGAF50000319956 fastq.gz 3.1 GB
EGAF50000319957 fastq.gz 3.2 GB
EGAF50000319958 fastq.gz 4.1 GB
EGAF50000319959 fastq.gz 4.2 GB
EGAF50000319960 fastq.gz 4.3 GB
EGAF50000319961 fastq.gz 4.3 GB
EGAF50000319962 fastq.gz 2.6 GB
EGAF50000319963 fastq.gz 2.6 GB
EGAF50000319964 fastq.gz 2.8 GB
EGAF50000319965 fastq.gz 4.5 GB
EGAF50000319966 fastq.gz 4.6 GB
EGAF50000319967 fastq.gz 2.7 GB
EGAF50000319968 fastq.gz 4.6 GB
EGAF50000319969 fastq.gz 4.7 GB
EGAF50000319970 fastq.gz 1.8 GB
EGAF50000319971 fastq.gz 1.8 GB
EGAF50000319972 fastq.gz 2.9 GB
EGAF50000319973 fastq.gz 2.9 GB
EGAF50000319974 fastq.gz 1.9 GB
EGAF50000319975 fastq.gz 1.9 GB
EGAF50000319976 fastq.gz 3.0 GB
EGAF50000319977 fastq.gz 3.0 GB
EGAF50000319978 fastq.gz 2.4 GB
EGAF50000319979 fastq.gz 2.3 GB
EGAF50000319980 fastq.gz 2.4 GB
EGAF50000319981 fastq.gz 2.4 GB
EGAF50000319982 fastq.gz 2.4 GB
EGAF50000319983 fastq.gz 2.4 GB
EGAF50000319984 fastq.gz 2.5 GB
EGAF50000319985 fastq.gz 2.5 GB
EGAF50000319986 fastq.gz 1.6 GB
EGAF50000319987 fastq.gz 1.6 GB
EGAF50000319988 fastq.gz 1.7 GB
EGAF50000319989 fastq.gz 1.7 GB
EGAF50000319990 fastq.gz 1.2 GB
EGAF50000319991 fastq.gz 1.2 GB
EGAF50000319992 fastq.gz 1.3 GB
EGAF50000319993 fastq.gz 3.8 GB
EGAF50000319994 fastq.gz 1.3 GB
EGAF50000319995 fastq.gz 3.8 GB
EGAF50000319996 fastq.gz 3.9 GB
EGAF50000319997 fastq.gz 2.3 GB
EGAF50000319998 fastq.gz 2.3 GB
EGAF50000319999 fastq.gz 1.8 GB
EGAF50000320000 fastq.gz 4.0 GB
EGAF50000320001 fastq.gz 2.4 GB
EGAF50000320002 fastq.gz 2.4 GB
EGAF50000320003 fastq.gz 1.8 GB
EGAF50000320004 fastq.gz 1.9 GB
EGAF50000320005 fastq.gz 1.9 GB
EGAF50000320006 fastq.gz 3.6 GB
EGAF50000320007 fastq.gz 3.6 GB
EGAF50000320008 fastq.gz 3.7 GB
EGAF50000320009 fastq.gz 3.7 GB
100 Files (524.3 GB)