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Sequencing data for the manuscript "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas"

Mapping the spatial organization of DNA-level somatic copy number changes in tumors can provide insight to understanding higher-level molecular and cellular processes that drive pathogenesis. We describe an integrated framework of spatial transcriptomics, tumor/normal DNA sequencing, and bulk RNA sequencing to identify shared and distinct characteristics of an initial cohort of eleven gliomas of varied pathology and a replication cohort of six high-grade glioblastomas.

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DUO:0000006
version: 2021-02-23

health or medical or biomedical research

This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.

Data access for "Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas"

1. Purpose: The purpose of this Data Use Agreement (DUA) is to establish the terms and conditions under which raw sequencing data associated with the publication titled " Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas" will be shared with external researchers to advance scientific research into the molecular pathogenesis of central nervous system (CNS) and spine malignancies. The data is provided for non-commercial, academic purposes only for studies only. 2. Data Description The data covered under this agreement includes Illumina-based exome sequencing of tumor specimens, paired blood specimens, bulk RNA-seq, and Visium FFPE sequencing data. Visium data without sequencing is available via NCBI GEO under record GSE242352. 3. Obligations of the Requesting Institution and Individuals a. Institutional Approval: This agreement must be signed by an authorized representative of the Requesting Institution, confirming that the institution will oversee compliance with its terms. b. Confidentiality. The Principal investigator and authorized users agree to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. c. Agree not to reidentify or conduct reidentification research. The Principal investigator and users agree not to link or combine these Data with other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User or is freely available without restriction. The Requesting Institution and Named Individuals must maintain the confidentiality of the data and take reasonable precautions to protect it from unauthorized access. d. Principal Investigator Approval: The agreement must also be signed by the Principal Investigator at the Requesting Institution, who will be responsible for the appropriate use of the data. e. Named Individuals: Only the Named Individuals listed in this agreement are permitted to access and use the data. Additional individuals must be pre-approved in writing by the Providing Institution. f. Data Use Restrictions: The data will be used solely for non-commercial, academic purposes and will not be shared, distributed, or sold to any third parties. g. Compliance with Laws: All data use will comply with applicable laws, regulations, and ethical guidelines, including but not limited to HIPAA, GDPR, or other relevant regulations. h. Acknowledgment: Any publication or presentation resulting from the use of this data must appropriately acknowledge the Providing Institution and cite the original publication. i. Data Destruction: Upon completion of the approved research, the data must be securely destroyed or returned to the Providing Institution unless otherwise agreed upon in writing.

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
EGAS50000000949 Exome Sequencing
EGAS50000000950 RNASeq
EGAS50000000951 Exome Sequencing
EGAS50000000952 Exome Sequencing
EGAS50000000953 RNASeq
EGAS50000000954 Transcriptome Analysis
EGAS50000000955 Exome Sequencing
EGAS50000000956 Transcriptome Analysis

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 Quality Report
Located in
EGAF50000349088 crai 1.3 MB
EGAF50000349089 bam 16.3 GB
EGAF50000349090 cram 5.5 GB
EGAF50000349091 crai 588.1 kB
EGAF50000349092 crai 456.1 kB
EGAF50000349093 crai 464.7 kB
EGAF50000349094 bai 2.6 MB
EGAF50000349095 cram 6.0 GB
EGAF50000349096 cram 4.6 GB
EGAF50000349097 crai 268.9 kB
EGAF50000349098 cram 2.4 GB
EGAF50000349099 cram 4.2 GB
EGAF50000349100 cram 4.3 GB
EGAF50000349101 cram 30.7 GB
EGAF50000349102 crai 389.7 kB
EGAF50000349103 crai 998.5 kB
EGAF50000349104 cram 2.2 GB
EGAF50000349105 crai 254.1 kB
EGAF50000349106 crai 245.1 kB
EGAF50000349107 cram 2.3 GB
EGAF50000349108 cram 3.7 GB
EGAF50000349109 cram 4.9 GB
EGAF50000349110 crai 266.4 kB
EGAF50000349111 cram 7.6 GB
EGAF50000349112 cram 5.2 GB
EGAF50000349113 cram 4.1 GB
EGAF50000349114 crai 1.6 MB
EGAF50000349115 cram 44.4 GB
EGAF50000349116 cram 5.5 GB
EGAF50000349117 cram 4.3 GB
EGAF50000349118 crai 107.9 kB
EGAF50000349119 cram 3.3 GB
EGAF50000349120 crai 346.5 kB
EGAF50000349121 cram 6.1 GB
EGAF50000349122 cram 4.3 GB
EGAF50000349123 crai 145.9 kB
EGAF50000349124 cram 27.2 GB
EGAF50000349125 cram 5.6 GB
EGAF50000349126 cram 28.1 GB
EGAF50000349127 bai 2.3 MB
EGAF50000349128 bai 2.3 MB
EGAF50000349129 bai 2.6 MB
EGAF50000349130 bai 2.4 MB
EGAF50000349131 bai 4.2 MB
EGAF50000349132 bam 15.0 GB
EGAF50000349133 bam 9.1 GB
EGAF50000349134 crai 220.2 kB
EGAF50000349135 bai 3.9 MB
EGAF50000349136 crai 204.5 kB
EGAF50000349137 crai 175.5 kB
EGAF50000349138 bai 7.4 MB
EGAF50000349139 bam 8.4 GB
EGAF50000349140 bai 3.7 MB
EGAF50000349141 bai 3.6 MB
EGAF50000349142 cram 38.4 GB
EGAF50000349143 cram 5.7 GB
EGAF50000349144 cram 23.8 GB
EGAF50000349145 cram 37.4 GB
EGAF50000349146 bam 4.0 GB
EGAF50000349147 crai 1.2 MB
EGAF50000349148 crai 793.9 kB
EGAF50000349149 bam 10.9 GB
EGAF50000349150 bai 3.7 MB
EGAF50000349151 bam 11.7 GB
EGAF50000349152 crai 246.7 kB
EGAF50000349153 crai 183.4 kB
EGAF50000349154 cram 5.3 GB
EGAF50000349155 crai 166.0 kB
EGAF50000349156 bai 4.3 MB
EGAF50000349157 bam 16.2 GB
EGAF50000349158 bai 4.2 MB
EGAF50000349159 bam 3.5 GB
EGAF50000349160 bai 2.3 MB
EGAF50000349161 bam 7.4 GB
EGAF50000349162 cram 6.6 GB
EGAF50000349163 cram 4.3 GB
EGAF50000349164 cram 4.4 GB
EGAF50000349165 crai 462.2 kB
EGAF50000349166 crai 604.3 kB
EGAF50000349167 crai 545.0 kB
EGAF50000349168 crai 574.2 kB
EGAF50000349169 cram 7.5 GB
EGAF50000349170 crai 259.2 kB
EGAF50000349171 cram 5.6 GB
EGAF50000349172 crai 202.4 kB
EGAF50000349173 cram 7.5 GB
EGAF50000349174 cram 3.2 GB
EGAF50000349175 cram 32.0 GB
EGAF50000349176 crai 1.2 MB
EGAF50000349177 crai 1.2 MB
EGAF50000349178 crai 976.0 kB
EGAF50000349179 cram 33.6 GB
EGAF50000349180 crai 1.0 MB
EGAF50000349181 crai 1.3 MB
EGAF50000349182 crai 258.4 kB
EGAF50000349183 crai 333.0 kB
EGAF50000349184 cram 3.1 GB
EGAF50000349185 crai 462.4 kB
EGAF50000349186 cram 3.9 GB
EGAF50000349187 crai 540.1 kB
EGAF50000349188 crai 374.0 kB
EGAF50000349189 crai 315.9 kB
EGAF50000349190 crai 266.0 kB
EGAF50000349191 cram 35.2 GB
EGAF50000349192 bam 3.0 GB
EGAF50000349193 bam 9.5 GB
EGAF50000349194 bam 15.3 GB
EGAF50000349195 bai 4.4 MB
EGAF50000349196 bam 9.6 GB
EGAF50000349197 bai 4.7 MB
EGAF50000349198 bam 9.6 GB
EGAF50000349199 bai 3.8 MB
EGAF50000349200 cram 3.5 GB
EGAF50000349201 cram 2.7 GB
EGAF50000349202 cram 5.3 GB
EGAF50000349203 cram 5.4 GB
EGAF50000349204 cram 34.3 GB
EGAF50000349205 bam 29.1 GB
EGAF50000349206 cram 3.6 GB
EGAF50000349207 crai 217.2 kB
EGAF50000349208 crai 343.4 kB
EGAF50000349209 bam 11.5 GB
EGAF50000349210 cram 4.9 GB
EGAF50000349211 crai 305.1 kB
EGAF50000349212 crai 455.7 kB
EGAF50000349213 cram 5.2 GB
EGAF50000349214 crai 549.8 kB
EGAF50000349215 crai 579.8 kB
EGAF50000349216 crai 633.8 kB
EGAF50000349217 crai 620.8 kB
EGAF50000349218 crai 351.4 kB
EGAF50000349219 cram 3.6 GB
EGAF50000349220 cram 5.2 GB
EGAF50000349221 cram 4.0 GB
EGAF50000349222 crai 151.7 kB
EGAF50000349223 crai 1.2 MB
136 Files (741.8 GB)