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.
- 07/04/2025
- 17 samples
- DAC: EGAC50000000579
- Technologies: Illumina NovaSeq 6000, NextSeq 2000
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
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|---|---|---|---|---|
| EGAF50000349088 | crai | 1.3 MB |
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| EGAF50000349089 | bam | 16.3 GB |
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| EGAF50000349090 | cram | 5.5 GB |
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| EGAF50000349091 | crai | 588.1 kB |
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| EGAF50000349092 | crai | 456.1 kB |
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| EGAF50000349093 | crai | 464.7 kB |
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| EGAF50000349094 | bai | 2.6 MB |
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| EGAF50000349095 | cram | 6.0 GB |
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| EGAF50000349096 | cram | 4.6 GB |
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| EGAF50000349097 | crai | 268.9 kB |
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| EGAF50000349098 | cram | 2.4 GB |
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| EGAF50000349099 | cram | 4.2 GB |
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| EGAF50000349100 | cram | 4.3 GB |
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| EGAF50000349101 | cram | 30.7 GB |
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| EGAF50000349102 | crai | 389.7 kB |
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| EGAF50000349103 | crai | 998.5 kB |
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| EGAF50000349104 | cram | 2.2 GB |
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| EGAF50000349105 | crai | 254.1 kB |
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| EGAF50000349106 | crai | 245.1 kB |
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| EGAF50000349107 | cram | 2.3 GB |
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| EGAF50000349108 | cram | 3.7 GB |
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| EGAF50000349109 | cram | 4.9 GB |
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| EGAF50000349110 | crai | 266.4 kB |
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| EGAF50000349111 | cram | 7.6 GB |
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| EGAF50000349112 | cram | 5.2 GB |
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| EGAF50000349113 | cram | 4.1 GB |
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| EGAF50000349114 | crai | 1.6 MB |
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| EGAF50000349115 | cram | 44.4 GB |
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| EGAF50000349116 | cram | 5.5 GB |
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| EGAF50000349117 | cram | 4.3 GB |
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| EGAF50000349118 | crai | 107.9 kB |
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| EGAF50000349119 | cram | 3.3 GB |
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| EGAF50000349120 | crai | 346.5 kB |
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| EGAF50000349121 | cram | 6.1 GB |
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| EGAF50000349122 | cram | 4.3 GB |
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| EGAF50000349123 | crai | 145.9 kB |
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| EGAF50000349124 | cram | 27.2 GB |
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| EGAF50000349125 | cram | 5.6 GB |
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| EGAF50000349126 | cram | 28.1 GB |
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| EGAF50000349127 | bai | 2.3 MB |
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| EGAF50000349128 | bai | 2.3 MB |
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| EGAF50000349129 | bai | 2.6 MB |
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| EGAF50000349130 | bai | 2.4 MB |
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| EGAF50000349131 | bai | 4.2 MB |
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| EGAF50000349132 | bam | 15.0 GB |
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| EGAF50000349133 | bam | 9.1 GB |
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| EGAF50000349134 | crai | 220.2 kB |
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| EGAF50000349135 | bai | 3.9 MB |
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| EGAF50000349136 | crai | 204.5 kB |
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| EGAF50000349137 | crai | 175.5 kB |
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| EGAF50000349138 | bai | 7.4 MB |
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| EGAF50000349139 | bam | 8.4 GB |
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| EGAF50000349140 | bai | 3.7 MB |
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| EGAF50000349141 | bai | 3.6 MB |
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| EGAF50000349142 | cram | 38.4 GB |
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| EGAF50000349143 | cram | 5.7 GB |
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| EGAF50000349144 | cram | 23.8 GB |
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| EGAF50000349145 | cram | 37.4 GB |
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| EGAF50000349146 | bam | 4.0 GB |
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| EGAF50000349147 | crai | 1.2 MB |
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| EGAF50000349148 | crai | 793.9 kB |
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| EGAF50000349149 | bam | 10.9 GB |
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| EGAF50000349150 | bai | 3.7 MB |
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| EGAF50000349151 | bam | 11.7 GB |
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| EGAF50000349152 | crai | 246.7 kB |
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| EGAF50000349153 | crai | 183.4 kB |
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| EGAF50000349154 | cram | 5.3 GB |
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| EGAF50000349155 | crai | 166.0 kB |
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| EGAF50000349156 | bai | 4.3 MB |
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| EGAF50000349157 | bam | 16.2 GB |
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| EGAF50000349158 | bai | 4.2 MB |
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| EGAF50000349159 | bam | 3.5 GB |
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| EGAF50000349160 | bai | 2.3 MB |
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| EGAF50000349161 | bam | 7.4 GB |
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| EGAF50000349162 | cram | 6.6 GB |
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| EGAF50000349163 | cram | 4.3 GB |
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| EGAF50000349164 | cram | 4.4 GB |
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| EGAF50000349165 | crai | 462.2 kB |
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| EGAF50000349166 | crai | 604.3 kB |
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| EGAF50000349167 | crai | 545.0 kB |
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| EGAF50000349168 | crai | 574.2 kB |
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| EGAF50000349169 | cram | 7.5 GB |
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| EGAF50000349170 | crai | 259.2 kB |
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| EGAF50000349171 | cram | 5.6 GB |
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| EGAF50000349172 | crai | 202.4 kB |
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| EGAF50000349173 | cram | 7.5 GB |
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| EGAF50000349174 | cram | 3.2 GB |
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| EGAF50000349175 | cram | 32.0 GB |
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| EGAF50000349176 | crai | 1.2 MB |
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| EGAF50000349177 | crai | 1.2 MB |
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| EGAF50000349178 | crai | 976.0 kB |
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| EGAF50000349179 | cram | 33.6 GB |
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| EGAF50000349180 | crai | 1.0 MB |
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| EGAF50000349181 | crai | 1.3 MB |
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| EGAF50000349182 | crai | 258.4 kB |
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| EGAF50000349183 | crai | 333.0 kB |
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| EGAF50000349184 | cram | 3.1 GB |
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| EGAF50000349185 | crai | 462.4 kB |
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| EGAF50000349186 | cram | 3.9 GB |
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| EGAF50000349187 | crai | 540.1 kB |
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| EGAF50000349188 | crai | 374.0 kB |
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| EGAF50000349189 | crai | 315.9 kB |
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| EGAF50000349190 | crai | 266.0 kB |
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| EGAF50000349191 | cram | 35.2 GB |
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| EGAF50000349192 | bam | 3.0 GB |
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| EGAF50000349193 | bam | 9.5 GB |
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| EGAF50000349194 | bam | 15.3 GB |
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| EGAF50000349195 | bai | 4.4 MB |
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| EGAF50000349196 | bam | 9.6 GB |
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| EGAF50000349197 | bai | 4.7 MB |
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| EGAF50000349198 | bam | 9.6 GB |
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| EGAF50000349199 | bai | 3.8 MB |
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| EGAF50000349200 | cram | 3.5 GB |
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| EGAF50000349201 | cram | 2.7 GB |
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| EGAF50000349202 | cram | 5.3 GB |
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| EGAF50000349203 | cram | 5.4 GB |
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| EGAF50000349204 | cram | 34.3 GB |
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| EGAF50000349205 | bam | 29.1 GB |
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| EGAF50000349206 | cram | 3.6 GB |
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| EGAF50000349207 | crai | 217.2 kB |
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| EGAF50000349208 | crai | 343.4 kB |
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| EGAF50000349209 | bam | 11.5 GB |
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| EGAF50000349210 | cram | 4.9 GB |
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| EGAF50000349211 | crai | 305.1 kB |
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| EGAF50000349212 | crai | 455.7 kB |
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| EGAF50000349213 | cram | 5.2 GB |
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| EGAF50000349214 | crai | 549.8 kB |
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| EGAF50000349215 | crai | 579.8 kB |
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| EGAF50000349216 | crai | 633.8 kB |
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| EGAF50000349217 | crai | 620.8 kB |
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| EGAF50000349218 | crai | 351.4 kB |
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| EGAF50000349219 | cram | 3.6 GB |
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| EGAF50000349220 | cram | 5.2 GB |
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| EGAF50000349221 | cram | 4.0 GB |
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| EGAF50000349222 | crai | 151.7 kB |
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| EGAF50000349223 | crai | 1.2 MB |
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| 136 Files (741.8 GB) | ||||
