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31 results for “ecDNA”
ecDNA machine learning modeling
<h3><strong>1. Today (2024-06-27), we discovered an issue with the labeling of sample groups in one of the supplementary figures (Supplementary Figure 14c) in our published article. We have corrected the figure and present it here, and we extend our apologies to all readers for any confusion this may have caused (although no report received).</strong></h3> <h3><strong>2. The source data of supplementary figure 13 in the accompanying article table has been found to have issues, which were identified as a result of improper Excel operation. Here, we have uploaded the correct data table</strong></h3> <p>--------------------------------------------------</p> <p> </p> <p>1. ecDNA_cargo_gene_modeling_data.csv.gz</p> <p>The dataset contains features from 386 TCGA tumors for modeling ecDNA cargo gene prediction. It was converted from R data format with the following code. NOTE: columns 'sample' and 'gene_id' are not used for actual modeling but for identifying, and sampling purposes.</p> <p>library(data.table)</p> <p>data = readRDS("~/../Downloads/ecDNA_cargo_gene_modeling_data.rds")</p> <p>colnames(data)[3] = "total_cn"</p> <p>data.table::fwrite(data, file = "~/../Downloads/ecDNA_cargo_gene_modeling_data.csv.gz", sep = ",")</p> <p> </p> <p>2. gcap_pcawg_WGS_result.tar.gz</p> <p>GCAP analysis results for PCAWG allele-specific copy number profiles derived from WGS.</p> <p> </p> <p>3. gcap_tcga_snp6_result.tar.gz</p> <p>GCAP analysis results for TCGA allele-specific copy number profiles derived from SNP6 array.</p> <p> </p> <p>4. gcap_Changkang_WES_result.tar.gz</p> <p>GCAP analysis results for SYSUCC Changkang allele-specific copy number profiles derived from tumor-normal paired WES.</p> <p> </p> <p>5. tcga_overlap_gene_wgs.rds, tcga_overlap_gene_snp.rds and tcga_overlap_gene_wes.rds</p> <p>These datasets contain TCGA gene-level copy number results in R data format from overlapping samples (dataset above). WGS from PCAWG, SNP array, and WES from GDC portal.</p> <p> </p> <p>6. cellline-batch1.zip & cellline-batch1.zip</p> <p> </p> <p>GCAP results of cell line batch 1 and batch 2.</p> <p> </p> <p>7. AA_cellline_wgs.zip</p> <p>AA software results for cell line batch 1.</p> <p> </p> <p>8. Batch2_AA_summary.xlsx</p> <p>AA software results for cell line batch 2.</p> <p> </p> <p>9. FISH-for-supp-file.zip</p> <p>Extended raw FISH images from 12 CRC samples.</p> <p> </p> <p>10. SNU216.zip</p> <p>Extended AA and GCAP analysis on SNU216.</p> <p> </p> <p>11. aa_ffpe.zip and AA_summary_table_of_6_erbb2_ffpe_samples.xlsx</p> <p>Extended AA running files (all results) and result summary data for 6 GCAP predicted ERBB2 amp clinical samples.</p> <p> </p> <p>12. source data of fig.4</p> <p> </p> <p>13. source data of supp fig.2 subplots</p> <p> </p> <p>13. source data of supp fig.15</p> <p> </p> <p>14. GCAP result data objects for three ICB cohorts. Both gene-level and sample-level data included.</p> <p> </p> <p>15. PDX-P68: processed (AA and CNV) data of P68 from WGS and WES data.</p> <p> </p> <p>16. source data of supp fig.13</p> <p> </p> <p>17. updated supplementary figure 14</p>
Toy example for Decoil-viz - vizualization module for ecDNA reconstructions
<p>This zenodo entry is a toy example for the Decoil-viz, the visualization module for ecDNA reconstructions generated by Decoil method.</p> <ul> <li>Find Decoil-viz repository under <a href="https://github.com/madagiurgiu25/decoil-viz">https://github.com/madagiurgiu25/decoil-viz</a>.</li> <li>Learn how to reconstruct ecDNA structures using Decoil (<a href="https://github.com/madagiurgiu25/decoil-pre">https://github.com/madagiurgiu25/decoil-pre)</a></li> </ul> <p>Please cite the paper: Giurgiu et al. 2024. <em>Genome Research</em>. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil". <a href="https://genome.cshlp.org/content/early/2024/08/21/gr.279123.124">Doi: 10.1101/gr.279123.124</a></p>
Study of the CHK1 Inhibitor BBI-355, an ecDNA-directed Therapy (ecDTx), and the RNR Inhibitor BBI-825, in Subjects With Tumors With Oncogene Amplifications
ClinicalTrials.gov study NCT05827614. IPD Sharing: NO. Countries: 1. Publications: 7.
ecPath: Predicting ecDNA status in Tumors from Histopathology Slide Images
Open the record for dataset details and reuse information.
ecDNA hubs drive cooperative intermolecular oncogene expression [ATAC-Seq]
GEO Series GSE175451. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
HPV integration generates cellular super enhancer and functions as ecDNA to regulate genome-wide transcription
GEO Series GSE195631. Homo sapiens. 77 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing.
ecDNA hubs drive cooperative intermolecular oncogene expression [RNA-Seq]
GEO Series GSE184566. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
ecDNA hubs drive cooperative intermolecular oncogene expression
GEO Series GSE159986. Homo sapiens. 63 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing.
MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC
GEO Series GSE281325. Homo sapiens. 19 samples. Type: Other.
MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC
GEO Series GSE247129. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing.
ecDNA hubs drive cooperative intermolecular oncogene expression [scRNA and scATAC-Seq]
GEO Series GSE160148. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
The Role of Extracellular DNA (ecDNA) in the Occurrence and Development of Gastric
ClinicalTrials.gov study NCT05956847. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
YY1 and Lig3 collaboratively regulate ecDNA biogenesis (CUT&Tag)
GEO Series GSE287200. Homo sapiens. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
YY1-mediated DNA looping promotes the generation of ecDNA (HiCUT)
GEO Series GSE287239. Homo sapiens. 2 samples. Type: Other.
ecDNA hubs drive cooperative intermolecular oncogene expression [ChIP]
GEO Series GSE159972. Homo sapiens. 21 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC
GEO Series GSE281326. Homo sapiens. 47 samples. Type: Expression profiling by high throughput sequencing; Other.
ecDNA hubs drive cooperative intermolecular oncogene expression [HiChIP]
GEO Series GSE159985. Homo sapiens. 4 samples. Type: Other.
Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution
GEO Series GSE226741. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing; Other.
Histone 3 lysine 56 acetylation (H3K56ac) regulates extrachromosomal DNA (ecDNA) hub biogenesis
GEO Series GSE296003. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Expression changes of ecDNA in colorectal epithelium-adenoma-adenocarcinoma evolution (mRNA)
GEO Series GSE226739. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.