This README.txt file was generated on 2019/12/20 by Miguel Julia. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Supplemetary Tables for Annexes 2 and 3 2. Author Information Principal Investigator Contact Information Name: Miguel Julia Institution: University of Kent Address: Email: mj308@kent.ac.uk 3. Date of data collection: 2015/09/20-2018/09/15 4. Geographic location of data collection: Canterbury, Kent 5. Information about funding sources that supported the collection of the data: University of Kent --------------------- DATA & FILE OVERVIEW --------------------- 1. File List - Annex 2: A. Filename: UKF-NB-3_all_variants.tsv Short description: Supplementary Table 1. Variants in UKF-NB-3. They are fully annotated by VEP and also include their presence in each of the ten clonal sub-lines. B. Filename: number_of_variants_samples.xls Short description: Supplementary Table 2. Number of each type of variant per sample, sub-classified by variants that were called and variants that had enough quality to pass the 30 QUAL Phred threshold. C. Filename: par.cancer.xls Short description: Supplementary Table 3. Mutations of UKF-NB-3 located in common cancer genes and neuroblastoma driver genes. D. Filename: ClinVar_filtered.xls Short description: Supplementary Table 6. UKF-NB-3 variants annotated in ClinVar. E. Filename: SIFT_filtered.xls Short description: Supplementary Table 7. UKF-NB-3 variants with SIFT prediction. F. Filename: PolyPhen2_filtered.xls Short description: Supplementary Table 8. UKF-NB-3 variants with PolyPhen-2 prediction. G. Filename: SIFTandPlyPhen2_filtered.xls Short description: Supplementary Table 9. Overlap of variants whose effect was predicted by both SIFT and PolyPhen-2. H. Filename: CNVs_clones.ods Short description: Supplementary Table 10. CNV variations of each gene in log2 scale. - Annex 3: A. Filename: description_table.xls Short description: Supplementary Table 3. Variants per sample. Between brackets is the number of gained variants of each type. In the second table we show the number of variants of the parental UKF-NB-3 cell line not detected in each of the clonal sub-lines (lost) and the de novo mutations. In both tables, the parental cell line row (par) refers to the number of its variants not detected in any of the clonal sub-lines. B. Filename: all_denovo_variants.tsv Short description: Supplementary Table 4. De novo variants in each clone and overlap across samples. C. Filename: genes.freqs.variants.PASS.all.tsv Short description: Supplementary Table 5. Frequency of mutated genes, considering all mutations. D. Filename: genes.freqs.variants.PASS.gained.tsv Short description: Supplementary Table 6. Frequency of mutated genes, considering only gained mutations E. Filename: genes.freqs.variants.PASS.denovo.tsv Short description: Supplementary Table 7. Frequency of mutated genes, considering only de novo mutaitons. 2. Relationship between files: In this supplementary materials folder you can find the Supplementary tables of Annex 2 and 3 that are cited but not included in the main document. The name of each archive is the same as te table cited in the document, and they are storaged in two different folders each of them corresponding to the Annex of their names. 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: https://kar.kent.ac.uk/79140/ 2. Methods for processing the data: https://kar.kent.ac.uk/79140/ 3. Instrument- or software-specific information needed to interpret the data: https://kar.kent.ac.uk/79140/ 4. Standards and calibration information, if appropriate: https://kar.kent.ac.uk/79140/ 5. Environmental/experimental conditions: https://kar.kent.ac.uk/79140/ 6. Describe any quality-assurance procedures performed on the data: https://kar.kent.ac.uk/79140/ 7. People involved with sample collection, processing, analysis and/or submission: Miguel Julia