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Mutagenesis in Medicine Data Access Committee

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sn206@cam.ac.uk

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This DAC controls 10 datasets

Dataset ID	Description	Technology	Samples
EGAD50000000036	Deposited here are whole-genome sequencing bam or fastq files from the experimental isogenic cell lines used in the study "The chemotherapeutic CX-5461 is extremely mutagenic and may increase cancer risk, Koh, Gene (2023)". The bam files were aligned to GRCh38/hg38 using BWA-MEM. The corresponding variant call data have been deposited on Mendeley Data, V2, doi: 10.17632/d58cv549v6.2	Illumina NovaSeq 6000	65
EGAD50000000209	Deposited here are whole-genome sequencing bam files from the experimental isogenic cell lines used in the study "Redefined indel taxonomy reveals insights into mutational signatures, Koh, Gene (2023)".	Illumina NovaSeq 6000	47
EGAD50000000228	Deposited here are time series bulk RNA-seq data generated from isogenic wild-type (WT), XPA and XPG gene knockouts hiPSC cells during cortical neuronal differentiation.	Illumina NovaSeq 6000	61
EGAD50000000230	Deposited here are time series bulk RNA-seq data generated from XP patients and controls as well as rescued patient hiPSC cells during cortical neuronal differentiation.	Illumina NovaSeq 6000	87
EGAD50000000232	Deposited here are WGS data generated from differentiated neural stem cells (NSCs) of NXPG-32 patient (XPG patient with neurodegeneration) and a matched healthy control CTRL-33.	Illumina NovaSeq 6000	9
EGAD50000001544	Deposited here are time series (6, 24 and 48hrs) bulk RNA-seq data generated from isogenic wild-type (WT) RPE1 untreated or treated with Brequinar (and other dNTP-pool disruptor compounds)	Illumina NovaSeq 6000	48
EGAD50000001602	Deposited here are WGS data generated from isogenic wild-type (WT) RPE1 untreated and treated with brequinar for 42 days (and other dNTP-pool disruptor compounds)	Illumina NovaSeq 6000	15
EGAD50000002036	Deposited here are 56 whole-genome sequencing BAM files from 15 Trp53f/w, 12 Trp53f/f, 14 Brca1f/f Trp53f/w, and 15 Brca1f/f Trp53f/f mouse mammary tumor samples sequenced on Illumina NovaSeq PE150. An additional 6 whole genome sequencing BAM files from corresponding normal tissues of mice are also included as controls (BPC_D666, B1PC_D840, BPTC_D992, PC_D503, PC_D720_Kid, PTC_H531). All samples were used in the study “Insights into BRCA1 and TP53 associated breast cancer development from integrated whole genome analysis of mouse model mammary tumors, Huo et al., 2026.”	Illumina NovaSeq 6000	62
EGAD50000002071	Deposited here are whole-genome sequencing data for 51 paired breast cancer DCIS and matched-normal samples taken from the same individual. Average sequence depth is 110x for DCIS samples and 39x for matched-normals. Matched-normals are from blood (n=14) or adjacent normal breast (n=37). Sequencing was performed on Illumina HIseqX (n=70) or Illumina Novoseq (n=32). They are a part of a broader project that uses high-depth WGS to investigate the somatic mutation genomic landscape of DCIS in order to uncover biological insights into breast cancer progression as well as possible methods to stratify DCIS patients for individualised therapy or disease monitoring.	Illumina HiSeq X	102
EGAD50000002237	Deposited here are whole-genome sequencing data for 26 paired breast cancer DCIS and matched-normal samples taken from the same individual. Average sequence coverage is 118x for DCIS samples and 41x for matched-normals. Matched-normal samples are from blood. Sequencing was performed on an Illumina HiseqX. Due to specific restrictions imposed by the ethical approval at sample collection, the use of the germline data is restricted to filtering of somatic mutation calls only and cannot be used outside this purpose.They are a part of a broader project that uses high-depth WGS to investigate the somatic mutation genomic landscape of DCIS in order to uncover biological insights into breast cancer progression as well as possible methods to stratify DCIS patients for individualised therapy or disease monitoring.	HiSeq X Ten	52