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• Bulk RNA-sequencing data from five lines of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons, to define the molecular response of astrocytes to misfolded alpha-synuclein.

  Samples were derived from five lines of human iPSC-derived (hiPSC-derived) astrocytes, both alone and in co-culture with neurons +/- alpha-synuclein oligomer treatment. Paired-end FASTQ files for each of the samples are provided.

  Dataset EGAD50000001109

• GATCI whole genome germline variants

  Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with GATK HaplotypeCaller to generate germline variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers

  Dataset EGAD00001005817

• GATCI whole genome somatic variants (SomaticSniper)

  Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with SomaticSniper to generate somatic variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers

  Dataset EGAD00001005818

• GATCI whole genome somatic variants (MuTect)

  Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with MuTect to generate somatic variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers.

  Dataset EGAD00001005822

• Somatic mutation and clonal evolution in the human bladder_WGS (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-genome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006113

• Somatic mutation and clonal evolution in the human bladder Novaseq (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-genome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006116

• Somatic mutation and clonal evolution in the human bladder_WES (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-exome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006115

• mRNA-seq data from ALL patients with NUP214::ABL1 disease

  Dataset contains mRNA-sequencing data (fastq files) from 2 patients with NUP214::ABL1 disease (one T-ALL and one B-ALL patient). Patient samples (peripheral blood or bone marrow) were taken at diagnosis (B-ALL) or relapse (T-ALL). mRNA was extracted from lymphoblasts and underwent paired-end sequencing (75bp) using the Illumina NextSeq platform. Transcriptomic data was used for identification of gene fusions, SNVs and InDels. mRNA-seq data for an additional B-ALL patient with NUP214::ABL1 disease utilised in this study has already been published (EGAS00001006460).

  Dataset EGAD50000001395

• DDD_1 hypermutated individual

  CRAM files and VCF for DDD_1 and their parents. Also de novo mutations file for hypermutated DDD_1 child as described in the manuscript ‘Genetic and chemotherapeutic influences of germline hypermutation’ by Kaplanis et al. which will be published in Nature shortly.

  Dataset EGAD00001008497

• Clonally selected lines after CRISPR/Cas editing are not isogenic

  The CRISPR-Cas9 system has enabled researchers to precisely modify/edit the sequence of a genome. A typical editing experiment consists of two steps: (i) editing cultured cells and (ii) selection of clones, which are presumed to be isogenic, with and without the intended edit. The application of the CRISPR-Cas9 system may result in off-target edits, while cloning would reveal culture-acquired mutations. We analyzed the extent of the former and of the latter by whole genome sequencing (WGS) involving separate genomic loci in three experiments conducted by three independent laboratories. In all experiments we hardly found any off-target edits, while we detected hundreds to thousands of single nucleotide mutations unique to each clone after relatively short culture of 10-20 passages. Notably, clones also differed in copy number alterations that were several kb to several mb in size, representing the largest source of genomic divergence among clones. This study in dbGaP includes data from experiments carried out by investigators at the Oklahoma Medical Research Foundation and Baylor College of Medicine (OMRF/BCM) involving an iPSC line derived from fibroblasts of a female patient (line c7) carrying a constitutional heterozygous variant (chr1:1,464,679 C>T; GRCh37) in exon 15 of the ATPase family, AAA domain containing 3A (ATAD3A) gene. The parental line was edited by introducing a double stranded break at the variant allele to correct the variant by homology directed repair. Two unedited control clones (clone7 and clone8) and one edited clone (SC20) were selected for WGS.

  Study phs003110