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MOMA - Bladder group DAC

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Lars Dyrskjøt
lars@clin.au.dk

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This DAC controls 15 datasets

Dataset ID	Description	Technology	Samples
EGAD00001006238	In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). RNA-seq was performed using the QuantSeq kit FWD HT kit (Lexogen) using 500 ng input RNA from 121 tumor samples. Data provided here consist of 780 fastq files for RNA-seq.	NextSeq 500	121
EGAD00001006239	In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.	Illumina NovaSeq 6000 NextSeq 500	330
EGAD00001006656	For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 535 patients. Sequencing of total RNA was performed using ScriptSeq-v2 RNA-Seq Library Preparation Kit (Illumina) and KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 500 ng for both kits. The dataset is composed of 1,596 fastq files.	Illumina HiSeq 2000 Illumina MiSeq Illumina NovaSeq 6000 NextSeq 550	535
EGAD00001006967	For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 47 patients used for validation. Sequencing of total RNA was performed using KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 100 to 500 ng. The dataset is composed of 94 fastq files.	Illumina NovaSeq 6000	47
EGAD00010001921	EPIC array data from 72 tumor samples with muscle invasive bladder cancer.	EPIC BeadChip (Illumina, San Diego, CA)	72
EGAD00010001943	SNP data from 49 paired samples (tumor/germline) with muscle invasive bladder cancer.	Illumina Infinium Human Global Screening Array GSAMD-24v2-0_20024620_a1 BeadChip	98
EGAD00010002038	SNP data for 473 tumor samples	Illumina Infinium Human Global Screening Array GSAMD-24v2-0_20024620_a1 BeadChip	473
EGAD00010002039	SNP data for 473 germline samples	Illumina Infinium OncoArray-500K	473
EGAD50000000730	A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 876 BAM files corresponding to the full WES dataset. Tumor and matched germline DNA were sequenced to a mean coverage of 132x (35x-338x) and 128x (31x-302x), respectively.	Illumina NovaSeq 6000	876
EGAD50000000731	A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). Additionally, tumor/germline samples from 4 patients were sequenced using Oxford Nanopore technology. This dataset contains 8 BAM files corresponding to the Long read sequencing data.	PromethION	8
EGAD50000000732	A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 876 BAM files corresponding to the full WES dataset. This dataset contains 392 BAM files corresponding to the full sWGS dataset. Tumor samples were sequenced to median coverage of 2.14x (1.24-9.01).	Illumina NovaSeq 6000	392
EGAD50000000733	A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 414 BAM files corresponding to the full total RNA-sequencing dataset.	Illumina HiSeq 2000 Illumina NovaSeq 6000	414
EGAD50000001380	For this dataset we performed total RNAseq on blood samples from 8 patients with muscle invasive bladder cancer. The data consists of 8 sets of paired fastq files with accompanying UMI fastq files. Sequenced on the Illumina NoveSeq6000 platform using S2 flow cells (v1.5,2x150 cycles), with a mean yield of 313 million reads.	Illumina NovaSeq 6000	8
EGAD50000001381	For this dataset we performed single cell RNAseq paired with single cell TCR-seq on tumor and blood samples from 4 patients. This dataset contains 4 tumor samples as well as 4 blood samples. Each sample is made up of 2 sets of paired fastq files. The first pair contains reads corresponding to RNA transcripts (_Transcripts in file name), while the second pair contain reads corresponding to TCRs (_VDJ in file name). Sequenced on the Illumina NovaSeq6000 platform in a paired-end run using an SP flow cell (v1.5, 300 cycles).	Illumina NovaSeq 6000	8
EGAD50000001382	For this dataset we performed bulk TCRseq on tumor and serial blood samples from patients with muscle invasive bladder cancer (n patients = 119, n blood = 209, n tumor = 28) or non-muscle invasive bladder cancer (n patients = 30, n blood = 56, n tumor = 19) for a total of 149 patients and 312 samples. Each sample consists of a paired fastq file. Sequenced on the Ilumina NovaSeq6000 platform using SP and S1 flow cells (v1.5, 2x101 cycles), with a mean yield of 42 million reads covering the CDR3β region.	Illumina NovaSeq 6000	312