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• Mutation analysis using a custom SureSelect panel

  All baseline samples and when available EOT were processed for high-resolution mutation analysis. We designed a SureSelectXT-HS custom panel (Agilent) covering 68 genes with a total size of 260kb using the Agilent SureDesign platform.

  Dataset EGAD00001006386

• RNA sequencing data pre-treatment and post-treatment for NABUCCO cohort 1

  NABUCCO cohort 1 sequencing data. The dataset includes RNA sequencing pre-treatment on tumor samples (n=18) and RNA sequencing post-treatment on bladder tumor samples (n=18).

  Dataset EGAD00001006855

• ChIP-sequencing fragment coverage

  Raw sequencing reads from H3K27ac ChIP and input DNA from lymphoblastoid cells of three TET2 mutation carriers and two wild-type family members were quality and adapter trimmed with cutadapt version 1.16 in Trim Galore version 0.3.7 using default parameters. Trimmed reads were aligned to hs37d5 reference genome using Bowtie2 (version 2.1.0). Duplicate reads were removed with samtools rmdup (v1.7). Fragment coverage of paired-end reads was calculated from bam files with BEDtools genomecov (v2.26.0).

  Dataset EGAD00010001671

• Single-cell transcriptomic analyses of peripheral blood mononuclear cells from patients with colorectal cancer metastasized to the peritoneum

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peripheral blood mononuclear cells (PBMC) from patients with colorectal cancer (CRC) and peritoneal metastases (PM). Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000247

• Bulk RNAseq of cultured fibroblasts

  Fastq files from bulk RNAseq of fibroblasts after culture and facs sorting (N=9). Sorted FAP+ CAF cells RNAs were extracted using Qiagen miRNeasy Kit (Qiagen, #217004) according to the manufacturer's instructions. Verification of RNA integrity and quality was performed using the Agilent RNA 6000 nano Kit (Agilent Technologies, #5067-1511). cDNA libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina, #20020594) followed by sequencing on NovaSeq (Illumina).

  Dataset EGAD50000000323

• Cityscape Serum peptide Mass Spec data

  Matrix of counts from the serum peptide mass spec data from patients enrolled in the CITYSCAPE trial, and the sample annotation. Specifically, serum samples at C1D1, C2D1, C3D1, SCRN were collected from a total of 132 patients and subject to Mass Spec at Biognosys. The current study focused on patients who have samples at both C1D1 and C2D1 (n = 64 pairs). Associated metadata also included.

  Dataset EGAD50000000369

• PBMC scRNA-seq data using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data and single-cell CITE-seq data collected from 16 patients enrolled in GO30103 trial, and the cell level annotation. Specifically, PBMCs at C1D1, C1D15 (2 weeks after treatment), C2D1 (3 weeks after treatment) and C4D1 (9 weeks after treatment) were collected and subject to 10x Genomics protocol. Associated metadata also included.

  Dataset EGAD50000000370

• RNA sequencing of BCP-LBL patients samples

  In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL patients, we performed RNA sequencing of 49 tissue samples from BCP-LBL patients. Because the material was available as FFPE, and had a relative low quality, we used a capture-based approach, where NGS libraries obtained from total RNA were captured in 4-plex, using a whole exome capture panel.

  Dataset EGAD50000000419

• Whole Exome Sequencing Bipolar cases matched controls performed at Broad Inst on cohort from Germany

  This research project was a collaboration between University Hospital Frankfurt and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 823 Bipolar case/control samples from collaborators in Germany. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing cram files.

  Dataset EGAD50000000563

• Whole Exome Sequencing of Bipolar cases, matched controls at Broad Inst on a cohort from Netherlands

  This research project was a collaboration between VU and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 943 Bipolar case/control samples from collaborators in the Netherlands. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and the samples were sequenced on Illumina HiSeqX machines producing cram files

  Dataset EGAD50000000619