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• OAK GO28915 Source Table

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000368

• GO30103 Source Tables

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000367

• Cityscape Source Tables

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000366

• RNAseq and ATACseq data, derived from HGSC cell lines pre- and post- treatment with an epigenetic compound

  These data consist of transcriptome and chromatin accessibility data (RNAseq and ATACseq respectively) derived from five High-Grade Serous Ovarian Carcinoma (HGSC) cell lines. HGSC lines included PEO1, PEO4, PEA2, OVCAR5 and OVCAR8. Samples were taken pre- and post-treatment with a novel epigenetic compound, HKMTi-1-005, which targets the activity of two histone methyltransferases, EZH2 and G9a.

  Dataset EGAD50000000064

• Molecular characterization of T-PLL by Next-Generation Sequencing

  Patients with T-cell prolymphocytic leukemia (T-PLL) were profiled with multiple OMICS approaches based on Next-Generation Sequencing (NGS). In total, data from RNA-Seq, Whole-Exome Sequencing, Whole-Genome Sequencing and amplicon panel analyses in 134 samples are available. All samples were processed as paired-end libraries on Illumina sequencing machines. The data are available as paired FastQ files.

  Dataset EGAD00001003825

• Genome and transcriptome sequence data from an appendix cancer patient

  Genome and transcriptome sequence data from an appendix cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001309

• Genome and transcriptome sequence data from a peritoneal mesothelioma patient

  Genome and transcriptome sequence data from a peritoneal mesothelioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001310

• Genome and transcriptome sequence data from a peritoneal mesothelioma patient

  Genome and transcriptome sequence data from a peritoneal mesothelioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001311

• TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

  Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only.study_refcenter AMC

  Dataset EGAD00001001635

• Genome and transcriptome sequence data from an atypical teratoid rhabdoid tumor patient

  Genome and transcriptome sequence data from an atypical teratoid rhabdoid tumor patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001655

• Genome and transcriptome sequence data from an atypical chronic lymphocytic leukemia patient

  Genome and transcriptome sequence data from an atypical chronic lymphocytic leukemia patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001656

• Genome and transcriptome sequence data from a parotid gland cancer patient

  Genome and transcriptome sequence data from a parotid gland cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001657

• Genome and transcriptome sequence data from an odontogenic ghost cell carcinoma patient

  Genome and transcriptome sequence data from an odontogenic ghost cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001658

• Trimmed bam-files from whole genome sequencing data from plasma DNA

  Single-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002254

• Genome and transcriptome sequence data from a locally advanced breast cancer patient

  Genome and transcriptome sequence data from a locally advanced breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004897

• Genome and transcriptome sequence data from a metastatic rectal carcinoma patient

  Genome and transcriptome sequence data from a metastatic rectal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004898

• Genome and transcriptome sequence data from a invasive ductal carcinoma of right breast patient

  Genome and transcriptome sequence data from a invasive ductal carcinoma of right breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004899

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004900

• Single cell RNA sequencing of colorectal cancer with diverse tissue dissociation protocols or fresh vs. frozen cell preparations.

  To evaluate 3 different tissue dissociation protocols or fresh vs. frozen cell preparations, we performed single-cell RNA sequencing on cancer or distant normal tissue dissociates from 2 colorectal cancer patients. Total 18,409 cells from 10 sample preparations were analyzed (5 primary colorectal cancer and 5 matched normal mucosa). The results suggest highly consistent cellular proportions were recovered with different sample preparation methods.

  Dataset EGAD00001005191

• Chromatin accessibility analysis of hepatocyte-like cell in vitro differentiation from iPSC in comparison to primary human hepatocytes

  Fastq files of ATAC-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE), hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 4) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as from 3 PHH donors.

  Dataset EGAD00001005934

• Single cell transcriptomes of in vitro differentiated hepatocyte-like cells in comparison to primary human hepatocytes

  Fastq files of deeply sequenced single cell RNA-seq data (Smartseq2, approx. 2 million reads / sample) of hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 3) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as PHH from 3 donors. Each replicate comprises 96 single cells.

  Dataset EGAD00001005946

• Profiling of H3K27ac landscape in five immune cell types from rheumatoid arthritis patients and healthy controls

  We collected peripheral blood mononuclear cells (PBMC) from 6 RA patients and 4 healthy controls, as well as synovial fluid (SF) from the same RA patients. We then sorted B cells, CD4+ and CD8+ T cells, regulatory T cells and monocytes using flow cytometry and profiled regions marked with H3K27ac using CUT&Tag.

  Dataset EGAD00001007003

• WES_SCLC_MDACC

  To identify genomic drivers present in limited-stage small cell lung cancer (LS-SCLC); To determine the overall tumor mutational burden in LS-SCLC; To determine genomic intratumor heterogeneity (ITH) in LS-SCLC.

  Dataset EGAD00001007004

• Low coverage WGS of plasma cfDNA

  This dataset includes FASTQ files of low coverage whole genome sequencing of cell free DNA from plasma samples. The samples include 271 plasma samples of patients with an adnexal mass and 125 plasma samples of healthy individuals.

  Dataset EGAD00001007748

• Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA

  Total RNA sequencing (SMARTer Stranded Total RNA-Seq Kit v2) data of extracellular RNA (exRNA) from liquid biopsies of a BRC0004PR PDX and SK-N-BE(2C) CDX mouse model, and total RNA sequencing profiles of the matching PDX tumors.

  Dataset EGAD00001008318