12213 results for "cancer rna-seq"

in 38.74 milliseconds.

• Proteogenomic Landscape of Curable Prostate Cancer

  Aligned RNA-seq sequences in this dataset are from the Proteogenomic Landscape of Curable Prostate Cancer study

  Dataset EGAD00001004875

• Deregulation of FOXF1/FENDRR from t(14;16)(q32;q24) defines a subtype of high risk lineage ambiguous leukemia

  Despite great progress in understanding the genomic basis of immature T-cell acute lymphoblastic leukemia/lymphoblastic lymphoma (T-ALL) and acute leukemias of ambiguous lineage (ALAL), there are still cases that lack defining genetic markers, complicating risk stratification and limiting targeted therapeutic options. Here, we describe a subtype of leukemia defined by the t(14;16)(q32;q24) translocation, which places the FOXF1 gene and its antisense long noncoding RNA gene FENDRR under the regulatory control of the BCL11B enhancer, leading to their ectopic transcriptional activation. Analysis of different high-throughput sequencing data, including WGS, RNA-seq, scDNA-seq, scRNA-seq, ChIP-seq, ATAC-seq, and HiChIP-seq, identified BCL11B-enhancer mediated deregulation of FOXF1/FENDRR as a hallmark of a subtype of high-risk lineage ambiguous leukemia that is potentially amenable to targeted therapeutic intervention.

  Study EGAS50000001255

• Spatial heterogeneity, stromal phenotypes, and therapeutic vulnerabilities in colorectal cancer peritoneal metastasis

  Peritoneal metastases (PM) in colorectal cancer (CRC) portend a poor prognosis. We sought to elucidate molecular features differentiating primary tumors (PTs) from PMs and actionable targets facilitating transcoelomic dissemination and progression. We performed multi-omic profiling of 217 samples from 136 patients, including 56 primary tumor (PT) and 120 PMs comprising 25 matched PT-PM pairs. Whole exome, and bulk RNA-seq analysis was conducted to identify underlying genomic aberrations and transcriptomic differences between primary and peritoneal lesions.

  Study EGAS50000000813

• SYSCOL Human colorectal cancer project pilot RNA-seq and germline genotyping

  Genotyping by array and Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001000880

• Genomic profiling of BRCA- mutant breast cancer tumors

  This data set contains whole exome sequencing (WXS) and RNA-Seq on germline BRCA- mutant tumors from 18 patients. BAM files are provided for WXS on tumor and germline samples. FASTQ files are provided for the RNA-Seq samples. Sequencing was done on an Illumina Hi-Seq 2500.

  Dataset EGAD00001008276

• Natural variation of circulating RNAs in human serum

  The Janus Serum Bank (JSB) is a population-based cancer research biobank. This dataset contains small RNA sequencing (RNA-seq) data of 520 JSB samples from cancer-free individuals. Sequencing libraries were indexed and 12 samples were sequenced per lane on a HiSeq 2500 (Illumina) to an average depth of 18 million reads per sample. The dataset files are raw FASTQ files from the sequencing machine (50bp, single-end sequencing)

  Dataset EGAD00001003968

• Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in HGSOC

  Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Long-read single-cell RNA sequencing (scRNA-seq), capturing full-length transcripts, lacked the depth to provide this information so far. Here, we increased the PacBio sequencing depth to 12,000 reads per cell, leveraging multiple strategies, including artifact removal and transcript concatenation, and applied the technology to samples from three human ovarian cancer patients. Our approach captured 152,000 isoforms, of which over 52,000 were novel, detected cell type- and cell-specific isoform usage, and revealed differential isoform expression in tumor and mesothelial cells. Furthermore, we identified gene fusions, including a novel scDNA sequencing-validated IGF2BP2::TESPA1 fusion, which was misclassified as high TESPA1 expression in matched short-read data, and called somatic and germline mutations, confirming targeted NGS cancer gene panel results. With multiple new opportunities, especially for cancer biology, we envision long-read scRNA-seq to become increasingly relevant in oncology and personalized medicine.

  Study EGAS00001006807

• Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data

  In this study, we performed systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, on both simulated and real single-cell RNA-seq datasets. We generated SMART-seq2 data for 70 CD45- single cells, which were derived from two colorectal cancer patients (P0411 and P0413). The average sequencing depths of these cells were 1.4 million reads per cell. We also generated tumor and adjacent normal bulk WES data, as well as tumor bulk RNA-seq data for these patients.

  Dataset EGAD00001005373

• ICGC Breast Cancer Project, RNA seq

  A comprehensive characterisation and analysis of human breast cancers through genome-wide approaches through transcriptomics.

  Dataset EGAD00001001323

• Single cell RNA sequencing of PBMC samples from CRC patients

  This data contains scRNA-seq on 14 PBMC samples from colorectal cancer patients.

  Dataset EGAD50000000841

• Molecular Characterization of Prostate Cancer Specimens by Bulk and Single Cell Analysis

  Version 1: We performed single-cell RNA-sequencing (scRNA-seq) of fresh biopsies from metastatic castration resistant prostate cancer. Additionally, where available, we performed matched bulk whole exome sequencing (WXS; tumor and normal paired) and whole transcriptome sequencing for the same individuals. We also performed bulk whole exome (WXS) and RNA-sequencing (RNA-Seq) from FFPE pre-treatment biopsies from patients with clinically localized high-risk prostate cancer.Version 2: We added data from a randomized phase 2 trial of radium-223 with or without pembrolizumab in patients with Metastatic Castration-Resistant Prostate Cancer (mCRPC) to bone. After enrollment, study participants underwent bone biopsy and were randomized 2:1 to receive radium-223 at 55 kBq/kg every 4 weeks + pembrolizumab at 200 mg every 3 weeks (Arm A, R223+P) or radium-223 at 55 kBq/kg every 4 weeks alone (Arm B, R223). Stratification factors were alkaline phosphatase ≥220 vs. Data generated includes bulk whole exome sequencing (WXS), ultra-low pass whole genome sequencing (WGS) at 0.1X coverage, and targeted-capture sequencing. The ultra-low pass sequencing was used as part of the selection criteria for the target capture sequencing. Note: Two subjects in this study are linked to phs001577 and phs000915 respectively.

  Study phs001988

• Metabolic Biomarkers in Thoracic Cancers

  Here we present RNA sequencing (RNA-Seq) of non-small cell lung cancer (NSCLC) and adjacent lung tissue. These samples were acquired from primarily untreated, surgically resected primary tumors. The first analysis published with this data was to determine the metabolic signatures between primary tumors and adjacent lung tissue.The associated clinical trial (NCT02095808) includes patients with many kinds of thoracic cancers, including NSCLC and other diseases, such as thymoma and esophageal adenocarcinoma. However, the current dbGaP data is focused on the NSCLCs described in the associated paper.

  Study phs003880

• DNTR sequencing data of paediatric acute lymphoblastic leukemia

  This study used the DNTR-seq method in leukaemia samples to profile the whole-genome and mRNA jointly in single cells. Direct tagmentation is used in a collection of single-cell whole genome sequencing (scWGS) methods, including DNTR-seq, which provide high quality data at ultra-low to low coverage. The overall goal was to characterize the genetic and transcriptional heterogeneity of cancer samples. To infer clonal structure and evolutionary history, copy number analysis based workflows were implemented. Bone marrow mononuclear cells from pediatric acute lymphoblastic leukemia samples were FACS sorted into 384 plates to generate the DNA and RNA profiles.

  Study EGAS50000001247

• Deconvolution of bulk RNA-Seq using single cell RNA-Seq

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Study EGAS00001006723

• Comparison of good PDX responders and bad PDX responders

  RNA-Seq raw data of untreated breast cancer xenografts known as good or bad acetalax responders.

  Dataset EGAD50000000876

• RNA-Seq of kidney cancer organoid biobank

  Dataset EGAD00001005318

• The function of circular RMST in neuroendocrine tumours

  Circular RNA (circRNA) is a class of noncoding RNA with regulatory potentials. Its role in the transdifferentiation of prostate and lung adenocarcinoma into neuroendocrine prostate cancer (NEPC) and small cell lung cancer (SCLC) remains unexplored. Here we identified circRMST as an exceptionally abundant circRNA predominantly expressed in NEPC using total RNA-seq profiling of patient samples. In addition, circRMST is also abundantly expressed in SCLC. Functional studies using shRNA, siRNA, CRISPR-Cas13 and Cas9 consistently demonstrate that circRMST is essential for tumour growth and the expression of ASCL1, a master regulator of neuroendocrine fate. Mechanistically, circRMST physically interacts with lineage transcription factors NKX2-1 and SOX2. Loss of circRMST induces NKX2-1 protein degradation through autophagy-lysosomal pathway and alters the genomic binding of SOX2, collectively leading to the loss of ASCL1 transcription.

  Study EGAS50000000897

• RNA-seq study of a Princess Margaret Cancer Centre human acute myeloid leukemia patient cohort

  The PMCC AML RNAseq dataset consists of 81 AML patient samples (clinical data in Supplemental Table 11 of manuscript), processed in two batches. These patient samples are able to engraft in the NSG (NOD.Cg PrkdcscidIl2rgtm1Wjl /SzJ) mouse model. Five patients (90543, 598, 90240, 110484, 100500) were included in both batches. Viaably frozen material from the Leukemia Tissue Bank at Princess Margaret Cancer Centre/ University Health Network were thawed by dropwise addition of X-VIVO + 50% fetal calf serum supplemented with DNase (100μg/mL final concentration, Roche). RNA was extracted from bulk peripheral blood mononuclear cells (PBMC) using the RNeasy Micro Kit (Qiagen Inc.). A paired-end 76 base-pair flow-cell lane Illumina High seq 2000 yielded an average of 240 million sequence reads aligning to genome per sample at the Genome Sciences Centre, BC Cancer Agency for cohort 1. Cohort 2 was subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Centre for Applied Genomics, Sick Kids Hospital.

  Study EGAS00001004792

• Genentech Colon Cancer Screen

  Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. Here we analyse systematically more than 70 pairs of primary human colon tumours by applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alterations. We have identified 36,303 protein-altering somatic changes that include several new recurrent mutations in the Wnt pathway gene TCF7L2, chromatin-remodelling genes such as TET2 and TET3 and receptor tyrosine kinases including ERBB3. Our analysis for significantly mutated cancer genes identified 23 candidates, including the cell cycle checkpoint kinase ATM. Copy-number and RNA-seq data analysis identified amplifications and corresponding overexpression of IGF2 in a subset of colon tumours. Furthermore, using RNA-seq data we identified multiple fusion transcripts including recurrent gene fusions involving R-spondin family members RSPO2 and RSPO3 that together occur in 10% of colon tumours. The RSPO fusions were mutually exclusive with APC mutations, indicating that they probably have a role in the activation of Wnt signalling and tumorigenesis. Consistent with this we show that the RSPO fusion proteins were capable of potentiating Wnt signalling. The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer.

  Study EGAS00001000288

• Cellular composition of spheres derived from lymph nodes of lung cancer patients

  To decipher the cell type composition within single spheres we performed RNA-Seq of 25 selected spheres of 4 different categories (including 8 signature-/balanced, 9 signature+/balanced, 1 signature-/aberrant, 7 signature+/aberrant). To track the individual cell types within single spheres we performed deconvolution analysis.

  Study EGAS00001007369

• GELATO clinical trial RNA-Seq data (metastatic lesions)

  RNA-Seq data of 46 matched lobular breast cancer metastatic samples obtained from 21 unique patients from GELATO clinical trial assayed at three timepoints: at baseline (directly after patient randomization), pre-atezolizumab (after induction treatment with carboplatin for two weeks) and on atezolizumab (after two cycles of atezolizumab combined with carboplatin). The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009834

• RNA-seq data from the MESOMICS project (French project of molecular characterization of malignant pleural mesothelioma)

  The dataset includes fastq files from 109 tumor samples as well as RNA-seq gene expression R data, RNA-seq transcript expression R data, RNA-seq gene counts matrix, RNA-seq transcript counts matrix, RNA-seq gene FPKM matrix RNA-seq transcript FPKM matrix for the 109 samples. The sequencing was done with HiSeq 2000 instrument.

  Dataset EGAD00001007024

• Recurrent DNMT3B gene rearrangements are associated with unfavorable outcome in dicentric (9;20)-positive pediatric BCP-ALL

  We provide clinical data sets of Array CGH, targeted RNA-seq, total RNA-seq, whole genome bisulfite (WGBS) and whole genome DNA sequencing (WGS) obtained from bone marrow (BM) or peripheral blood (PB) mononuclear cells of 57 pediatric patients with dicentric chromosome dic(9;20) positive Acute lymphocytic leukemia (ALL), from which in 6 cases DNMT3B gene rearrangement was identified. This data is complemented by total RNA-seq and WGBS of samples from 4 additional ALL patients with a t(12;21) translocation and ETV6-RUNX1 gene fusion. DNA was isolated from BM or PB B-lymphocytes using Qiagen QIAamp DNA Blood Midi Kit to perform i) Array CGH of 58 dic(9;20) positive samples by hybridizing 500ng DNA using a Agilent 400K SurePrint G3 Custom CGH Human Genome Microarray (e-Array design 84704) ii) WGBS of 6 DNMT3B rearrangement positive samples and 4 ETV6-RUNX1 positive samples using Tecan TrueMethyl oxBS-Seq module for library preparation and Illumina NovaSeq 6000 platform to run 2x151 cycles iii) WGS of DNMT3B rearrangement positive samples using Illumina Lotus DNA Library Prep Kit followed by sequencing running 2x160 cycles on an Illumina NovaSeq 6000 platform. RNA was isolated from PB B-lymphocytes using the PerkinElmer Chemagic 360 instrument, followed by i) targeted RNA-seq of 56 dic(9;20) positive samples prepared using Illumina TruSight RNA Pan-Cancer Panel and sequenced on an Illumina MiSeq platform running 2x75 cycles ii) total RNA-seq of 6 DNMT3B rearrangement positive samples and 4 ETV6-RUNX1 positive samples utilizing TruSeq Stranded Total RNA Library Prep Gold kit and running 2x100 cycles on an Illumina NovaSeq 6000 platform.

  Dataset EGAD00001011122

• A Phase I Study with a Personalized Neoantigen Cancer Vaccine in Melanoma

  Effective anti-tumor immunity in humans has been associated with presence of T cells targeting neoantigens that arise from non-silent tumor-specific mutations. Here we conducted whole-exome sequencing of tumor and normal cells from individual patients to identify mutations. We assessed the expression of mutated alleles by RNA-sequencing of tumor. We demonstrated the feasibility, safety and immunogenicity of a vaccine that targets up to 20 personal neoantigens predicted to be presented by the autologous patient tumor.Antigen-specific CD8+ T cells that can recognize and eliminate cancer cells play a crucial role in anti-tumor immune responses. Here we conducted single-cell sequencing of cells infiltrating melanoma specimens originating from 4 patients and determine the TCR clonality of the CD8+ tumor infiltrating cells. We investigated the relationship between T cell clonality and phenotypic cell states coupling single-cell transcriptome to single-cell TCR seq. The surface expression of a panel of protein was detected in parallel using CITE-Seq antibodies. Sorted tumor and peripheral blood specimens were processed in parallel.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out matched ribosome profiling (Ribo-seq), RNA-sequencing, and whole genome sequencing on one of the patients, as well as Ribo-seq on an additional patient. We used it to discover novel or unannotated open reading frames (nuORFs), their expression levels, as well as somatic mutations within them to predict potential neoantigens.

  Study phs001451

• SAPCS Blood RNA-seq of prostate cancer patients

  The study aims to quantify the gene expression in blood samples in 20 prostate cancer patients under the Southern African Prostate Cancer Study (SAPCS). The objective is to identify a list of differentially expressed genes.

  Study EGAS50000000702

• Pheno-seq profiles of single clonal tumor spheroids derived from a patient with colorectal cancer

  Pheno-seq is a new approach that integrates high-throughput imaging and transcriptomic profiling of clonal spheroids/organoids to dissect functional tumor cell heterogeneity in 3D cell culture systems. The method is based on the iCELL8 technology (TakaraBio) that uses barcoded nanowells and a micro-solenoid valve dispenser. The CRC_spheroid dataset contains demultiplexed RNA-sequencing profiles (FASTQ file format, NextSeq 500) of 95 clonal tumor spheroids derived from a patient with colorectal cancer.

  Dataset EGAD00001004131

• Genomic Profiling of Melanoma

  This study reports on genomic profiling [whole-exome sequencing (WXS), bulk RNA sequencing (RNA-seq), and/or single-cell RNA sequencing (scRNA-seq)] of patient-derived melanoma samples and matched normal samples. The goal is to elucidate the genetic and cellular basis of sun-exposed and sun-shielded melanomas and to relate these findings to survival and regional metastasis. Specimens were collected by the Tissue Resource Core of the Yale SPORE in Skin Cancer with participants' informed signed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with a Human Investigative Committee protocol. The melanomas used for sequencing were from fresh or snap-frozen tumors, or from short-term cell cultures. The cell cultures were routinely checked for mycoplasma contamination and were discarded when found positive. Matching normal DNA was from circulating lymphocytes or normal skin. We also include 77 WES-sequenced samples from the Yale Spitzoid neoplasm repository, which collects specimen and data according to a protocol approved by the Yale Human Investigative Committee.

  Study phs000933

• Rio Dataset

  Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer. RNA-Seq data for paired baseline and end of treatment samples

  Dataset EGAD00001006120

• Smart-seq3 scRNA-seq of cells from primary (OV2295) and metastatic (OV2295R2) high-grade serous ovarian cancer cell-line

  In this project, single cells extracted from two high-grade serous ovarian cancer cell-lines, one primary (OV2295) and one metastatic (OV2295R2), where split into two 384 well plates and libraries were prepared using Smart-seq3 single cell RNA sequencing (Hagemann-Jensen et al, 2020).

  Study EGAS00001006868

• RNA-seq study of a Princess Margaret Cancer Centre human acute myeloid leukemia patient cohort

  The PMCC AML RNAseq dataset consists of 81 AML patient samples (clinical data in Supplemental Table 11 of manuscript), processed in two batches. These patient samples are able to engraft in the NSG (NOD.Cg PrkdcscidIl2rgtm1Wjl /SzJ) mouse model. Five patients (90543, 598, 90240, 110484, 100500) were included in both batches. Viaably frozen material from the Leukemia Tissue Bank at Princess Margaret Cancer Centre/ University Health Network were thawed by dropwise addition of X-VIVO + 50% fetal calf serum supplemented with DNase (100μg/mL final concentration, Roche). RNA was extracted from bulk peripheral blood mononuclear cells (PBMC) using the RNeasy Micro Kit (Qiagen Inc.). A paired-end 76 base-pair flow-cell lane Illumina High seq 2000 yielded an average of 240 million sequence reads aligning to genome per sample at the Genome Sciences Centre, BC Cancer Agency for cohort 1. Cohort 2 was subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Centre for Applied Genomics, Sick Kids Hospital.

  Dataset EGAD00001006576

• RNA sequencing data from 10 patient derived colorectal cancer organoids

  This dataset comprises RNA-sequencing data from ten colorectal cancer (CRC) organoids, derived from histologically verified primary tumor tissues of patients undergoing surgical resection. Paired-end sequencing produced 20 FASTQ.gz files. The organoids were cultured in Geltrex-based droplets using PDO culture medium and harvested for RNA extraction. Total RNA was isolated and subjected to full-length mRNA sequencing, producing high-quality RNA-seq data. The dataset includes transcriptomic profiles of seven microsatellite stable (MSS) and three microsatellite instable (MSI) tumors, providing a valuable resource for the analysis of non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline. This dataset aids in uncovering potential immunotherapy targets in CRC, particularly in hard-to-treat low-TMB MSS cases.

  Dataset EGAD50000000962

• Transcriptome profiling for Korean Early Onset Gastric Cancer

  To identify transcriptome profile in this unique subset of gastric cancers, RNA-seq analyses were performed using frozen cancer tissue. Adjacent normal tissue of the same patients were used in differently expressed gene selection and fusion gene prediction.

  Dataset EGAD00001002187

• Semibulk RNA-seq analysis as a convenient method for measuring gene expression statuses in a local cellular environment

  For two cases of breast cancers, semibulk RNA-seq and single cell RNA-seq were performed.

  Study JGAS000387

• Chordoma_Sequencing_Project_Whole_Genome

  This is a continuation of the Chordoma Sequencing Project, prelim #G0175-122-CF. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. The Chordoma Foundation will fund the RNA Sequencing/Methylation and SNP6 costs for this project while the whole genome and library sequencing will be covered under the CGP, 2012-2013 core WTSI internal funding. An additional sequencing of three cancer cell lines will be added to this work, financed by the Chordoma Foundation. In this project, the Chordoma foundation will pay for the additional costs of methylation, RNA Seq,

  Study EGAS00001000409

• RNA-seq of high-grade serous ovarian cancer in long-term survivors (MOCOG study)

  RNA-seq dataset of high-grade serous ovarian cancer (HGSC) tumours from long-term survivors performed as part of the Multidisciplinary Ovarian Cancer Outcomes Group (MOCOG) study. The dataset includes fastq files from 56 HGSC tumours (53 primary tumours and 3 recurrent tumours) from 53 long-term survivor patients. Libraries were generated using the Illumina Stranded mRNA Prep and 150 bp paired-end sequencing was performed to a minimum of 100 million reads on Illumina NovaSeq 6000 instruments.

  Dataset EGAD00001008537

• Divergent WNT Signaling and Drug Sensitivity Profiles within Hepatoblastoma Tumors and Organoids

  Hepatoblastoma, the most prevalent pediatric liver cancer, almost always carries a WNT-activating CTNNB1 mutation, yet exhibits notable molecular heterogeneity. To characterize this heterogeneity and identify novel targeted therapies, we perform comprehensive analysis of hepatoblastomas and tumor-derived organoids using single-cell RNA-seq/ATAC-seq, spatial transcriptomics, and high-throughput drug profiling. We identify two distinct tumor epithelial signatures: hepatic ‘fetal’ and WNT-high ‘embryonal’, displaying divergent WNT signaling patterns. The fetal group is enriched for liver-specific WNT targets, while the embryonal group is enriched in canonical WNT target genes.

  Study EGAS50000000561

• Multi-omics datasets (WES, RNA-seq) of mesothelioma MIST4 study, a phase II PD-L1/VEGF blockage clinical trial

  This study comprises 26 mesothelioma patients with whole exome and RNA sequencing, designed to examine the efficacy and correlates of response to dual inhibition of programmed death-ligand 1 and vascular endothelial growth factor inhibition.

  Study EGAS50000001818

• BELLINI clinical trial bulk RNA-Seq data: cohorts A, B & С

  RNA-Seq data of 78 breast cancer primary tumors obtained from 45 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (15 patients, 25 samples) received nivolumab for 4 weeks, patients in cohort B (15 patients, 28 samples) received nivolumab + ipilimumab for 4 weeks, and patients in cohort C (15 patients, 25 samples) received nivolumab + ipilimumab for 6 weeks. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000808

• RNA-seq of oropharynx cancer cases from University of Michigan

  This dataset consists of 67 bulk RNA-seq data (sorted aligned BAM files) from formalin-fixed paraffin-embedded (FFPE) oropharynx tumor samples from the University of Michigan (UM). Samples were collected as part of the UM Head and Neck SPORE between 2008-2014. Library preparation was performed using the ribo-depletion method with the FastSelect kit and sequenced on the NovaSeq 6000 at the UM Advanced Genomics Core, resulting in 150bp paired-end reads. Raw reads were trimmed using Cutadapt (v3.4) and aligned to hg38 and high-risk HPV genomes using STAR (v2.7.9a). 62 of 67 samples were determined to be HPV RNA-positive.

  Dataset EGAD50000001306

• High-grade serous ovarian cancer refined with single-cell RNA-sequencing

  We performed single-cell RNA-sequencing of 18,403 cells unbiasedly collected from 7 treatment-naive HGSOC tumours. For each phenotypic cluster of tumour or stromal cells, we identified specific transcriptomic markers. Next, we explored which phenotypic clusters correlate with overall survival based on expression of these transcriptomic markers in 1467 bulk RNA-seq tumours. By evaluating molecular subtype signatures in single cells, we assessed to what extent a phenotypic cluster of tumour or stromal cells contributes to each molecular subtype.

  Study EGAS00001004987

• Response and Resistance to ER-Directed Therapy in Metastatic Breast Cancer

  Despite the reduction in cancer recurrence and mortality provided by hormonal therapy, estrogen receptor positive (ER+) metastatic breast cancer (MBC) remains the most common cause of breast cancer death, resulting in more than 20,000 deaths in the U.S each year. Although several therapeutic options exist to target the estrogen receptor, resistance to these therapies invariably occurs. Genetic mechanisms of acquired resistance to targeted therapies in ER+ MBC are not well understood. To address this, we developed a prospective biopsy protocol where multiple research biopsies are collected from metastatic samples and used for pathology, ER/PR/HER2, OncoPanel (a CLIA 300 gene sequencing panel), whole exome sequencing (WES), transcriptome sequencing (RNA-Seq), and single-cell RNA-seq (scRNA-seq). In some cases, tissue is used for cell line and xenograft generation. Archival primary biopsies are also obtained when possible for parallel genomic studies. Patients are followed and serial metastatic biopsies are obtained. This data will be used to determine the landscape of genomic alterations in treatment-resistant ER+ MBC, and compared to data generated by TCGA for treatment-naive ER+ primary breast cancer. Comparison of genomic studies from resistant, metastatic specimens with corresponding pre-treatment primary samples will allow us to identify genomic association with resistance to specific therapies. Analysis of the serial metastatic biopsies collected over the course of multiple treatments will also shed light on tumor evolution under selective therapeutic pressure.NoteA subset of the MBC blood biopsies that are included in our study can be accessed and downloaded from the phs001977 accession.Another subset of patients in this study participated in a clinical trial (NCT02871791) and have their data deposited in the current study as well.

  Study phs001285

• SCANDARE HNSCC 3' Tag RNA-seq

  SCANDARE (NCT03017573) is a multicentric biobanking study, enrolling adult patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC), triple negative breast cancer (TNBC), ovarian and cervical cancer. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Since its launch in 2017 at Institut Curie, SCANDARE has enabled the longitudinal collection and preservation of samples for in-depth analyses. Here, we describe molecular alterations in 264 FFPE samples at baseline from 90 HNSCC patients using 3'-tag RNA-seq technology, with FASTQ files deposited in the dataset.

  Dataset EGAD50000001655

• Comprehensive RNA repository of tissue and plasma from patients with esophageal cancer or precursor lesions

  A comprehensive RNA repository (both coding and non-coding) from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were collected. This dataset includes both mRNA and small RNA sequencing data (fastq.gz files) of all tissue and plasma samples. In total,102 RNA-seq libraries from 51 samples (17 plasma and 34 tissue samples) were sequenced (plasma mRNA libraries were sequenced twice).

  Dataset EGAD00001006857

• Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

  In this study, we describe a systematic analysis of pseudogene 'transcription' from an RNA-Seq resource of 293 samples, from 13 cancer and normal tissue types. We observed a highly prevalent, genome-wide expression of pseudogenes that could be categorized as universally expressed or lineage- and/or cancer-specific. We also explored disease subtype specificity and functions of selected expressed pseudogenes. We provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.

  Study phs000525

• Comparison of capture-based method for transcriptome profiling of formalin-fixed paraffin embedded tumor samples

  Background: The need for fresh frozen (FF) tissue limits implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. Methods: Transcriptomic analysis of 32 FFPE tumor samples from 11 patients was performed using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. Results: The Spearman's correlation coefficients between the global expression profiles of the three capture-based methods from FFPE and matched FF-TruSeq were high (rho = 0.72-0.9, p < 0.05). A significant correlation between the expression of key immune genes between individual capture-based methods and FF-TruSeq (rho = 0.76-0.88, p < 0.05) was observed. All exome capture-based methods reliably detected outlier expression of actionable genes, including ERBB2, MET, NTRK1, and PPARG. In urothelial cancer samples, the Agilent assay was associated with the highest molecular subtype concordance with FF-TruSeq (Cohen's k = 0.7, p < 0.01). Both Agilent and IDT detected all the clinically relevant fusions that were initially identified in FF-TruSeq. Conclusion: All exome capture-based methods had comparable performance and concordance with FF-TruSeq. By enabling the interrogation of FFPE tumor samples, our findings will enable the implementation of RNA-seq in the clinic to guide precision oncology approaches.

  Study EGAS00001005255

• Hereditary Gastric Cancer Syndromes: An Integrated Genomic and Clinicopathologic Study of the Predisposition to Gastric Cancer

  Gastric cancers are cancers of the stomach. Hereditary cancers are passed from parent to child. Researchers want to gather data about hereditary gastric cancers. Bulk RNA sequencing (RNA-seq) of signet ring cells (SRCs) and adjacent non-SRC epithelium (NEP) was performed on laser-capture microdissected (LCM) regions of interest found in risk-reducing total gastrectomy specimens from hereditary diffuse gastric cancer (HDGC) patients (Clinicaltrials.gov ID: NCT03030404). Twenty patients (6 male, 14 female) with confirmed HDGC were identified. Analysis of differentially expressed genes (DEGs) demonstrated upregulation of certain individual epithelial–mesenchymal transition (EMT) and proliferation genes. SRC regions had significant enrichment in pathways involved in T cell signaling. CIBERSORTx predicted significant increases in the presence of regulatory T cells (Tregs) specific to SRC regions.

  Study phs003422

• RNA-seq SE

  Transcriptomics of single-end RNA-seq data

  Study EGAS00001006521

• RNA-seq PE

  Transcriptomics of paired-end RNA-seq data

  Study EGAS00001006522

• OncoCis: Annotation of cis-regulatory mutations in cancer

  RNA-seq dataset used for the validation of CDK6 cis-regulatory mutation annotated by OncoCis. NB bam files for manuscript A_Proteomic_Chronology_of_Gene_Expression_through_the_Cell_Cycle_in_Human_Myeloid_Leukemia_Cells are now available at the following link:http://www.ebi.ac.uk/ena/data/view/ERP008483

  Dataset EGAD00001001019

• Single-cell RNA-seq data from metastatic ovarian cancer for quality control study

  This study includes treatment-naïve fresh tissue sample from 4 HGSOC patients.

  Dataset EGAD00001006984

• RNA-Seq on GeparSixto tissue samples

  RNA-Seq on GeparSixto tissue samples

  Study EGAS00001007124

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence

  ChIP-seq for AR, FOXA1 and H3K27ac in primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment. RNA-seq expression data of primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment.

  Dataset EGAD00001008562

• RNA-Seq and small RNA-Seq of tuberous sclerosis complex cortical tubers and age-matched controls.

  This dataset contains both standard RNA-Seq and small RNA-Seq of TSC related cortical tubers and age matched cortical controls. For the standard RNA-Seq paired-end sequencing was carried out. Each sample was split across multiple lanes. For the files available here the multiple lanes have been merged together, resulting in one forward and one reverse .fastq file for each sample. Small RNA-Seq was carried out on the same samples that underwent standard RNA-Seq. Again paired-end sequencing was carried out. The files here are raw and will need to be undergo quality control and trimming.

  Dataset EGAD00001003444

• RNA-seq of lung neuroendocrine tumors

  RNA-seq of lung neuroendocrine tumors

  Study EGAS50000000058

• Single Cell Transcriptomic Analysis of Cellular Heterogeneity in Human Colorectal Tumours

  1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms.

  Dataset EGAD00001002727

• H3K27ac and RNA-seq data of neuroblastoma PDXs and/or primary tumors

  This study includes H3K27ac ChIP-seq and RNA-seq data of 6 neuroblastoma PDXs. It also contains RNA-seq data of 3 pairs of neuroblastoma tumors obtained at diagnosis and relapse. The MAP-GR-B25-NB-1 PDX was derived from the relapse of pair 1.

  Study EGAS00001002505

• CASCADE tumour transcriptome data

  RNA-Seq data from 20 fresh-frozen postmortem samples from three patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.

  Dataset EGAD00001009492

• The UC San Diego Chronic Lymphocytic Leukemia (CLL) Study

  The UC San Diego Chronic Lymphocytic Leukemia Study is designed to identify genetic, epigenetic, and transcriptional changes important for CLL. This data release consists of samples collected to 1) identify genomic changes associated with CLL progression using serially collected tumor samples; 2) characterize the transcriptional consequences of SF3B1 mutation through RNA-seq; and 3) characterize the expression profiles of ROR1+ vs. ROR1- tumors. The samples were collected from participants at the University of California, San Diego Moores Cancer Center and the data was generated at UC San Diego or in collaboration with the BC Cancer Agency Genome Sciences Centre.

  Study phs000767

• Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas

  Spitzoid melanoma is a specific morphologic variant of melanoma that most commonly affects children and adolescents and ranges on the spectrum of malignancy from low-grade to overtly malignant. These tumors are generally driven by fusions of ALK, RET, NTRK1/3, MET, ROS1 and BRAF. However, in approximately 50% of cases, no genetic driver has been established. Clinical whole genome and transcriptome sequencing (RNA-Seq) of a spitzoid tumor from an adolescent revealed a novel gene fusion of MAP3K8, encoding a serine−threonine kinase that activates MEK. The patient who had exhausted all other therapeutic options was treated with a MEK inhibitor and underwent a transient clinical response. We subsequently analyzed spitzoid tumors from 49 patients by RNA-Seq and found in-frame fusions or C-terminal truncations in 33% of cases. The fusion transcripts and truncated genes all contained MAP3K8 exons 1-8 but lacked the autoinhibitory final exon. Data mining of RNA-Seq from the Cancer Genome Atlas (TCGA) uncovered analogous MAP3K8 rearrangements in 1.5% of adult melanomas. Thus, MAP3K8 rearrangements - uncovered by comprehensive clinical sequencing of a single case - are the most common genetic event in spitzoid melanoma, are present in adult melanomas, and could be amenable to MEK inhibition.

  Study EGAS00001003430

• Resistance studies in Lung Cancer

  The purpose of the study was to compare gene expression profiles from a cohort of crizotinib-resistant ALK-rearranged lung tumors and a cohort of treatment-naive ALK-rearranged lung tumors. Expression profiles were generated by RNA-seq. In parallel, gene expression profiles were obtained from ALK-rearranged lung cancer cell lines in the presence or absence of the ALK inhibitor TAE684. Gene expression profiles were also obtained from ALK-rearranged cells ectopically expressing genes associated with ALK inhibitor resistance that were identified from a functional genetic study.

  Study phs000855

• Comprehensive peripheral blood immunoprofiling reveals five immunotypes with immunotherapy response characteristics in cancer patients

  The lack of comprehensive diagnostics and consensus analytical models for evaluating the status of a patient’s immune system has hindered a wider adoption of immunoprofiling for treatment monitoring and response prediction in cancer patients. To address this unmet need, we developed an immunoprofiling platform that uses multiparameter flow cytometry and RNA-seq to characterize immune cell heterogeneity in the peripheral blood of healthy donors and patients with advanced cancers. Using unsupervised clustering, we identified five immunotypes with unique distributions of different cell types, and gene expression profiles.

  Study EGAS50000000286

• Gene signature for predicting homologous recombination deficiency in triple-negative breast cancer

  We developed a gene expression-based classifier for homologous recombination deficiency (HRD) in breast cancer patients using WES and RNA-seq data obtained from 94 TNBC samples from a Malaysian hospital-based cohort (MyBrCa). This classifier was able to predict for high levels of a mutational signature associated with HRD in an additional MyBrCa TNBC validation cohort (this EGA study) as well as in TNBCs from TCGA. We also validated the classifier on a NanoString platform with both fresh frozen and FFPE tissue.

  Study EGAS00001006518

• Genomic and Transcriptomic Profiling of Patients with Malignant Pleural and Peritoneal Mesothelioma: The NCI Cohort

  Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. Better understanding of mesothelioma genomics and transcriptomics could advance novel therapies. We performed whole-exome sequencing (WXS) of germline and tumors of 122 patients, and RNA-sequencing (RNA-Seq) of tumor samples of 100 patients with pleural, peritoneal, and tunica-vaginalis mesothelioma.The biospecimens used in this study were collected as a part of the Mesothelioma Natural History Protocol (https://clinicaltrials.gov/ct2/show/NCT01950572), wherein, samples were collected from subjects with malignant mesothelioma as listed in the eligibility criteria below and written consent from each participant was obtained before sample acquisition.

  Study phs002207

• RNA sequencing data from glioblastoma primary cell lines treated with indisulam

  This study aimed to develop NovumRNA, a bioinformatics pipeline designed to predict non-canonical tumor-specific antigens (ncTSAs) from human tumor RNA-sequencing data, potentially broadening the target pool for cancer neo-epitope-based immunotherapies. The splicing-modulating drug indisulam was investigated for its potential to induce aberrant transcriptomes, potentially increasing ncTSAs, subsequently predicted by NovumRNA. Four glioblastoma primary cell lines were derived from patient Cavitron Ultrasonic Aspirator (CUSA) material, cultured as neurospheres, and treated with indisulam or vehicle control. RNA was extracted at 6 and 16 hours post-treatment and sequenced using the NovaSeq platform. The resulting RNA-seq data was analyzed with NovumRNA, using healthy brain GTEx samples as controls, to identify and validate ncTSAs induced by indisulam treatment. NovumRNA is available at: https://github.com/ComputationalBiomedicineGroup/NovumRNA.

  Study EGAS50000000680

• June 2016 data update for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  June 2016 data update (bam/fastq for CEMT0062, CEMT0068, CEMT0072, CEMT0086, CEMT0087 ChIP-Seq and RNA-Seq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001002239

• Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

  This dataset comprises FASTQ files for single-cell RNA-seq and single-cell ATAC-seq data. These data were generated using 10x Genomics' multiome kit. In this cohort, there are 25 samples from 17 human cancer patients.

  Dataset EGAD00001015782

• Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome

  To evaluate the potential of an integrated clinical test to detect diverse classes of somatic and germline mutations relevant to pediatric oncology, we performed three-platform whole-genome (WGS), whole exome (WES) and transcriptome (RNA-Seq) sequencing of tumors and normal tissue from 78 pediatric cancer patients in a CLIA-certified, CAP-accredited laboratory. Our analysis pipeline achieves high accuracy by cross-validating variants between sequencing types, thereby removing the need for confirmatory testing, and facilitates comprehensive reporting in a clinically-relevant timeframe. Three-platform sequencing has a positive predictive value of 97-99%, 99% and 91% for somatic SNVs, indels and structural variations, respectively, based on independent experimental verification of 15,225 variants. We report 240 pathogenic variants across all cases, including 84 of 86 known from previous diagnostic testing (98% sensitivity). Combined WES and RNA-Seq, the current standard for precision oncology, achieved only 78% sensitivity. These results emphasize the critical need for incorporating WGS in pediatric oncology testing.

  Study EGAS00001002217

• Whole Genome Sequencing of HCC

  The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors using whole genome (WGS) and whole exome sequencing (WGS), integrated with DNA methylation and RNA sequencing (RNA-seq) data. The present series corresponds to 24 whole genome sequencing (12 Tumoral/Non-tumoral pairs). Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.

  Study EGAS00001002888

• Regulatory Changes in Glioblastoma Brain Tumors and Xenografts Wave 1

  Non-coding elements in our genomes that play critical roles in complex disease are frequently marked by highly unstable RNA species. Sequencing nascent RNAs attached to an actively transcribing RNA polymerase complex can identify unstable RNAs, including those templated from gene-distal enhancers (eRNAs). However, nascent RNA sequencing techniques remain challenging to apply in some cell lines and especially to intact tissues, limiting broad applications in fields such as cancer genomics and personalized medicine. Here we report the development of chromatin run-on and sequencing (ChRO-seq), a novel run-on technology that maps the location of RNA polymerase using virtually any frozen tissue sample, including samples with degraded RNA that are intractable to conventional RNA-seq. We used ChRO-seq to develop the first maps of nascent transcription in 23 human glioblastoma (GBM) brain tumors and patient derived xenografts. Remarkably, >90,000 distal enhancers discovered using the signature of eRNA biogenesis within primary GBMs closely resemble those found in the normal human brain, and diverge substantially from GBM cell models. Despite extensive overall similarity, 12% of enhancers in each GBM distinguish normal and malignant brain tissue. These enhancers drive regulatory programs similar to the developing nervous system and are enriched for transcription factor binding sites that specify a stem-like cell fate. These results demonstrate that GBMs largely retain the enhancer landscape associated with their tissue of origin, but selectively adopt regulatory programs that are responsible for driving stem-like cell properties. We also identified enhancers and their associated transcription factors that regulate genes characteristic of each known GBM subtype, and discovered a core group of transcription factors that control the expression of genes associated with clinical outcomes. This study uncovers new insights into the molecular etiology of GBM and introduces ChRO-seq which can now be used to map regulatory programs contributing to a variety of complex diseases.

  Study phs001646

• RNA-seq of PDAC patient-derived xenograft tumors

  This dataset contains single cell RNA-seq data of stromal cells derived from two PDX models (N = 2 in total) and bulk RNA-seq data of two PDX models treated with gemcitabine and our novel antibody-drug conjugate, C6-EBET (N = 59 in total). Bulk RNA-seq experiments were performed with Agilent SureSelect Strand Specific RNA Library Prep Kit (Agilent). Single cell RNA-seq experiments were performed with Chromium Single Cell 3' Reagent Kits v2 Chemistry (10x Genomics).

  Dataset EGAD00001010130

• Breast Cancer - immune clusters - RNA-seq

  In this study we use expression data from breast cancer tumors to define immune clusters in breast cancer. Immune clusters have gradual levels of immune infiltration. In the intermediate immune infiltration cluster, we found a worse prognosis which is independent of known clinicopathological features. We also found the immune clusters associated with treatment response. Further using gene expression data and deconvolution algorithms to dissect the immune contexture of the clusters.

  Dataset EGAD00001004985

• Whole exome sequencing of advanced gastric cancer

  To define the cellular characteristics of malignant ascites of advanced gastric cancer patients and search for therapeutic strategies, we obtained 5 malignant ascites and 1 cerebrospinal fluid from five patients with gastric cancer. We analyzed single-cell RNA-seq data of 180 cells from 4 malignant ascites and 1 cerebrospinal fluid metastasis using Fluidigm® C1™ System. Whole exome sequencing data was also generated from blood or tumor tissue.

  Dataset EGAD00001005740

• RNA-seq analysis of TGF-β-induced transcriptional changes in 19TT cancer-associated fibroblasts

  The dataset contains 6 samples, three biological replicates for vehicle-treated 19TT cells, and three biological replicates for TGF-β-treated 19TT cells. The dataset was generated by the next generation high throughput sequencing. Strand specific transcriptome library construction is completed by enriching mRNA from total RNA, sequenced by DNBSEQ high throughput platform.

  Dataset EGAD50000001350

• CRUK Accelerator: oesophageal adenocarcinoma whole exome and RNA-seq raw sequencing data

  Whole exome and RNASeq raw sequencing data for a cohort of 7 male patients with oesophageal adenocarcinoma. Median age at diagnosis was 68. Tumour tissue and PBMCs were used for whole exome sequencing and RNA sequencing. This data was generated as part of a study funded by a Cancer Research UK Centres Network Accelerator Award Grant (A21998).

  Dataset EGAD00001008489

• bulk RNA-seq of the 5 HCC patients which also have the single cell T cell RNA-seq data

  bulk RNA-seq data of the 5 HCC patinets. Single cell RNA seq data of these patients was under the accession number EGAD00001003337

  Dataset EGAD00001004148

• In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Dataset EGAD00001009688

• ovarian cancer sample RNA-seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to bulk RNA-sequencing on 17 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy. - Group C1, Epithelial Ovarian Cancer(EOC) patients with estrogen responsiveness : 6 samples - Group C2, Epithelial Ovarian Cancer(EOC) patients with estrogen non-responsiveness : 10 samples - non-classified 1-sample

  Dataset EGAD50000000613

• Metastases of a cancer of unknown primary (CUP)

  RNA seq analysis of 6 CUP metastases (each in triplicate), analysed by paired sequencing with NextSeq 500. Whole exome sequencing of 15 CUP metastases, analysed by paired sequencing with NextSeq 500.

  Dataset EGAD00001005963

• WCDT deep RNA-seq

  This dataset includes fastq files for total RNAseq of 104 patient biopsies with metastatic castration resistant prostate cancer. The RNAseq libraries were rRNA depleted and sequenced at 150bp paired-end on Illumina Novaseq.

  Dataset EGAD00001008799

• Comprehensive genomic characterization of early stage bladder cancer - Total RNA-seq data

  This study looks at the non muscle invasive bladder cancer subtypes based on totRNAseq data of 414 bladder cancer samples collected in different European centers within the UROMOL project. All samples were sequenced using paired reads on Illumina platforms. The reads are mapped to hg38.

  Study EGAS50000000512

• RNA-Seq dataset for Genomic rearrangements in Pediatric Cancer

  RNA-Seq data for systematic gene fusion detection in Pediatric Cancer

  Dataset EGAD00001008152

• Small-RNA sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

  Single-end 75 basepair small-RNA sequencing of 90 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. Samples were prepared using the NEXTFLEX® Small RNA-Seq Kit v3 (Bioo Scientific ). Samples were sequenced at the molecular genomics core (Peter MacCallum Cancer Centre) using 50bp single end sequencing on the Illumina NextSeq 500 (Illumina, USA). This dataset contains raw sequencing reads in FASTQ format.

  Dataset EGAD50000000501

• BLUEPRINT EpiVar RNA-seq for Naive naive CD4+ T-cells

  BLUEPRINT EpiVar RNA-seq for Naive naive CD4+ T-cells

  Study EGAS00001000752

• Single-cell RNA-seq, single-cell TCR-seq, single-cell ATAC-seq, and CITE-seq of human tonsillar CD4+ T cells

  To describe human tonsillar CD4+ T cells, especially IL10+ Foxp3- follicular CD4+ T cells (Tfr1, T follicular regulatory type 1), human tonsillar CD4+ T cells were analyzed with single-cell RNA-seq, single-cell TCR-seq, single-cell ATAC-seq, and CITE-seq.

  Study JGAS000805

• Single-cell RNA-seq, single-cell TCR-seq, single-cell BCR-seq, and CITE-seq of B and T cells

  To describe human tonsillar CD4+ T cells, especially IL10+ Foxp3- follicular CD4+ T cells (Tfr1, T follicular regulatory type 1), human tonsillar CD4+ T cells were analyzed with single-cell RNA-seq, single-cell TCR-seq, single-cell ATAC-seq, and CITE-seq.

  Study JGAS000827

• A Genomic Approach to Improved Diagnosis and Treatment of Neuroendocrine Tumors

  These are RNA-Seq samples from patients undergoing surgery for small bowel and pancreatic neuroendocrine tumors. Normal tissue, primary tumors, lymph nodes, and liver metastases were collected at surgery and stored in RNAlater until RNA extraction was carried out for RNA-Seq.

  Study phs001772

• Integrative Analysis for Multi-Omics Data in Non-Small-Cell Lung Cancer

  We conducted epigenetic and transcriptomic mapping of primary non-small cell lung tumors and non-neoplastic tissues. 20 non-neoplastic lung tissues and 18 non-small cell lung tumors were obtained from Biorepository and Tissue Technology Shared Resource at Moores Cancer Center, UC San Diego. All tumor samples were in pathological stages I and II. 8 pairs of samples were "matched", meaning that the tumor and normal tissues came from the same patient. Microfluidic oscillatory washing–based chromatin immunoprecipitation followed by sequencing (MOWChIP-seq) was used to profile the binding of H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3. SmartSeq-2 was used to map mRNA expression. We identified a large number of differentially modified regions for both epigenetic and transcriptomic markers between tumors and normal tissues. Deep learning model showed extensive transcription factor network rewiring. Raw sequencing data of the ChIP-seq and RNA-seq libraries are available through this dbGaP submission.

  Study phs003113

• Pooled Mutant KRAS-Targeted Long Peptide Vaccine Combined with Nivolumab and Ipilimumab for Patients with Resected MMR-p Colorectal and Pancreatic Cancer

  We developed INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach to combine molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4+ and CD8+ populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility. Data available through dbGaP include scRNA-seq with matched TCR-seq.

  Study phs003425

• RNA-Seq - Characterization of a Breast Patient-derived Tumor Organoid biobank from an underserved population of patients

  RNA-seq datasets of patient and patient-derived organoids

  Study EGAS50000000683

• van Hijfte GBM dataset 2022/A (single-nucleus RNA-seq)

  van Hijfte GBM dataset 2022/A (single-nucleus RNA-seq) 1x GBM

  Study EGAS00001006920

• Evaluation of triple negative breast cancer with heterogeneous immune infiltration

  This dataset contains the raw RNA-seq data (FASTQ files) of the samples used in the study title: "Evaluation of triple negative breast cancer with heterogeneous immune infiltration". The dataset is composed of 3 patients with 6 samples per patient (3 with high TILs and 3 with low TILs).

  Dataset EGAD00001010280

• Ribodepletion RNA-Seq of 8 samples and polyA RNA-Seq of 22 samples

  Ribodepletion RNA-Seq of 8 samples and polyA RNA-Seq of 22 samples

  Dataset EGAD00001004993

• March 2017 data update (bam/fastq) (containing H3K27ac for CEMT_87, RNA-Seq for CEMT_141, CEMT_142, CEMT_145, CEMT_146, H3K27me3, H3K9me3, H3K4me3, H3K4me1, ChIP-Seq Input for CEMT_88, CEMT_90 and CEMT_91) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2017 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003272

• Childhood Cancer Data Initiative (CCDI): NCI-COG Pediatric MATCH Precision Medicine Clinical Trial

  The National Cancer Institute-Children's Oncology Group (NCI-COG) Pediatric Molecular Analysis for Therapy Choice (MATCH) trial provides a framework for biomarker-driven early phase trials of targeted therapies in pediatric and young adult cancer patients across the United States. Pediatric MATCH enrolled more than 1,300 patients with treatment-refractory cancers, offering access to molecular screening and investigational targeted therapies. To further advance this, matched diagnostic, refractory tumor, and normal samples from Pediatric MATCH cases were molecularly characterized, creating one of the largest comprehensive data sets available for childhood cancers. This analysis has the potential to provide novel insights into the genetics of refractory pediatric, adolescent, and young adult cancers, as well as inform potential therapeutic strategies. The following molecular characterization assays were performed: Tumor whole exome sequencing (WES) Tumor whole genome sequencing (WGS) Tumor RNA sequencing (RNA-seq) Blood whole exome sequencing (WES) Blood whole genome sequencing (WGS)

  Study phs002883

• RNA-seq and scRNA/TCR-seq data for publication: "Pharmacological inhibition of nonsense-mediated mRNA decay enhances anti-tumour immunity"

  RNA-seq and scRNA/TCR-seq data from patient-derived fragments (PDFs) analysed in publication by R. Vendramin, H. Fu, S. Fernandez Patel, Y. Zhao et al.

  Study EGAS50000001208

• Genomic profiling of subcutaneous patient derived xenograft models of solid childhood cancer

  The pediatric cancer cohort in this study included 70 PDX models from 65 different individuals. This cohort included a total of 16 different pediatric solid tumor subtypes, including fourteen Wilms tumors, thirteen hepatoblastomas, thirteen osteosarcomas, ten germ cell tumors, four neuroblastomas, three clear cell sarcomas, two adrenal cortical carcinomas, two leydig cell tumors, two medulloblastomas, one embryonal rhabdomyosarcoma (ERMS), one Ewing sarcoma, one pleomorphic sarcoma, one adenocarcinoma, one glioblastoma, one mesothelioma and one ovarian tumor. Notably, we have five samples with multiple PDX models from same patient, including two cases with duplicates (564 and 564-Dup, 1796 and 1796-Dup), one case with two different metastasis (560-SM, 560-LM), one case with two blocks from same tumor (1939 and 1939-Dup), and one case with different primary tumor from same patient (2264 and 1932). We have a total of 353 sequencing data, including 82 RNA sequencing data (RNA-seq), 138 whole-exome sequencing (WES) and 135 low-pass whole-genome sequencing (WGS). For RNA-seq data, we have 61 PDXs and 21 PTs; for WES, we have 67 PDXs, 30 PTs and 40 matched normal germlines; for WGS, we have 64 PDXs, 30 PTs and 40 matched normal germlines. Of which, 19 PT-PDX paired RNA-seq, 28 paired PT-PDX paired WES and WGS were included.

  Dataset EGAD00001009863

• RNA-seq analysis of human primary keratinocytes and skin

  Bulk and single cell RNA-seq analysis of human keratinocyte and human skin

  Study EGAS00001002981

• Single-Cell RNA-Sequencing of Human Prostatectomy Tissue

  The tissue microenvironment in prostate cancer is profoundly altered. How prostate cancer cells and their precursors mediate those changes is unclear, in part due to the inability to longitudinally study the disease evolution in human tissues. To overcome this limitation, we performed extensive single-cell RNA-sequencing (scRNA-seq) to assess the transcriptional profiles of the tissue microenvironment in prostate tissues from prostatectomies from men diagnosed with prostate cancer. For each subject, benign-enriched and tumor-enriched tissues were collected from the peripheral zone of the prostate. Our studies of human tissues revealed that cancer cell-intrinsic activation of MYC signaling was the top up-regulated pathway in human cancers, representing a common denominator across the well-known molecular and pathological heterogeneity of human prostate cancer. Numerous non-malignant cell states in the tumor microenvironment (TME), including non-cancerous epithelial, immune, and fibroblast cell compartments, were conserved across individuals, suggesting that these cell types may be a sequelae of the convergent MYC activation in the cancer cells.

  Study phs003480

• Transcriptomic hallmarks and RNA isoform diversity in human neurodegenerative disease

  Single-cell RNA-sequencing (scRNA-seq) has enabled high-throughput RNA analysis at an unprecedented resolution. One staple analysis in scRNA-seq is identifying differentially expressed genes (DEGs) between two populations. However, the mRNA isoforms have often been overlooked in these transcriptomic analyses due to technical limitations. In order to investigate the mRNA isoforms at the single-cell level, we used a targeted single-nucleus long-read RNA-sequencing method combining single-nucleus short-read RNA-seq (snRNA-seq), target gene enrichment, and Iso-Seq. We performed snRNA-seq and targeted single-nucleus Iso-Seq (snIso-Seq) on 25 human frontal cortices from individuals with AD, DLB, or PD, and age-matched controls. Our short-read transcriptome analysis revealed that DLB samples had more overlapping DEGs with AD than PD despite sharing pathological hallmarks with PD. We observed vast RNA isoform diversity in the 50 genes targeted, including genes that were not differentially expressed in our short-read data. We also identified several novel isoforms that are not included in the reference annotation. Our data collectively characterize the transcriptome of various neurodegenerative diseases and illuminate the mRNA isoform diversity.

  Study EGAS50000000132

• RNA-seq analysis of human peri-implantitis samples

  Bulk RNA-seq analysis of human biopsy material collected from implant sites with peri-implantitis.

  Study EGAS50000000369