2919 results for "RNA AND sequencing OR transcriptome"

in 81.80 milliseconds.

• Natural variation of circulating RNAs in human serum

  Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In these studies, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed more than 10 billion Illumina reads from more than 500 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). Our results suggest that many circulating RNAs in serum can be potential biomarkers and they are associated with different traits including age, sex, smoking, body size etc.

  Study EGAS00001002814

• Spatial multi-omic map of human myocardial infarction

  We applied an integrative single-cell genomics strategy with single nucleus RNA sequencing (snRNA-seq) and single nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) together with spatial transcriptomics from the same tissue mapping human cardiac cells in homeostasis and after myocardial infarction (MI) at unprecedented spatial and molecular resolution. We profiled in total 31 samples from 23 patients including four non-transplanted donor hearts as controls and samples from tissues with necrotic tissue areas (ischemic zone, IZ), border zone (BZ), and the non-affected left ventricular myocardium (remote zone, RZ) of patients with acute MI.

  Dataset EGAD00001008952

• RNA seq of MPNST tumour samples

  RNA sequencing of 10 MPNST tumour samples as part of a larger study of MPNST. Article: Lyskjær et al, 2020, J Pathol, "H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours".

  Study EGAS00001004528

• Single cell sequences in patients with malignant tumors

  We perfomed single cell RNA and TCR sequencing of 2 lung adenocarcinoma patients and 3 head and neck squamous cell carcinoma to assess the detailed biological mechanisms of resistance to immune checkpoint inhibitors.

  Study JGAS000480

• RNA-seq following miR-130a overexpression (OE) in human CD34+cord blood cells

  We performed RNA-seq on CD34+ human cord blood (CB) cells transduced with Control or miR-130a OE lentiviruses to identify differentially expressed genes. Sorted CD34+ cells from 3 independent cord blood pools were transduced with lentiviruses containing mOrange (mO) reporter gene. mO+ cells were sorted 3 days post-transduction and RNA was harvested for library preparation and sequencing.

  Study EGAS00001005868

• Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

  The goal of the sequencing study was to determine the neoantigen profile of melanoma patients. We performed whole exome sequening of the tumor and respective patien matched PBMC samples (2x50nt) and RNA-sqeuencing of the tumor samples. The was analyzed for somatic point mutaions, using the RNA-Seq data to determine mutation expression. This study contains the exome seq data.

  Study EGAS00001003306

• Childhood Cancer Data Initiative (CCDI): Comprehensive Genomic Sequencing of Pediatric Cancer Cases (CMRI/KUCC)

  This study provides paired tumor normal genomic sequencing data from approximately 200 children with cancer, including both solid tumors and leukemias, done by the Children’s Mercy Research Institute (CMRI) and University of Kansas Cancer Center (KUCC). These data include whole genome sequencing (generally, ~20x), whole exome sequencing (generally, ~300x), bulk RNA sequencing (generally, ~80 million reads), and single-cell RNA and ATAC sequencing (>50,000 reads/cell). Additional phenotypic, pathologic, and genetic data, gathered clinically for these samples, are also provided.

  Study phs002529

• Multiregion Whole Exome and Smart-Seq3 single cell RNA sequencing of Breast Tumors

  Multiple regions were cut out of each tumor extracted form breast cancer patients and two experiments were run: - Whole exome sequencing on each of the regions plus an adjacent normal tissue sample - Smart-Seq3 Single cell RNA sequencing on EPCAM+ CD45- sorted cells from different tumor regions

  Study EGAS00001006851

• Sequencing Lymphoma

  This repository contains sequencing data to describe the genomic profiles of several B-cell lymphomas including follicular lymphoma and Hodgkin lymphoma. We have used several different high throughput sequencing technologies to interrogate genomic DNA and RNA from tumor cells obtained from lymph node biopsies and normal cells obtained from skin biopsies and peripheral blood mononuclear cells. A number of sequencing platforms for DNA, RNA, and protein were used to generate the data. These platforms include exome sequencing and a custom capture panel (NimbleGen) that targets 7.05 MB corresponding to the exons and splice sites of 1716 genes related to lymphoma biology (WUSM-LP). Other platforms include single-cell RNA-seq and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), which was used to describe transcriptional and proteomic changes in immune cell subsets within lymphoma patients pre- and post-therapy.

  Study phs001229

• Genetic architecture of microRNA expression and its link to complex diseases in the Japanese population

  We mapped microRNA expression quantitative trait loci by quantifying microRNA expression using small RNA sequencing.

  Study JGAS000504

• Kidney_tumour_DNA

  This is a bulk DNA and RNA sequencing study of human renal tumours

  Study EGAS00001002486

• Transcriptomic Profiles of Neoantigen-Reactive T Cells in Human Gastrointestinal Cancers

  This study explores the transcriptomic profiles of neoantigen-reactive tumor-infiltrating lymphocytes (TILs) from human bile duct and pancreatic cancer. The submitted data are bulk tumor RNA-Seq, tumor and germline whole-exome sequencing from 10 patients, and single cell RNA-Seq data from TIL of 5 of these patients.

  Study phs002765

• Genomic Analysis of Follicular Lymphoma

  We included tumors from newly diagnosed or untreated follicular lymphoma in this study. Samples consented to the University of Iowa and Mayo Clinic Lymphoma Specialized Program of Research Excellence (SPORE) were included for data sharing. RNA was extracted from 1) CD19 sorted B cells from tumor cell suspension frozen in dimethyl sulfoxide (DMSO; RNA Tumor B Cell, n=77), 2) tumor cell suspensions frozen in DMSO (RNA Tumor DMSO, n=78), and 3) tumor tissue sections frozen in optimal cutting temperature compound (OCT; RNA Tumor OCT, n=53). For RNA sequencing, library preparation was done using the Illumina TruSeq RNA Exome Kit and sequenced with 100 nucleotide paired-end reads using the HiSeq 4000. DNA was extracted from 1) tumor cell suspensions frozen in DMSO (DNA Tumor DMSO, n=78), 2) tumor tissue sections frozen in OCT (DNA Tumor OCT, n=33), and 3) germline DNA from peripheral blood (n=102) and from normal tissue adjacent tumor (n=9). For whole exome sequencing (WES), library preparation was done using the Agilent SureSelect XT kit and sequenced with 100 nucleotide paired-end reads using the Illumina HiSeq 4000.

  Study phs002989

• An integrated molecular study of 20 hepatoblastoma pairs using whole genome sequencing and RNA sequencing

  Hepatoblastoma is an uncommon malignant liver cancer occurring in infants and children. The mutant background of hepatoblastoma has not been fully demonstrated. The aim of this study is to genomically depict the mutational landscape of hepatoblastoma through an integrative analysis of whole genome sequencing and RNA sequencing of 20 hepatoblastomas from Chinese individuals.

  Study EGAS00001002772

• Whole Exome Sequencing of Localized Prostate Cancer Patients

  We performed whole-exome sequencing on localized prostate cancer patients to validate tumor content as part of a single-cell RNA sequencing study of localized prostate cancer patients.

  Study EGAS00001005685

• Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a METABRIC patient sample

  Fusion transcripts and their exact breakpoints were identified in RNA-seq data (30X) of an ER-,HER2+ breast cancer. DNA-level breakpoints associated with the fusion events were determined by analyzing whole genome sequencing (WGS) data (30X) from the same donor. The RNA-seq and WGS data for this case were generated on the Illumina platform using standard protocols. The patient (MB-0152) derives from the METABRIC cohort for which array based copy number and gene expression data were previously described (EGAS00000000083).

  Study EGAS00001002475

• Combined – whole blood and skin fibroblasts - transcriptomic analysis in Psoriatic arthritis.

  Whole blood RNA sequencing was performed longitudinally in 27 subjects with PsA at the beginning, one month and six months after treatment and response to therapy was defined at 6 months. As control groups 7 healthy individuals and 9 subjects with rheumatoid arthritis were recruited combined with public RNA-sequencing datasets from patients with psoriasis and systemic lupus erythematous. Differential expression analysis and weighted gene co-expression network analysis were performed to identify gene expression signatures, while deconvolution and flow cytometry to characterize the peripheral blood immune cell profile. RNA sequencing of skin fibroblasts was performed in a subset of affected (n=3) and healthy individuals (n=3) combined with CellChat to identify the blood-skin fibroblasts interaction network.

  Study EGAS00001006288

• Mutational Landscape of Plasmablastic Lymphoma

  Plasmablastic lymphoma (PBL) represents a clinically heterogeneous subtype of aggressive B-cell non-Hodgkin lymphoma. Although targeted sequencing studies and a single center whole exome sequencing (WES) study in HIV+ patients recently revealed several genes, associated with PBL pathogenesis, the global mutational landscape and transcriptional profile of PBL remain elusive. To inform on disease-associated mutational drivers, mutational patterns and perturbed pathways in HIV+ and HIV- PBL we performed WES and RNA-sequencing (RNA-seq) of 34 PBL tumors.

  Study EGAS00001004906

• 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

• Transcriptome Changes in ASD (NRXN1α+/-) iPSC-derived neurons

  NRXN1 deletions are identified as one of major rare risk factors for autism spectrum disorder (ASD) and other neurodevelopmental disorders. ASD has 30% co-morbidity with epilepsy and the latter is associated with excessive neuronal firing. NRXN1 encodes hundreds of presynaptic neuro-adhesion proteins categorized as NRXN1α/β/γ. Previous studies on cultured cells show that the short NRXN1β primarily exerts excitation effect, whereas the long NRXN1α which is more commonly deleted in patients involves in both excitation and inhibition. However, patient-derived models are essential for understanding functional consequences of NRXN1α deletions in human neurons Quantitative RNA sequencing was performed by BGI using 50bp single-end strategy with BGI-SEQ500 sequencing device on iPSC-derived cortical neurons from 6 control lines; (2VC1, 3VCX1, 3VC2, 4C3, 4CX1, NCRM-1) of 4 healthy donors, and 4 NRXN1α+/- lines; (ND1C1, ND2C11, ND2CX1, ND4-1C2) from 3 ASD patients.

  Study EGAS00001005536

• RNA-seq study of human long-term and short-term hematopoietic stem cells from umblical cord blood with lentiviral overexpression of S1PR3

  To investigate the molecular and biological pathways altered by S1PR3OE in human hematopoietic stem cells (HSC), we performed RNA-sequencing (RNA-seq) of LT- and ST-HSC 3 days after transduction with control or S1PR3 overexpression (OE) lentiviral vectors. LT-HSC and ST-HSC from 3 pool of CB lin- were FACS-purified, cells were prestimulated for 4 hours and transduced with lentiviral vectors. At day 3, 2000-5300 BFP+ cells were FACS-purified for RNA isolation with a PicoPure kit. We were able to isolate only 1600-1800 BFP+ cells from LT-HSC control samples as opposed to 4000-5400 BFP+ cells from S1PR3OE samples. Thus, we pooled all control BFP+ LT-HSC cells into one sample for RNA-seq analysis. BFP- LT-HSC from control vector transduction were purified from CB1 as an additional LT-HSC control. Nextera libraries generated from 10 ng RNA from 5 LT-HSC samples (2 controls, 3 S1PR3OE) and 6 ST-HSC samples (3 controls, 3 S1PR3OE) were subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Center for Applied Genomics, Sick Kids Hospital.

  Study EGAS00001004798

• Blood neutrophils in COPD derive from activated progenitors in the bone marrow

  Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

  Dataset EGAD00001008788

• Blood neutrophils in COPD derive from activated progenitors in the bone marrow sc Seqwell

  Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

  Dataset EGAD00001008908

• Blood neutrophils in COPD derive from activated progenitors in the bone marrow sc Rhapsody

  Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

  Dataset EGAD00001009704

• Spatiotemporal immune atlas of the first clinical-grade gene-edited pig-to-human kidney xenotransplant

  Pig-to-human xenotransplantation is rapidly approaching the clinical arena; however, it is unclear which immunomodulatory regimens will effectively control human immune responses to pig xenografts. We transplanted a gene-edited pig kidney into a brain-dead human recipient on pharmacologic immunosuppression and studied the human immune response to the xenograft using spatial transcriptomics and single-cell RNA sequencing. Human immune cells were uncommon in the porcine kidney cortex early after xenotransplantation and consisted of primarily myeloid cells. Both the porcine resident macrophages and human infiltrating macrophages expressed genes consistent with an alternatively activated, anti-inflammatory phenotype. No significant infiltration of human B or T cells into the porcine kidney xenograft was detected. Altogether, these findings provide proof of concept that conventional pharmacologic immunosuppression is sufficient to restrict infiltration of human immune cells into the xenograft early after compatible pig-to-human kidney xenotransplantation.

  Dataset EGAD50000000359

• Longitudinal single-cell transcriptomic study in patient-derived xenografts of pediatric T-ALL

  In this study, we conducted single cell full length total RNA sequencing (VASA-seq) on 13 matched pediatric T-ALL PDX samples at initial diagnosis and relapse, along with 5 non-relapsing PDX samples collected at initial diagnosis. We identified a subpopulation of T-ALL cells with stem-like cell features that expands substantially at relapse indicating resistance to first-line therapy. Chemotherapy resistance was further validated through functional testing: Two samples were subjected to in-vitro drug testing, treated with Cytarabine for three days, followed by single-cell transcriptomic analysis using 10x Genomics. Additionally, in-vivo drug testing was conducted on one sample, involving re-engraftment into mice and treatment with a combination of Vincristine, Doxorubicin, and Dexamethasone. Single-cell transcriptomic analysis using 10x Genomics was performed after 0, 15 and 30 days of treatment.

  Dataset EGAD50000000831

• Brain tumor sequencing data

  This study contains tumor DNA (with matched normal) for 1 medulloblastoma and 1 ependymoma patient. Tumor RNA sequencing data is also present for the medulloblastoma patient

  Study EGAS00001006352

• RNA-seq following miR-130a knock-down (KD) in Flag-tag AML1-ETO Kasumi-1 cells

  We performed RNA-seq on Flag-tag AML1-ETO Kasumi-1 cells transduced with Control or miR-130a KD lentiviruses to identify differentially expressed genes. Kasumi-1 cells were transduced in 3 independent replicates for control and miR-130a KD samples with lentiviruses containing GFP reporter gene. GFP+ cells were sorted 3 days post-transduction and RNA was harvested for library preparation and sequencing.

  Study EGAS00001005866

• Gene Fusion Discovery through RNA Sequencing of Human Glioblastoma Stem Cell Lines

  We used massively parallel, paired-end sequencing of expressed transcripts (RNA-seq) to detect novel gene fusions in short-term cultures of glioma stem-like cells freshly isolated from nine patients carrying primary glioblastoma multiforme (GBM). The culture of primary GBM tumors under serum-free conditions selects cells that retain phenotypes and genotypes closely mirroring primary tumor profiles as compared to serum-cultured glioma cell lines that have largely lost their developmental identities.

  Study phs000505

• Spinocerebellar ataxia type 3 RNA-sequencing study

  RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

  Study EGAS00001004241

• Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer

  We generated a collection of patient-derived pancreatic normal and cancer organoids. We performed whole genome sequencing, targeted exome sequencing, and RNA sequencing on organoids as well as matched tumor and normal tissue if available. This dataset is a valuable resource for pancreas cancer researchers, and those looking to compare primary tissue to organoid culture. In our linked publication, we show that pancreatic cancer organoids recapitulate the mutational spectrum of pancreatic cancer. Furthermore, RNA sequencing of organoids demonstrates the presence of both transcriptional subtypes of pancreas cancer.

  Study phs001611

• Whole genome and RNAseq analysis of pediatric osteosarcoma

  Integrative analysis whole genome sequencing and RNA-seq in pediatric osteosarcoma primary tumors and patient derived tumor xenografts.

  Study EGAS00001003201

• RNA seq before and after cold pressor test

  The cold pressor test (CPT) is a widely used pain provocation test to investigate both pain tolerance and cardiovascular responses. Twenty-two females were phenotypically assessed before and after a CPT, and blood samples were taken for RNA-sequencing.

  Study EGAS00001006690

• Nasopharyngeal RNASeq Comparing SARS-CoV-2+ Patients and SARS-CoV-2 Negative Control Subjects

  The goal of this analysis was to compare RNAs enriched in the upper respiratory tract of SARS-CoV-2 patients and SARS-CoV-2 negative controls. RNA-sequencing of RNA isolated from the viral transport medium associated with nasopharyngeal swab samples from SARS-CoV-2+ patients and SARS-COV-2 negative controls.

  Study phs002433

• RNA-Seq of Whole Blood from Patients with Intracranial Aneurysms

  Rupture of intracranial aneurysms (IAs) causes intracranial hemorrhaging that leads to high rates of neurological deficits and death. Although rupture rates are low, clinicians must decide whether to treat or monitor these potentially dangerous lesions. In the current clinical practice, the most common metric to measure risk of rupture is aneurysm size. However, clinical data show that small aneurysms can also rupture. As a result, alternative clinical stratification scores have been proposed, including the PHASES (Population, Hypertension, Age, Size, Earlier subarachnoid hemorrhage, and Site) score based on patient demographics and IA characteristics to stratify ruptured and unruptured IAs, and the Rupture Resemblance Score (RRS) that stratifies ruptured and unruptured IAs based on hemodynamic and morphological properties. However, all metrics require imaging on digital subtraction angiography (DSA), which is invasive, expensive, requires the use of X-rays, and is associated with transient or permanent neurological and non-neurological complications. We hypothesize that individuals with dangerous IAs have detectable gene expression differences in their blood that could be used as biomarkers to determine rupture risk. We propose to use whole blood transcriptomes to develop a "one-stop" diagnostic test that can detect the presence of IAs and determine the risk of rupture based on circulating RNA expression biomarkers using our prototype AneuScreenTM platform. We aim to develop and validate biomarkers to predict risk, as calculated by the currently-used metric of aneurysm size, the clinical PHASES score, and the RRS. Here, we collected blood samples from consented individuals who were receiving cerebral imaging at the Gates Vascular Institute (Buffalo, NY) for intracranial aneurysm. RNA extracted from blood samples (n=43) was subjected to RNA-sequencing and added to our existing database (n=44). When combined with our previous data, we had transcriptome data from 68 aneurysms (after additional sample filtering). This dataset was stratified into low- and high-risk according to IA size, PHASES score, and RRS score. Differentially expressed genes were identified and used to construct predictive models. Fastq files and basic demographic information for the 43 newly-sequenced intracranial aneurysm samples on this project will be available through dbGaP.

  Study phs003072

• WGS analysis of a glioma initiating cell line

  We here obtained whole-genome sequencing data to analyze transcription factor binding sequences and somatic mutations found in our RNA-seq analysis of glioma initiating cells.

  Study JGAS000096

• Sequencing data for CLL patients

  Single-cell RNA-sequencing and other genome-wide approaches were applied to a cohort of CLL patients receiving Venetoclax treatment to study mechanisms of resistance.

  Study EGAS00001005815

• 10x dataset of an obese human subject

  Biopsies from visceral adipose tissue from the omental depot (OAT) were obtained from an obese individual with participant informed consent obtained after the nature and possible consequences of the studies were explained under protocols approved by the Institutional Review Boards of the Perelman School of Medicine at the University of Pennsylvania, the Children’s Hospital of Philadelphia, or the Tel Aviv Sourasky Medical Center. The obese donor underwent bariatric surgery, the lean donor underwent cholecystectomy. OAT samples were placed in 1 mL of DMEM, and finely minced under sterile conditions before digestion in 50 mL of DMEM with 3 mg/1 mL collagenase IV (Gibco). Samples were incubated at 37°C in a rotating oven for 20-60 min. Adipocyte and stromal vascular fractions (SVF) were separated by centrifugation, and red blood cells (RBCs) were removed from the SVF by histopaque gradient (Sigma). Single-cell RNA-sequencing libraries were prepared using the Chromium platform (10x genomics), and sequenced on the MiSeq 500 or HiSeq 2500 Sequencing System (Illumina).

  Dataset EGAD00001005101

• MARS-seq dataset of five obese human subjects and a lean human subject

  Biopsies from visceral adipose tissue from the omental depot (OAT) were obtained from five obese individuals and one lean donor with participant informed consent obtained after the nature and possible consequences of the studies were explained under protocols approved by the Institutional Review Boards of the Perelman School of Medicine at the University of Pennsylvania, the Children’s Hospital of Philadelphia, or the Tel Aviv Sourasky Medical Center. The obese donors underwent bariatric surgery, the lean donor underwent cholecystectomy. OAT samples were placed in 1 mL of DMEM, and finely minced under sterile conditions before digestion in 50 mL of DMEM with 3 mg/1 mL collagenase IV (Gibco). Samples were incubated at 37°C in a rotating oven for 20-60 min. Adipocyte and stromal vascular fractions (SVF) were separated by centrifugation, and red blood cells (RBCs) were removed from the SVF by histopaque gradient (Sigma). Single-cell RNA-sequencing libraries were prepared using the MARS-seq pipeline, and sequenced on the MiSeq 500 or HiSeq 2500 Sequencing System (Illumina).

  Dataset EGAD00001005100

• Dataset for urologic_cancer-RNA

  Rare cancer sequencing data of 75 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008851

• Pediatric Patient-Derived-Xenograft development in MAPPYACTS – international pediatric cancer precision medicine trial in relapsed and refractory tumors

  Pediatric patients with recurrent and refractory cancers are in most need for new treatments. This study developed patient-derived-xenograft (PDX) models within the European MAPPYACTS cancer precision medicine trial (NCT02613962). To date, 131 PDX models were established following heterotopical and/or orthotopical implantation in immunocompromised mice: 76 sarcomas, 25 other solid tumors, 12 central nervous system tumors, 15 acute leukemias, and 3 lymphomas. PDX establishment rate was 43%. Histology, whole exome and RNA sequencing revealed a high concordance with the primary patient’s tumor profile, human leukocyte-antigen characteristics and specific metabolic pathway signatures. A detailed patient molecular characterization, including specific mutations prioritized in the clinical molecular tumor boards are provided. Ninety models were shared with the IMI2 ITCC Paediatric Preclinical Proof-of-concept Platform (IMI2 ITCC-P4) for further exploitation. This new PDX biobank of unique recurrent childhood cancers provides an essential support for basic and translational research and new treatments development in advanced pediatric malignancies.

  Dataset EGAD00001011048

• Verification of BCR reconstruction from single-cell RNA-seq using BraCeR

  This dataset was made to verify the computational reconstruction of B cell reseptors from single-cell RNA-seq using BraCeR. The dataset contains BCR-derived reads from single-cell RNA-seq from 13 cells using the Smart-seq2 protocol, as well as targeted BCR-sequencing data from the same cells.

  Dataset EGAD00001004199

• RNA-Seq Pair End

  RNA analysis of two patients 11 and 15 with WGS done on Illumina HiSeq2000. For research purpose and authorised user only.

  Dataset EGAD00001003429

• Preclinical Modeling of Leiomyosarcoma Identifies Susceptibility to Transcriptional CDK Inhibitors through Antagonism of E2F-Driven Oncogenic Gene Expression

  Leiomyosarcoma (LMS) is a smooth muscle-derived mesenchymal cancer commonly found to have recurrent loss of tumor suppressor genes and a poorly defined oncogenic program. Empiric cytotoxic chemotherapy is the standard systemic treatment for LMS, and while more targeted and effective therapies are urgently needed, insights into therapeutic vulnerabilities in LMS have been limited by available preclinical models. We generated a panel of LMS patient-derived xenograft (PDX) models and evaluated fidelity to their tumors of origin using RNA sequencing and ultra-low passage whole-genome sequencing (ULP-WGS). Data available at dbGaP include RNA sequencing and ULP-WGS of primary tumors and early and late passages of PDX. 

  Study phs002587

• Oesophageal adenocarcinoma scRNAseq from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains single-cell RNA-seq generated from the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19) and additional donors with Barrett's oesophagus using the 5' Single Cell Gene Expression assay from 10x Genomics. Samples were generated from oesophageal tumours, Barrett's oesophagus, and normal oesophagus and gastric tissues, with the aim of generating a reference atlas for cell types found in normal and disease-associated tissue states in the upper GI tract. This reference atlas was used as the basis for a deconvolution workflow to estimate the cell composition of bulk transcriptomes from these tissues, and to assess cell type-specific expression patterns of potential predictive biomarkers for immunochemotherapy regimens in this setting.

  Dataset EGAD00001009401

• ProstOmics - Spatial Transcriptomics

  Spatial transcriptomics data (ST) from 32 human prostate tissue samples originating from 8 prostate cancer patients (5 patients with post-surgery relapse). The ST data was acquired using the Visium Spatial Gene Expression kit which resulted in over 20 000 spatially defined spots for the 32 tissue samples. The raw transcriptomics data is RNA-seq. The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Each ST spot has metadata such as sample origin, histology class (stroma, normal epithelium, cancer of various grading etc), number of cells and estimated cell type fractions. Patient metadata include information of age at surgery, time (months) until reported relapse, total follow-up time, pre-surgery PSA, post-surgery T-stage and metastasis status.

  Dataset EGAD50000000603

• SPECTA Lung cancer RNA FASTQ files

  SPECTA Lung cancer RNA FASTQ files (Illumina TST170 targeted analysis)

  Dataset EGAD00001006222

• BPH Tissues for Cell Culture and Analysis - Spatial Transcriptomics Identifies Candidate Stromal Drivers of Benign Prostatic Hyperplasia

  The study goal was to apply spatial transcriptomics to identify candidate stromal drivers of benign prostatic hyperplasia (BPH). Laser microdissection (LCM) with RNA-seq of the stroma adjacent to hyperplastic and budding BPH ducts identified secreted factors including IGF1 and CXCL13. Single‐cell RNA sequencing (scRNA‐seq) revealed their co-expression from BPH fibroblasts. Additional studies sought to define similarities to embryonic prostate development, as well as therapeutic applications. Subjects were those who underwent prostatectomy for prostate or bladder cancer, with concurrent BPH, and who consented to use of surplus tissue for research studies. LCM/RNA-seq studies included 5 patients, and scRNA-seq studies included 1 patient. Phenotypic data submitted to this study include patient age, sex, prostate size, and international prostate symptom score (IPSS). Sequencing was done on an Illumina NovaSeq 6000 (LCM/RNAseq) and Illumina HiSeq X-Ten (scRNA-seq). The data processing pipeline utilized Kallisto (LCM/RNA-seq) and Cell Ranger (scRNA-seq). Data submitted are raw sequencing (Fastq) files.

  Study phs003477

• Understanding human fetal pancreas development using subpopulation sorting and RNA sequencing

  To decipher the populations of cells present in the human fetal pancreas and their lineage relationships, we developed strategies to isolate pancreatic progenitors, endocrine progenitors and endocrine cells. Transcriptome analysis of the individual populationsrevealed a large degree of conservation among vertebrates in the drivers of gene expression changes occurring at different steps of differentiation, althoughnotably, sometimes, different members of the same gene family are expressed. The transcriptome analysis establishes a resource to identify novel genes and pathways involved in human pancreas development. Single cell profiling further captured intermediate stages ofdifferentiation and enabled us to decipher the sequence of transcriptional events occurring during human endocrine differentiation. Furthermore, we evaluate how well individual pancreatic cells derived in vitro from human pluripotent stem cells mirror the natural processoccurring in human fetuses. This comparison uncovers a few differences at the progenitor steps, a convergence at the steps of endocrine induction and the current inability to fully resolve endocrine cell subtypes in vitro.

  Study EGAS00001003127

• Single-cell RNA sequencing on 5063 single T cells isolated from peripheral blood, tumour and adjacent normal tissues from six hepatocellular carcinoma patients.

  Single-cell RNA sequencing on 5063 single T cells isolated from peripheral blood, tumour and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional properties of these individual cells, coupled with the assembled T cell receptor (TCR) sequences, were used to delineate the molecular subtypes, lineage, and functional properties of each T cell group. For five HCC patient, the exome-seq data of matched normal/tumor and bulk RNA-seq data of tumor are also available.

  Study EGAS00001002072

• RNA-seq of Liver Cancer

  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 161 RNA-seq samples from tumors with matched WES or WGS. 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 EGAS00001002879

• Single cell RNA sequencing of CD19 CAR T-cell infusion products

  We performed single cell RNA sequencing of remnants from CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma. Libraries were prepared using 10X 5’ GEX chemistry and sequenced on an Illumina HiSeq 4000 to obtain >50,000 reads per cell.

  Study EGAS00001004576

• Oxford Nanopore RNA sequencing for HLA typing

  A targeted RNA-based method for typing of 12 classical HLA genes using Oxford Nanopore sequencing. In the method, were enriched HLA genes from cDNA of 50 individuals using gene-specific reverse primers. The library molecules were then barcoded, pooled into 2 separate gene pools, and sequenced on MinION R9.4 SpotON flow cells.

  Study EGAS00001004918

• Total RNA sequencing from the TNT trial (NCT00532727)

  Primary tumours from 186 TNT participants (13 matched recurrences) were profiled using total RNA-sequencing. Four transcriptional DDR-related and 25 immune-related signatures were evaluated. We assessed their association with objective-response-rate (ORR) and progression-free-survival (PFS) and performed conditional inference forest clustering to integrate multi-modal data.

  Study EGAS00001007398

• Pediatric HGG WES and RNA-Seq

  Paediatric high-grade glioma (pHGG) is the leading cause of paediatric brain tumour death. Here we performed RNA and whole exome sequencing on pHGG samples to analyse transcriptomic and genetic alterations associated with this devastating disease, and to understand the relationship between them.

  Study EGAS00001005687

• RNA-Seq Single End

  RNA analysis of six patients 34, 35, 36, 37, 38 and 39 with WGS done on Illumina HiSeq2500. For research purpose and authorised user only.

  Dataset EGAD00001003430

• Characterization of Macrophage-Tropic HIV Infection of Central Nervous System Cells and the Influence of Inflammation

  In this study, we utilize macrophage-tropic and T cell-tropic HIV-1 Env proteins to establish accurate infection profiles for multiple CNS cells under basal and interferon alpha (IFN-α) or lipopolysaccharide (LPS)-induced inflammatory states. We found that macrophage-tropic viruses confer entry advantages in primary myeloid cells, including monocyte-derived macrophages, microglia, and induced pluripotent stem cell (iPSC)-derived microglia. Following 24-h IFN-α or LPS treatments, total RNA was harvested from 100,000 to 200,000 cells using an RNeasy RNA isolation kit (Qiagen, 74004). RNA was quantified using a NanoDrop spectrophotometer and TapeStation electrophoresis prior to library preparation. cDNA libraries were prepared using the KAPA RNA HyperPrep kit (Roche, 08098115702). Paired-end RNA sequencing was performed on a NovaSeq S4 platform at a read length of 100 bp, resulting in approximately 60 million reads per sample.

  Study phs003306

• Whole Exome and RNA Sequencing of 22 Patient-Derived Xenografts from Estrogen Receptor-Positive Breast Cancers

  We performed RNA and whole exome sequencing on 22 patient-derived xenografts (PDX) from estrogen receptor-positive (ER+) breast cancers, in the presence and absence of estradiol (E2) supplementation. Exome coverage across more than 3,500 clinically relevant genes that previously were covered below 20X (~2.72Mb) was achieved. On average, 11.2Gb of unique sequence data were generated with 95.3% of the bases in the exome design covered to 20x read depth or greater. RNA sequencing was generated from xenograft tumors. Between 50 and 85M total reads were performed. The average strand-specificity and rRNA rate was 98% and 1.5%, respectively. Transcripts for 17,000 to 27,087 genes were detected in these samples.

  Study phs003324

• Wnt Activity Reveals Context-Dependent Genetic Effects on Gene Regulation in Neural Progenitors

  In this study we aimed to identify context-dependent regulatory functions of common genetic variation after stimulation of the canonical Wnt pathway. Fetal cortical tissue between 14 and 21 gestation weeks was subjected to RNA-Sequencing (242 samples) and ATAC-Sequencing (222 samples) to profile expression and chromatin accessibility, respectively. Considering donor genotypes, we were able to identify eQTLs, caQTLs, as well as response QTLs of both categories. The dataset provided here includes 242 RNA-sequencing files in bam format and 222 ATAC-sequencing files in bam format. We also provide 83 donor genotypes in VCF format (hg38).

  Study phs003642

• Very Low Tumor Mutation Burden Identifies Inflamed Recurrent Glioblastomas Responsive to Cancer Immunotherapy

  A subset of available tumors (with matched blood) from patients enrolled in a phase I clinical trial testing a recombinant poliovirus, published by Desjardins et al. NEJM 2018 (PMID:29943666), were analyzed by whole exome sequencing and RNA-seq. It was discovered that low tumor mutation burden correlated with survival outcome, and also discovered that low tumor mutation burden correlated with higher inflammatory gene signatures by RNA-seq.

  Study phs002270

• PEDS-PLAN - Pediatric Precision Laboratory Advanced Neuroblastoma Therapy

  A multi-center clinical trial for newly diagnosed high-risk neuroblastoma patients. Molecular tumor boards selected one of six targeted agents based on tumor-normal whole exome sequencing and tumor RNA sequencing data.

  Study phs002303

• Analysis of genomic alterations in dedifferentiated liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000182

• Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers

  Thyroid cancer is the most common endocrine malignancy. This dataset encompasses two types of thyroid cancer : anaplastic which is the most de-differentiated and aggressive one, and papillary which is the most common one. We profiled 14 patients, including 10 papillary and 4 anaplastic thyroid carcinomas, using both single nuclei RNA sequencing and spatial transcriptomics to link single cell resolution RNA sequencing with tissue morphology and better understand inter and intratumoral thyroid cancer heterogeneity.

  Study EGAS00001007574

• Genetic Effects on miRNA Expression During Mid-Gestation Neocortical Development

  In this study we aimed to find common genetic variants that influence miRNA expression during mid-gestation neocortical development. Small RNA-sequencing from 212 fetal cortical tissue samples between 14 and 21 weeks gestation were used to profile miRNA expression. Combined with donor genotypes, we were able to find miRNA-eQTLs during neocortical development. The dataset provided here includes 212 Small RNA-sequencing files in FASTQ format from cortical wall samples. Also provided here are 212 donor genotypes in PLINK format (hg19).

  Study phs003106

• GATA6 expression distinguishes classical and basal-like subtypes in advanced pancreatic cancer.

  PURPOSE: To determine the impact of basal-like and classical subtypes in advanced PDAC and to explore GATA6 expression as a surrogate biomarker. EXPERIMENTAL DESIGN: Within the COMPASS trial patients proceeding to chemotherapy for advanced PDAC undergo tumour biopsy for RNA sequencing. Overall response rate (ORR) and overall survival (OS) were stratified by subtypes and according to chemotherapy received. Correlation of GATA6 with the subtypes using gene expression profiling, in situ hybridization (ISH) were explored. RESULTS: Between December 2015-May 2019, 195 patients (95%) had enough tissue for RNA sequencing; 39 (20%) were classified as basal-like and 156 (80%) as classical. RECIST response data were available for 157 patients; 29 basal-like and 128 classical where the ORR was 10% vs. 33% respectively (p=0.02). In patients with basal-like tumours treated with modified FOLFIRINOX (mFFX) (n=22) the progression rate was 60% compared to 15% in classical PDAC (p= 0.0002). Median OS in the intention to treat population (n=195) was 9.3 months for classical vs. 5.9 months for basal-like PDAC (HR 0.47 95% CI 0.32-0.69, p=0.0001). GATA6 expression by RNAseq highly correlated with the classifier (p<0.001) and ISH predicted the subtypes with sensitivity of 89% and specificity of 83%. In a multivariable analysis, GATA6 expression was prognostic (p=0.02). In exploratory analyses, basal-like tumours, could be identified by keratin 5, were more hypoxic and enriched for a T cell inflamed gene expression signature. CONCLUSIONS: The basal-like subtype is chemoresistant and can be distinguished from classical PDAC by GATA6 expression.

  Dataset EGAD00001006081

• RNA, ATAC, ChIP datasets from Ankylosing Spondylitis patients and Healthy Controls

  This dataset consists of functional genomic data from 20 Ankylosing Spondylitis patients and 35 Healthy Controls taken from CD4+ T cells, CD8+ T cells and CD14 Monocytes. It contains 364 paired end fastq files consisting of 104 total RNA-seq samples and 116 ATAC samples, for ChIP there are 46 H3K4me3 samples, 46 H3K27ac samples and 3 H3K4me1 samples, along with 49 paired input samples. The samples were sequenced on Illumina HiSeq4000, Illumina NextSeq500 and Illumina NovaSeq 6000 platforms.

  Dataset EGAD00001008758

• Longitudinal single-cell transcriptomic study in patient-derived xenografts of pediatric T-ALL

  In this study, we conducted single cell full length total RNA sequencing (VASA-seq) on 13 matched pediatric T-ALL PDX samples at initial diagnosis and relapse, along with 5 non-relapsing PDX samples collected at initial diagnosis. We identified a subpopulation of T-ALL cells with stem-like cell features that expands substantially at relapse indicating resistance to first-line therapy. Chemotherapy resistance was further validated through functional testing: Two samples were subjected to in-vitro drug testing, treated with Cytarabine for three days, followed by single-cell transcriptomic analysis using 10x Genomics. Additionally, in-vivo drug testing was conducted on one sample, involving re-engraftment into mice and treatment with a combination of Vincristine, Doxorubicin, and Dexamethasone. Single-cell transcriptomic analysis using 10x Genomics was performed after 0, 15 and 30 days of treatment.

  Study EGAS50000000582

• raw RNA-seq data from patients infected with COVID-19 or influenza

  Dataset consists of fastq files from bulk RNA-seq done on peripheral blood acquired from two well characterised hospitalised cohorts, a cohort of patients infected with influenza and a cohort of patients infected with SARS-CoV-2 during the first wave of the pandemic and prior to availability of COVID-19 treatments and vaccines.

  Dataset EGAD00001008505

• Genentech Small Cell Lung Cancer (SCLC) Screen

  Exome capture, RNA-Seq, whole genome sequencing of set of Small Cell Lung Cancer samples.

  Study EGAS00001000334

• Tumor reactive γδ T cells contribute to a complete response to PD-1 blockade in a Merkel cell carcinoma patient

  Single cell RNA and TCR sequencing of gamma delta T cells from two Merkel cell carcinoma patients

  Study EGAS50000000102

• G-SAM: Transcriptional Evolution of Glioblastomas Treated With Standard of Care

  Collection of mostly matching primary and recurrent glioblastoma RNA-seq sample pairs, also matching with an earlier DNA sequencing study

  Study EGAS00001005436

• The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia

  Acute lymphoblastic leukaemia (ALL) is the most common childhood malignancy, and implementation of risk-adapted therapy has been instrumental in the dramatic improvements in clinical outcomes. A key to risk-adapted therapies includes the identification of genomic features of individual tumors, including chromosome number (for hyper- and hypodiploidy) and gene fusions, notably ETV6-RUNX1, TCF3-PBX1 and BCR-ABL1 in B-cell ALL (B-ALL). RNA-sequencing (RNA-seq) of large ALL cohorts has expanded the number of recurrent gene fusions recognized as drivers in ALL, and identification of these new entities will contribute to refining ALL risk stratification. We used RNA-seq on 126 ALL patients from our clinical service to test the utility of including RNA-seq in standard of care diagnostic pipelines to detect gene rearrangements and IKZF1 deletions. RNA-seq identified 86% of rearrangements detected by standard of care diagnostics. KMT2A-rearrangements (MLL), whilst usually identified, were the most commonly missed by RNA-seq as a result of low expression. RNA-seq identified rearrangements that were not detected by standard of care testing in nine patients. These were found in patients who were not classifiable using standard molecular assessment. We developed an approach to detect the commonest IKZF1 deletion from RNA-seq data and validated this using a RQ-PCR assay. We applied an expression classifier to identify Ph-like B-ALL patients. T-ALL proved a rich source of novel gene fusions which have clinical implications or provide insights into disease biology. Our experience shows that RNA-seq can be implemented within an individual clinical service to enhance the current molecular diagnostic risk classification of ALL.

  Study EGAS00001004212

• Combined PDCD1, BRAF and MAP2K7 Inhibition in BRAFV600E Colorectal Cancer: A Phase 2 Trial

  In this study, we evaluated the clinical efficacy of combined PDCD1, BRAF, and MAP2K7 inhibition in metastatic BRAFV600E Colorectal Cancer (CRC) patients (NCT03668431). We performed bulk whole exome sequencing (WXS) and bulk RNA sequencing (RNA-Seq) in 35 pre-treatment tumor biopsies and matching germline for tumor mutational burden (TMB), BM1/BM2 transcriptional subtypes, and consensus molecular subtypes (CMS) analysis, which were previously reported to affect prognosis and response to therapy (PMIDs: 32047001, 27354468, and 26457756). Analysis of bulk data showed that TMB, BM1/BM2 subtypes, and CMS did not correlate with clinical response in this study. Analysis of single cell RNA sequencing (scRNA-Seq) data of tumor epithelial cells from 23 paired day 0 and day 15 tumor biopsies revealed greater induction of tumor cell-intrinsic immune programs and more complete MAPK inhibition in patients with better clinical outcome.

  Study phs003178

• Adipocytes Regulate Fibroblast Function and Their Loss Contributes to Fibroblast Dysfunction in Inflammatory Diseases

  We profiled live synovial cells from 16 individuals with no diagnosed arthritis using single-cell RNA sequencing. Our study was designed to provide a reference single cell RNA sequencing dataset for researchers interested in studying arthritic synovium, providing sequencing data on healthy synovial cells for comparison to cells from diseased synovial tissues. Synovial tissue was collected post-mortem from three different sources between 2019-2021: the National Disease Research Interchange, a collaboration with Rush University and the Gift of Hope, and the Brigham and Women's Hospital Autopsy Department. To be included in the study, patients had to be between the ages of 18 to 72 and have no diagnosed arthritis or autoimmune diseases. Additionally, this study includes bulk RNA sequencing data of cultured primary synovial fibroblasts isolated from three rheumatoid arthritis patents. Cells were stimulated with either cortisol, fat conditioned media, TGFβ, TNFα, fat conditioned media with mifepristone, TGFβ with fat conditioned media, or TNFα with fat conditioned media. Cells were harvested 4 or 22 hours later and lysates collected for sequencing. Data from this study submitted to the Gene Expression Omnibus (GEO) may be accessed via accession number GSE233504.

  Study phs003304

• Profiling of childhood neuroblastoma and the immune microenvironment by single-cell sequencing of RNA and TCR

  Neuroblastoma tumor cells and their tumor microenvironment are studied by single-cell RNA sequencing of primary neuroblastoma tumors and neuroblastoma-infiltrated tissues/metastases. Both diagnostic samples, taken pre-treatment and samples taken after induction chemotherapy at surgical resection and biopsies from relapse samples are included.  For a number of patients single-cell RNA sequencing of blood samples (controls) are included and additionally we performed single-cell T cell receptor sequencing (TCR) on the tumor and blood samples. With this study, we will focus on identifying differences in tumor cells and their (immune) microenvironment 1) before and after treatment or at relapse and 2) between primary tumors and infiltrated tissues/metastases. Moreover, with TCR sequencing we aim to unveil immune cell dynamics in patients with neuroblastoma.

  Study EGAS00001006823

• Genome-Wide Characterization of Pancreatic Adenocarcinoma Patients Using Next Generation Sequencing

  In this study, we whole genome sequenced tumor/normal pairs from three pancreatic adenocarcinoma patients to separately characterize each patient with respect to somatic alterations. For 2 patients for whom tumor RNA was available, we also performed RNA sequencing to evaluate gene expression changes. While additional sequencing is needed to improve our understanding of the disease, the information acquired from this study contributes to our knowledge base on pancreatic cancer and helps to establish a foundation for identifying and developing more efficacious treatments for patients.

  Study phs000550

• Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2

  Single cell RNA sequencing (scRNA-seq) is widely used for profiling transcriptomes of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently-used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data by the two platforms from the same samples of CD45- cells, we systematically evaluated their features using a wide spectrum of analysis. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data better. For 10X-based data, we observed higher noise for mRNA in the low expression level. Despite the poly(A) enrichment, approximately 10-30% of all detected transcripts by both platforms were from non-coding genes, with lncRNA accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can better detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected different sets of differentially expressed genes between cell clusters, indicating the complementary nature of these technologies. Our comprehensive benchmark analysis offers the basis for selecting the optimal scRNA-seq strategy based on the objectives of each study.

  Dataset EGAD00001005448

• WXS and RNA-seq raw sequence data for TG project

  WXS sequence data from 112 samples, RNA-seq sequence data from 117 samples, all sequence data are raw sequence data in fastq format, sequenced by Illumina platform.

  Dataset EGAD00001007989

• Subclonal evolution of four ER+ breast cancers determined by WGS and scRNA-Seq

  We analyzed the subclonal evolution of four ER+ breast cancers over 2-15 years using whole-genome sequencing (WGS) and single-cell RNA-Seq (scRNA-Seq). For each patient we analyzed 2-6 cancer samples, generally metastatic pleural effusions or ascites, by WGS, along with germline DNA. Two of the samples per patient were selected for single-cell RNA-Seq.

  Study EGAS00001002436

• Count Me In (CMI): The Metastatic Prostate Cancer (MPC) Project (CMI-MPCproject)

  Count Me In - The Metastatic Prostate Cancer Project: A Patient-Driven Research Initiative to Accelerate Metastatic Prostate Cancer Research The Metastatic Prostate Cancer Project (MPCproject; http://mpcproject.org/) is a research study that empowers men with metastatic and advanced prostate cancer to partner directly with researchers by sharing their samples and clinical information, with the ultimate goal of accelerating scientific discoveries that have clinical impact. The MPCproject enables any man with metastatic or advanced prostate cancer in the US and Canada to participate in cutting-edge genomic and molecular research, regardless of where they live. Metastatic or advanced prostate cancer patients visit the project website and complete an online questionnaire of basic information about themselves and their cancer. Enrolled patients are mailed saliva and blood draw kits, which can be used to extract germline DNA and cell-free DNA (cfDNA), respectively. The study team contacts participants' healthcare institutions to obtain medical records and a portion of archived tumor samples. Whole exome sequencing is performed on tumor DNA, germline DNA, and cfDNA, and transcriptome sequencing is performed on tumor RNA. De-identified data, including linked genomic, clinical, and patient-reported data, are shared via public databases on a recurring pre-publication basis. Participants are regularly provided with updates on the study.

  Study phs001939

• RNA-seq of uncultured CD112high and CD112low long-term(LT) human hematopoietic stem cells (HSC) and cultured and lentiviral transduced (CTRL, INKA1-OE) LT- and short-term HSC from umbilical cord blood

  We performed RNA-sequencing to elucidate the biological pathways (1) altered by INKA1 overexpression in LT-HSC and ST-HSC that may contribute to the induced transient restraint in generating proliferative hematopoietic output in vivo and in vitro; and (2) that underlie the differential in vitro priming and regeneration phenotypes of CD112high and CD112low LT-HSC. Therefore, we prospectively isolated indicated subpopulations from 3 independent human umbilical cord blood pools and subjected them either to RNA-sequencing directly or following culture, lentiviral transduction and purification of the transduced cell fractions.

  Study EGAS00001004768

• DIPG RNA and exome sequencing

  DIPG is a paediatric high-grade glioma that diffusely infiltrates the brainstem and is the leading cause of paediatric brain tumour death. Here we performed RNA and whole exome sequencing on DIPG and control samples to analyse transcriptomic and genetic alterations associated with this devastating disease, and to understand the relationship between them.

  Study EGAS00001004749

• 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

• CD8+ Tumor-Infiltrating Lymphocyte Abundance is a Positive Prognostic Indicator in Nasopharyngeal Cancer

  This retrospective tissue study explores the prognostic significance of tumour-infiltrating lymphocyte (TIL) populations in NPC, using a combination of RNA sequencing and immunohistochemistry.

  Study EGAS00001006396

• ADCC Pilot RNAseq Study on Posterior Cingulate Astrocytes in Alzheimer's Disease

  In this study, RNA sequencing was performed on astrocytes microdissected from the posterior cingulate cortex of Alzheimer's disease subjects and healthy elderly controls.

  Study phs000745

• TCRseq

  T cell receptor sequencing of tumor samples. Briefly, DNAse I treated tumor RNA samples were subjected to library preparation using AmpliSeq Immune Repertoire Panel (Illumina) and sequenced using NextSeq500.

  Study EGAS50000000258

• Transcriptional Reference Map of Human Natural Killler Cells

  Here we performed single-cell RNA sequencing of both bulk NK and sorted NK subsets to establish a transcriptional reference map of human natural killer cells.

  Study EGAS50000000014

• Type I Interferon and Cycling Lymphocytes in Macrophage Activation Syndrome

  We performed immune profiling of peripheral blood mononuclear cells from patients with Still's disease and macrophage activation syndrome (MAS) using bulk RNA sequencing and single-cell RNA sequencing. Three groups were included in the study: healthy controls, patients with Still's disease without macrophage activation syndrome, and patients with Still's disease and macrophage activation syndrome. We found that macrophage activation syndrome is associated with transcriptomic signatures of interferon upregulation and cell cycling. We identified cycling lymphocytes within T cell and NK cell populations that are correlated with MAS disease activity. All sequencing data are available through dbGaP.

  Study phs003310

• Whole blood RNA sequencing of individuals from Nepal

  This study utilized blood samples collected in Lalitpur, Nepal as part of the Strategic Typhoid Alliance across Africa and Asia (STRATAA) study. The dataset comprises whole blood RNAseq of 376 febrile individuals from Nepal. Blood was collected in PAXgene tubes and sent to Monash University (Melbourne, Australia) where RNA was extracted using the PAXgene Blood RNA kit before being sent to the Wellcome Sanger Institute (Hinxton, UK) for sequencing. Library prep used NEBNext Ultra II RNA custom kits on an Agilent Bravo WS automation platform with poly(A) pulldown. After PCR, plates were purified using Agencourt AMPure XP SPRI beads and libraries were quantified using Biotium Accuclear Ultra high sensitivity dsDNA Quantitative kits. Pooled libraries were normalised to 2.8 nM. Samples were globin depleted using KAPA RNA HyperPrep with RiboErase. Libraries were then subjected to 2x100bp paired-end sequencing on Illumina NovaSeq. Each library was sequenced to an average of 80 million reads. The STRATAA study was approved by the Nepal Health Research Council (NHRC, ref 283 306/2015) and OxTREC (Oxford Tropical Research Ethics Committee, ref 39-15). All participants provided informed consent for human genetic tests.

  Dataset EGAD00001011131

• Genome-wide integrative analysis of pediatric pancreatoblastoma

  Pancreatoblastoma is the most common pancreatic malignancy of young children, but its molecular pathogenesis remains poorly understood. To understand the molecular pathogenesis of pancreatoblastoma, we comprehensively analysed the whole exome sequencing, RNA sequencing, SNP array, and methylation array data of pancreatoblastoma.

  Study JGAS000088

• Comprehensive molecular and clinicopathological profiling of desmoid tumors

  Previous studies have not clearly identified a prognostic factor for desmoid tumors (DT). Whole-exome sequencing and/or RNA sequencing were performed in 64 cases of DT to investigate the molecular profiles in combination with the clinicopathological characteristics.

  Study JGAS000270

• Illumina TSO500 RNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Illumina TSO500 RNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Dataset EGAD00001015397

• CMML Collection of WES, WGS, RNA-Seq and ERRBS data

  We first performed a comprehensive analysis of the genome of 66 chronic myelomonocytic leukemia cases using whole exome (N=49) or whole genome (N=17) sequencing for paired leukemic-control DNA. Then, we realized serial analysis of whole exome sequence in 17 cases, completed with serial RNA sequencing and DNA methylation analysis in 9 cases, including patients treated or not with hypomethylating agents.

  Study EGAS00001001264

• Whole Exome Sequencing of 60 tumor/normal matched liver Cancers (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 60 whole exome tumor/normal pairs with matched RNA-seq. 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 EGAS00001003063

• Identification of Recurrent SMO and BRAF Mutations in Ameloblastomas

  RNA-seq data from two cases of ameloblastoma was analyzed for candidate gene fusions and point mutations. Recurrent point mutations identified in the RNA-seq data, as well as mutations identified with limited panel targeted deep sequencing, were validated as somatic. Expanding to a larger cohort of 28, one of two activating mutations was found in 80% of cases. No recurrent gene fusions events were identified.

  Study phs000739

• RNAseq from blood CD34+ cells

  This dataset contains paired-end RNA sequencing data of blood CD34+ cells from random blood donors (155 paired-end FastQ files). The data were used to perform expression quantitative trait locus (eQTL) analysis.

  Dataset EGAD00001008194

• Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens

  Enriched tumor epithelium, tumor-associated stroma, and whole tissue were collected by laser microdissection from thin sections across spatially separated levels of ten high-grade serous ovarian carcinomas (HGSOCs) and analyzed by mass spectrometry, reverse phase protein arrays, and RNA sequencing. Unsupervised analyses of protein abundance data revealed independent clustering of an enriched stroma and enriched tumor epithelium, with whole tumor tissue clustering driven by overall tumor “purity.” Comparing these data to previously defined prognostic HGSOC molecular subtypes revealed protein and transcript expression from tumor epithelium correlated with the differentiated subtype, whereas stromal proteins (and transcripts) correlated with the mesenchymal subtype. Protein and transcript abundance in the tumor epithelium and stroma exhibited decreased correlation in samples collected just hundreds of microns apart. These data reveal substantial tumor microenvironment protein heterogeneity that directly bears on prognostic signatures, biomarker discovery, and cancer pathophysiology and underscore the need to enrich cellular subpopulations for expression profiling.

  Dataset EGAD00001008344

• The polarity and specificity of antiviral T lymphocyte responses determine susceptibility to SARS-CoV-2 infection in cancer patients and healthy individuals

  We monitored patient's anti SARS-CoV-2 immune responses using an in vitro cross presentation assay. The goal of this study was to identify immune correlates of clinical protection against SARS-CoV-2 infection. Briefly, peripheral blood mononuclear cells of patient were divided into a monocyte and lymphocyte. Monocyte were differentiated into monocyte derived dendritic (mo-DC)cells using GM-CSF and Interferon alpha. Mo-DC were then loaded with SARS-CoV-2 culture lysates , or VeroE86 lysates. SARS-CoV-2 loaded mo-DC were then used to stimulates their autologous lymphocytes and T cell cytokine secretion was monitored in the supernatant. We discriminated patients producing IL-2 and patients producing IL-5. RNA sequencing was performed for 18 patients, to identify gene profile associated with IL-2 or IL-5 production.

  Dataset EGAD00001008538

• Sequencing data for oesophageal and related samples - Ganguli et al (RNA)

  Data supporting: "TBC" Ganguli et al (RNA for 394 samples)

  Dataset EGAD00001011190

• RNA sequencing of Human Organoid Lines

  The study will use RNA sequencing to aid in benchmarking different culture conditions in a set of genetically annotated human organoid lines. The data will be used to assess whether there are any clonal differences introduced when culturing these lines in different conditions.

  Dataset EGAD00001007971