14970 results for "cancer studies using rna-seq"

in 28.19 milliseconds.

• RNAseq of pre- and post-5AZA-treated head and neck cancer patients refractory to anti-PD-1 therapy

  RNA sequencing (RNA-seq) was performed on baseline (before low-dose 5-aza treatment) and on-treatment (low-dose 5-aza treatment for 5 or 10 days) tumor samples from eight participants with head and neck cancer who were refractory to anti-PD-1 therapy. RNA library preparations, sequencing reactions, and initial bioinformatics analyses were conducted at GENEWIZ, LLC. In total, 16 150-bp pair-end RNAseq data were generated.

  Dataset EGAD50000001010

• Pulldown_cytosine_deaminases

  We are looking at the causal factors behind hyper-mutator phenotypes found in previous Breast Cancer sequencing studies.

  Study EGAS00001000233

• Gene Expression of Small Cell Carcinoma of the Ovary-Hypercalcemic Type (SCCOHT)

  Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer afflicting young women at a median age of 24 years. SCCOHTs are characterized by loss of protein expression of SWI/SNF chromatin remodeling ATPases SMARCA4 and SMARCA2 through mutation and epigenetic silencing, respectively. This study aims to establish gene expression profiles of this cancer through RNA-Seq of fourteen pathologically confirmed cases of SCCOHT tumors.

  Study phs001528

• Common Variant GWAS, Genetics & Epidemiology of Colorectal Cancer Consortium (GECCO)

  Genetics & Epidemiology of Colorectal Cancer Consortium (GECCO) is a collaborative effort which aims to accelerate the discovery of colorectal cancer-related variants by discovering, replicating and fine-mapping Genome Wide Association Study (GWAS) findings, conducting a meta-analysis of GWAS data, and investigating how genetic variants are modified by environmental risk factors. The coordinating center for this consortium is based at the Fred Hutchinson Cancer Research Center (Principal investigator: Ulrike Peters). The GECCO Consortium is utilized in the following dbGaP individual studies. To view genotypes, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001078 GECCO Consortium. phs000965 VITAL phs001056 DALS phs001077 WHI Colorectal Cancer phs001092 PMH CCFR phs001094 PLCO phs001104 ASTERISK phs001113 DACHS phs001114 HPFS phs001128 PHS phs001129 NHS phs001170 Colo2and3 phs001171MEC Colorectal Cancer

  Study phs001078

• Cell Type-Specific and Disease-Associated eQTL in the Human Lung

  This study was conducted to investigate the genetic control of gene expression in a cell-type and context-specific manner in the human lung. We performed single-cell RNA-sequencing (scRNA-seq) of lung tissue from 66 Interstitial Lung Disease (ILD) cases and 48 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types. The scRNA-seq data presented here include previously published (PMID 34262047) and unpublished samples. ILD tissue samples were obtained from lungs removed at the time of lung transplantation at either Vanderbilt University Medical Center (VUMC) or the Norton Thoracic Institute (NTI). Control tissue samples were obtained from lungs declined for organ donation either at the Donor Network of Arizona (DNA) or VUMC. The self-reported ethnicities of donors were 66.7% European, 9.6% African American, 17.5% not available (N/A), and 6.1% other. The smoking history includes 46.5% ever smoker, 29.8% never smoker, 23.7% N/A. For genotyping, flash-frozen tissue in DNA/RNA shield was homogenized via a bullet blender. Genomic DNA was extracted using Zymo Quick DNA/RNA microprep plus kit. Library preparation and low-pass Whole Genome Sequencing (WGS) were carried out at TGen or by Gencove Inc. At TGen, libraries were prepared using PCR-free Watchmaker kits (Watchmaker Genomics) with 200 ng input. Genomes were sequenced on NovaSeq at low coverage (typically 0.4–1x). The resulting sequence data were processed and imputed using Gencove's imputation platform.

  Study phs003521

• Targeted Long-Read Sequencing of the Ewing Sarcoma 6p25.1 Susceptibility Locus

  Ewing Sarcoma (EwS) is rare but the second most common cancer in children, adolescents and young adults. Recent studies suggest germline variation in or around GGAA microsatellites may interact with fusion oncoprotein binding causing changes in binding affinity and potentially impacting enhancer activity on nearby target genes. This study aims to better understand germline variation around EwS susceptibility regions by performing long-range haplotype sequencing of these regions using PacBio sequencing. Our analysis focused on characterizing variation in GGAA microsatellite length as well as germline variants in or around the microsatellite and their association with EwS risk.

  Study phs003159

• Breast Cancer FRT RNA seq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001000338

• High-throughput sequencing data for study of molecular drivers of resistance to castration in localised prostate cancer

  Aligned whole-genome sequencing and RNA-seq of localised prostate cancer for study 'Loss of SNAI2 in prostate cancer correlates with clinical response to androgen deprivation therapy'.

  Dataset EGAD00001006640

• Ribosomal Depleted Total RNA-Seq of PBMCs and Skin from Controls and Systemic Sclerosis Patients

  This study involved prospective collection of skin biopsies and peripheral blood mononuclear cell (PBMC) samples from controls with no self-reported history of autoimmune or inflammatory disease and cases with Rheumatologist-confirmed systemic sclerosis: limited cutaneous systemic sclerosis (lcSSc), diffuse cutaneous systemic sclerosis (dcSSc), very early diagnosis of systemic sclerosis (VEDOSS), and systemic sclerosis sine scleroderma (SSS). Some SSc cases were sampled at a 6 month routine follow-up visit. PBMCs were collected and lysed immediately. Skin punches were stabilized in RNAlater until extraction. All RNA-Seq libraries were created using Takara/Clontech ribosomal depletion kits, and sequenced on either a HiSeq2500 or HiSeq3000.

  Study phs002902

• Reference Profiles of ExRNAs in Normal Human Pregnancy

  In this study, we did a comprehensive exRNA profiling of plasma and serum specimens from healthy pregnant women, sampled at different gestational time points, and including subjects with diverse geographical and ethnic backgrounds. This study also contains samples from male and female healthy donors to provide a baseline. The aim of this study is to identify miRNAs that can predict the gestation age and to build a miRNA profile across gestation using small RNA-seq data.

  Study phs003182

• Characteristics and Inflammatory Markers in Children with Eosinophilic Esophagitis (EoE)

  The overall protocol for the samples used in this study collects medical information, blood, and biopsy samples from children with eosinophilic esophagitis (EoE) over time to understand clinical characteristics and disease pathogenesis. Our patient population has confirmed EoE and symptoms of esophageal dysfunction characteristic endoscopic findings of EoE. Fibroblasts isolated from esophageal tissue samples from 2 subjects with active EoE and 2 control subjects were evaluated using single cell RNA-sequencing (scRNA-seq).

  Study phs003869

• B Cell Lymphocytosis and Reprogramming due to a CARD11 Bi-Allelic Gain-of-Function Mutation

  This is a single-cell RNA sequencing (scRNA-seq) study using peripheral blood mononuclear cells (PBMC) from 2 healthy donors and 2 patients with B cell Expansion with NF-κB and T cell Anergy (BENTA). Samples were not hashed or multiplexed. The 10X Genomics Platform was used for sequencing. Principal findings include transcriptome changes due to mono- or bi-allelic mutations in the gene CARD11. FASTA files will be available through dbGaP.

  Study phs004115

• Space Associated Stem Cell Hallmarks of Aging in Astronauts

  This study examined the effects of the stress of space, specifically low earth orbit, on hematopoietic stem and progenitor cells (HSPCs) that maintain lifelong hematopoiesis and immune responses. Enriched CD34+ HSPCs were derived from 7 astronauts before, during and after 10 and 21-day ISS missions on the International Space Station. The samples were used as input to whole transcriptome sequencing by bulk RNA-Seq performed at The Scripps Research Institute Next Generation Sequencing Core on Illumina NextSeq 2000 sequencer and single cell RNA-Seq performed at The Salk Institute for Biological Studies on Illumina NovaSeq X Plus sequencer. Subsequent expression, RNA editing, and retrotransposon analyses were performed to assess HSPC and immune subpopulation survival dynamics. Overall, these analyses revealed space-associated stem cell hallmarks of aging (SASHA), including spaceflight dependent alterations in HSPC survival and self-renewal, ADAR1, telomere maintenance, mobilization and cell cycle gene expression, combined with space-induced clonal hematopoietic mutations, APOBEC3C activation and retrotransposon deregulation to warrant countermeasure development to enable long-duration spaceflight. Post-spaceflight analysis revealed increased C-to-T and clonal hematopoiesis-associated mutations, repetitive element and base deaminase deregulation, decreased telomere maintenance gene expression, and decreased self-renewal capacity compared to ground controls. These results demonstrate the space-associated aging effects in HSPCs after month-long exposure to LEO, providing insights into utilizing the LEO environment to model space-accelerated aging and other age-related malignancies.

  Study phs004267

• Encompassing view of spatial and single-cell RNA-seq renews the role of the microvasculature in human atherosclerosis

  Atherosclerosis is a pervasive contributor to ischemic heart disease and stroke. Despite the advance of lipid lowering-therapies and antihypertensive agents, the residual risk of an atherosclerotic event remains high and developing therapeutic strategies has proven challenging. This is due to the complexity of atherosclerosis with a spatial interplay of multiple cell types within the vascular wall. Here we generate an integrative high-resolution map of human atherosclerotic plaques combining single-cell RNA-seq from multiple studies and spatial transcriptomics data from 12 human specimens, with different stages of atherosclerosis. We show cell-type and atherosclerosis-specific expression changes and spatially constrained alterations in cell-cell communication. We highlight the possible recruitment of lymphocytes via ACKR1 endothelial cells of the vasa vasorum, the migration of vascular smooth muscle cells towards the lumen by transforming into fibromyocytes, and cell-cell communication in the plaque region, indicating an intricate cellular interplay within the adventitia and the subendothelial space in human atherosclerosis.

  Dataset EGAD50000000936

• RNA-seq of Toxoplasma gondii response in human macrophages

  Toxoplasmosis is a zoonotic disease caused by a ubiquitous protozoan parasite called Toxoplasma gondii, which can infect all mammal and bird species throughout the world. seroprevalence varies widely between countries. Studies have estimated that between 7-34% of people in the UK have been infected with T. gondii. The vast majority of these people will not have noticed any symptoms, however about 10% of people develop a mild to moderate self limiting flu-like illness. Following the acute active stage of the infection the parasite persists in the body in the form of cysts, particularly in heart and skeletal muscle and nervous system tissues, for many years, and usually for life. In immunocompetent persons these cysts do not pose a health risk. We will use RNA-seq to quantify the transcriptional response of macrophages to T gondii infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001003241

• Single MII oocyte mRNA expression from women

  This dataset contains 14 paired-end FASTQ sequences from mRNA-Seq on single human M-II stage oocytes that were collected from ovarian tissue from unstimulated patients undergoing fertility preservation treatments due to cancer diagnoses, which did not influence ovarian function. Cumulus-oocyte-complexes were matured in vitro according Gruhn et al (Science 365: 1466-1469) and short term flash frozen prior to lysis, RNA extraction, full length cDNA preparation and amplification using the Ultra-low-input SMART-Seq2 v4 kit from Takara Clonetech. Further, these cDNA were used to prepare libraries for sequencing according the Nextera XT DNA library preparation kit from Illumina

  Dataset EGAD00001005971

• snRNAseq prostate cancer

  single-nucleus RNA seq characterization of human fresh frozen prostate cancer samples and non-malignant controls for the same patients. Biopsies were sectioned in 100 micron thick sections, adjacent to those used for spatial transcriptomics.

  Dataset EGAD50000001633

• Transcriptomic profiling of prostate cancer metastasis xenograft models

  RNA-seq profiling of 2 prostate cancer xenograft mouse models, each at the intact state (n=3), castrated state (n=4) and castrated + AR replacement (n=3).

  Dataset EGAD00001006551

• Paired RNA-Seq data from 17 samples of different tumors

  Paired RNA sequencing data (21 runs/ 17 samples) of different tumors. The samples were prepared using the Illumina TruSeq stranded mRNA Kit. The sequencing was done on Illumina HiSeq 4000.

  Dataset EGAD00001009706

• RNA-SEQ data from 13 CAF (Cancer Associated Fibroblast) samples sorted from fresh high-grade ovarian carcinoma

  Dataset EGAD00001003460

• Single-cell RNA-Seq analysis of thymic ILC1 progenitors and NK cell differentiation This analysis involved a multiplexed sequencing run to study thymic innate lymphoid cells (ILCs) and NK progenitors. The generated data requires a demultiplexing file to separate and identify the individual sample tags for downstream analysis.

  This dataset contains multiplexed single-cell RNA sequencing (scRNA-seq) data from human thymic tissue, focusing on ILC1 progenitors and NK cell differentiation. The data were generated using the BD Rhapsody system and sequenced on the Illumina NovaSeq S4 platform. A demultiplexing file is required to assign sample identities.

  Dataset EGAD50000001157

• T-ALL RNA-Seq raw data files

  Bone marrow or peripheral blood samples were collected of adult patients at first diagnosis of T-precursor acute lymphoblastic leukemia. RNA was isolated from mononuclear cells and subjected to mRNA library prep using Poly-A selection and sequencing on a NovaSeq 6000 system. Obtained gene expression profiles and gene fusion calls were used to allocate samples to molecular disease subtypes.

  Study EGAS50000000213

• Comparison between b2m KO and US2 expressing iPSC lines

  This dataset contains bulk RNA-seq transcriptomic profiles from a human induced pluripotent stem cell (hiPSC) line and three engineered derivatives: B2M knockout, EGFP overexpression, and US2 overexpression, alongside the parental line. Total RNA integrity was assessed using the Experion RNA StdSens 1K Analysis Kit on the Bio-Rad Experion Automated Electrophoresis System prior to library preparation and sequencing. Libraries were sequenced on an Illumina NovaSeq 6000 generating ~20 million reads per sample. Raw read quality was assessed with FastQC, reads were aligned to the human reference genome hg38 (Ensembl release 109) using STAR, and alignment/library QC metrics (e.g., orientation, composition, coverage) were evaluated with Picard.

  Dataset EGAD50000002321

• RNA sequencing data from patient derived colorectal cancer organoids

  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 pipeline was utilized to analyze RNA-seq data from ten patient-derived colorectal cancer (CRC) organoids, representing seven microsatellite stable (MSS) and three microsatellite instable (MSI) tumors. The goal was to explore the ncTSA landscape in CRC, particularly in MSS cases, which typically exhibit low tumor mutational burden and limited response to current immunotherapies. The study identified comparable ncTSA burdens across MSI and MSS tumors, suggesting new avenues for immunotherapy targeting non-canonical antigens in CRC. NovumRNA is available at: https://github.com/ComputationalBiomedicineGroup/NovumRNA.

  Study EGAS50000000685

• 10xchromium 3' v3 sequencing from cerebellum, lung, and heart aligned to GRCh38 genome

  Each run contains single cell RNA-seq data from unbiased sampling of single cells from the indicated human tissue. Single cell suspensions were prepared using enzymatic dissociation followed by tituration. The samples were processed using the 10XChromium 3' v3 sequencing pipeline, sequenced on an Illumina NovaSeq 6000, and analyzed using the cellranger software and aligned to the human GRCh38 genome version 93.

  Dataset EGAD00001006110

• Peripheral clonal expansion of T cells (scRNA-seq)

  Single-cell RNA-seq of tumor-infiltrating lymphocytes from 14 cancer patients before treatment, taken from tumor, normal adjacent tissue, and peripheral blood. Dataset consists of paired-end FASTQ files, including replicate libraries and runs.

  Dataset EGAD00001005464

• HBCC Postmortem Psychiatric Molecular Studies

  This postmortem study examines molecular, genetic and epigenetic signatures in the brains of hundreds of subjects with or without mental disorders conducted by the DIRP NIMH Human Brain Collection Core (HBCC). The brain tissues are obtained under protocols approved by the CNS IRB (NCT00001260), with the permission of the next-of-kin (NOK) through the Offices of the Chief Medical Examiners (MEOs) in the District of Columbia, Northern Virginia and Central Virginia. Additional samples were obtained from the University of Maryland Brain and Tissue Bank (contracts NO1-HD-4-3368 and NO1-HD-4-3383) (http://www.medschool.umaryland.edu/btbank/ and the Stanley Medical Research Institute: http://www.stanleyresearch.org/brain-research/). Clinical characterization, neuropathological screening, toxicological analyses, and dissections of various brain regions were performed as previously described (Lipska et al. 2006; PMID: 16997002). All patients met DSM-IV criteria for a lifetime Axis I diagnosis of psychiatric disorders including schizophrenia or schizoaffective disorder, bipolar disorder and major depression. Controls had no history of psychiatric diagnoses or addictions. SNP array: Array-based genotyping was performed on most samples published in this collection. The number of SNPs assayed via Illumina chips varied between 650,000 and 5 Million. Cerebellar tissue was generally used for genotyping studies. # Diagnosis SNP Array 1 Anxiety Disorder 1 2 Autism Spectrum Disorder 13 3 Bipolar Disorder 114 4 Control 387 5 Eating Disorder (ED) 2 6 Major Depressive Disorder (MDD) 186 7 Obsessive Compulsive Disorder (OCD) 5 8 Post-Traumatic Stress Disorder (PTSD) 0 9 Schizophrenia 220 10 Other 7 11 Tic Disorder 3 12 Undetermined 1 13 Williams Syndrome 2 Table: Numbers of samples in each diagnostic category. DNA extraction: 45-80 mg of cerebellar tissue was pulverized for DNA extractions. The QIAamp DNA mini Kit (Qiagen) method was employed for tissue DNA extraction. The tissue was initially lysed using Tissue Lyser (Qiagen) and extractions were accomplished according to manufacturer's protocol. The DNA was captured in 500uL elution buffer. The concentrations were measured using Thermo Scientific's NanoDrop 1000/NanoDrop ONE. The mean yield was 128.85 uG (+/- 79.48), the mean ratio of 260/280 was 1.87 (+/- 0.105), and the mean ratio of 260/230 was 2.48 (+/-1.75). Genotyping methods: Three types of Illumina Beadarray chips were used: HumanHap650Y, Human1M-Duo, and HumanOmni5M-Quad (San Diego, California). The genotyping was done according to the manufacturer's protocol (Illumina Proprietary, Catalog # WG-901-5003, Part # 15025910 Rev.A, June 2011). Approximately, 400ng DNA was used and each DNA sample was QC tested for 260/280 ratio by nanodrop and DNA band intactness on 2% agarose gel. Briefly, the samples were whole-genome amplified, fragmented, precipitated and resuspended in appropriate hybridization buffer. Denatured samples were hybridized on prepared Bead Array Chips. After hybridization, the Bead Chip oligonucleotides were extended by a single fluorescent labeled base, which was detected by fluorescence imaging with an Illumina Bead Array Reader, iScan. Normalized bead intensity data obtained for each sample were loaded into the Illumina Genome Studio (Illumina, v.2.0.3) with cluster position files provided by Illumina, and fluorescence intensities were converted into SNP genotypes. Microarray: We generated RNA expression data using array technology for psychiatric subjects compared to non-psychiatric subjects as controls. We used tissues from three different brain regions i.e. hippocampus, dorsolateral prefrontal cortex (DLPFC), and dura mater for a large cohort of individuals (total number 552 subjects for hippocampus, 800 for DLPFC and 146 for dura). Total RNA was extracted from ~100 mg of tissue using the RNeasy kit (Qiagen) according to the manufacturer's protocol. RNA quality and quantity were examined using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc), respectively. Samples with RNA integrity number (RIN) # Diagnosis DLPFC Hippo Dura 1 Anxiety Disorder 1 0 0 2 Autism Spectrum Disorder 14 6 0 3 Bipolar Disorder 90 49 0 4 Control 336 270 75 5 Eating Disorder (ED) 2 1 0 6 Major Depressive Disorder (MDD) 144 87 0 7 Obsessive Compulsive Disorder (OCD) 5 3 0 8 Post-Traumatic Stress Disorder (PTSD) 6 0 0 9 Schizophrenia 192 125 71 10 Other 5 6 0 11 Tic Disorder 3 3 0 12 Undetermined 1 1 0 13 Williams Syndrome 2 1 0 Table: Numbers of samples in each diagnostic category. RNA-Seq of Dorso-lateral prefrontal cortex: All brains were collected and the dorsolateral prefrontal cortical (DLPFC) samples dissected at the HBCC, DIRP, NIMH. Dorsolateral prefrontal cortex (DLPFC) specimens were dissected from right or left hemisphere of frozen coronal slabs. The study was funded by the DIRP, NIMH under contract (#HHSN 271201400099C) with Icahn School of Medicine at Mount Sinai,1106402 One Gustave L. Levy Place, Box 3500, New York NY 10029-6574. RNA extraction, library preparation and sequencing were performed under contract at Icahn School of Medicine. The Common Mind Consortium (CMC) provided project management support. RNA isolation: Total RNA from 468 HBCC samples was isolated from approximately 100 mg homogenized tissue from each sample by TRIzol/chloroform extraction and purification with the Qiagen RNeasy kit (Cat#74106) according to manufacturer's protocol. Samples were processed in randomized batches of 12. The order of extraction for schizophrenia, bipolar, and MDD disorders and control samples was assigned randomly with respect to diagnosis and all other sample characteristics. The mean total RNA yield was 24.2 ug (+/- 9.0). The RNA Integrity Number (RIN) was determined by 4200 Agilent TapeStation System. Samples with RIN DLPFC RNA-Seq quantified expression data are provided for 364 samples. Data were generated, QC'd, processed and quantified as follows: RNA library preparation and sequencing: All samples submitted to the New York Genome Center for RNAseq were prepared for sequencing in randomized batches of 94. The sequencing libraries were prepared using the KAPA Stranded RNAseq Kit with RiboErase (KAPA Biosystems). rRNA was depleted from 1ug of RNA using the KAPA RiboErase protocol that is integrated into the KAPA Stranded RNAseq Kit. The insert size and DNA concentration of the sequencing library was determined on Fragment Analyzer Automated CE System (Advanced Analytical) and Quant-iT PicoGreen (ThermoFisher) respectively. Schizophrenia Bipolar Control 89 65 210 Table: Numbers of samples in each diagnostic category. RNA-Seq of subgenual anterior cingulate cortex (sgACC): All the 200 post-mortem brain samples (61 controls; 39 bipolar disorder; 46 schizophrenia; 54 major depressive disorder) were collected by the HBCC, DIRP, NIMH. RNA Extraction and Quality Assessment: Tissue from sgACC was pulverized and stored at -80°C. Total RNA was extracted from 50-80 mg of the tissue using QIAGEN RNeasy Lipid Tissue Mini Kit (QIAGEN, Cat. # 74804) with DNase treatment (QIAGEN, Cat. # 79254). The RNA Integrity Number (RIN) for each sample was assessed with high-resolution capillary electrophoresis on the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, California). The concentration of RNA and their 260/280 ratio (2.1+/- 0.032 SD) were determined with NanoDrop (Thermo Scientific). RNA sequencing: Stranded RNA-Seq libraries were constructed after rRNA depletion using Ribo-Zero GOLD (Illumina). RNA sequencing was performed at National Institute of Health Intramural Sequencing Center (NISC). Schizophrenia Bipolar Control MDD 46 39 61 54 Table: Numbers of samples in each diagnostic category. Whole Genome Sequencing: All brains were collected and dissected at the HBCC, DIRP, NIMH. This study generates whole genome sequencing data using sequencing of DNA in the dorsolateral prefrontal cortex (DLPFC), anterior cingulate cortex (ACC) or cerebellum of 443 individuals with schizophrenia, bipolar disorder and major depressive disorder and non-psychiatric controls. The study was funded by the DIRP, NIMH under contract (#HHSN 271201400099C) with Icahn School of Medicine at Mount Sinai,1106402 One Gustave L. Levy Place, Box 3500, New York NY 10029-6574. DNA extraction, library preparation and sequencing were performed under contract at Icahn School of Medicine. The Common Mind Consortium (CMC) provided project management support. All specimens were dissected from right or left hemisphere of frozen coronal slabs. DNA Library Preparation and Sequencing: All samples submitted to the New York Genome Center for WGS were prepared for sequencing in randomized batches of 95. The sequencing libraries were prepared using the Illumina PCR-free DNA sample preparation Kit. The insert size and DNA concentration of the sequencing library was determined on Fragment Analyzer Automated CE System (Advanced Analytical) and Quant-iT PicoGreen (ThermoFisher) respectively. A quantitative PCR assay (KAPA), with primers specific to the adapter sequence, was used to determine the yield and efficiency of the adaptor ligation process. Performed on the Illumina HiSeqX with 30X coverage. Schizophrenia Bipolar Control 115 78 230 Table: Numbers of samples in each diagnostic category. ChIP-Seq: All brains were collected and the dorsolateral prefrontal cortical (DLPFC) samples dissected at the HBCC, DIRP, NIMH. This study generates epigenetic data using sequencing of DNA after chromatin immunoprecipitation (ChIP-Seq) for marks H3K4me3 and H3K27ac in the dorsolateral prefrontal cortex (DLPFC). Dorsolateral prefrontal cortex (DLPFC) specimens were dissected from right or left hemisphere of frozen coronal slabs. The study was funded by the DIRP, NIMH under contract (#HHSN 271201400099C) with Icahn School of Medicine at Mount Sinai,1106402 One Gustave L. Levy Place, Box 3500, New York NY 10029,6574. Chromatin precipitation, library preparation and sequencing were performed under contract at Icahn School of Medicine. The Common Mind Consortium (CMC) provided project management support. Chromatin immunoprecipitation (ChIP) assays for histone marks H3K4me3 and H3K27ac were carried out using Native ChIP. Micrococcal Nuclease (MNase) (Sigma, N3755) treatment was used to digest chromatin into mononucleosomes. The following antibodies were used for chromatin pull-down: anti-H3K4me3 (Cell Signaling, Cat# 9751BC, lot 7) and anti-H3K27ac (Active Motif, Cat# 39133, Lot # 31814008). Histone modification-enriched genomic DNA fragments were recovered using Protein A/G magnetic beads (Thermo Scientific, 88803-88938 or Millipore 16-663), and then washed, eluted, and treated with RNAse A and proteinase K. Final ChIP DNA products were isolated using phenol-chloroform extraction followed by ethanol precipitation. The efficiency of each ChIP assay was validated using Qubit concentration measurement and qPCR for positive (GRIN2B, DARPP32) and negative (HBB) control genomic regions. Only ChIP assays that passed quality control were further processed for library preparation and sequencing; this included ChIP DNA that was not detectable on Qubit but showed a good signal and expected enrichment patterns in qPCR. HISTONE_MARK H3K27ac H3K4me3 Input Bipolar 56 4 7 Control 158 11 24 Schizophrenia 79 11 12 Table: Numbers of individuals in each assay grouped by histone mark or input.Long-Read Whole-Genome Sequencing (WGS) Cohort Description: Brain specimens were obtained from the Human Brain Collection Core (HBCC), part of the NIH NeuroBioBank. Samples were collected under protocols approved by the NIH CNS Institutional Review Board (IRB) (NCT03092687), with informed consent from next-of-kin (NOK). Collection was coordinated through the Offices of the Chief Medical Examiners (MEOs) in Washington, D.C., Northern Virginia, and Central Virginia. Clinical metadata and documentation are publicly available via the NIMH Data Archive (NDA) (Collection #3151) https://nda.nih.gov/edit_collection.html?id=3151 Eligibility Criteria No clinical diagnosis of major neuropsychiatric or neurodegenerative diseaseNo diagnosis of cognitive impairment during life All individuals were confirmed to be neurologically normal at time of deathDemographics Initial cohort size: 155 individuals Ancestry: All individuals self-identified as African or African-admixed Mean age at death: 44.2 years (range: 18–85 years) Sex distribution: 36.4% femaleSample Processing: Frozen frontal cortex tissue was dissected and processed according to the public protocol: https://www.protocols.io/view/processing-human-frontal-cortex-brain-tissue-for-p-kxygxzmmov8j/v2. High-molecular-weight DNA was extracted and libraries were prepared using the Oxford Nanopore Technologies (ONT) LSK-114 kit. Sequencing was performed using ONT PromethION flow cells (R10.4.1 chemistry) Data Processing and Quality Control: Basecalling: Conducted using Guppy v6.38 Read Alignment: Reads were aligned to the GRCh38 reference genome using minimap2 Sample Identity Verification: Sample identity was validated by comparing ONT-derived SNP calls with matched short-read WGS genotypes to ensure concordance and prevent sample swaps Variant Calling and Phasing: Reads were base-called with Guppy v6.38. Reads were aligned to GRCh38 using minimap2. We verified sample identity by cross-checking ONT SNV calls with the existing short-read WGS genotypes, confirming no sample switches. The napu pipeline (https://github.com/nanoporegenomics/napu_wf) produced; haplotype-resolved assemblies, joint small-variant (SNV/indel) calls, and multi-caller structural-variant sets, all reported on GRCh38 and phased where possible. Raw signal data were basecalled to obtain 5-methyl-cytosine (5mC) status; methylation tags were added to the phased BAM files. Genome-wide methylation summaries are provided in BED format.Dataset Filtering and Exclusions: All 155 samples underwent sequencing and SNP-based ancestry inference 8 samples were excluded due to ancestry inconsistent with African or African-admixed background 1 sample was excluded due to insufficient sequencing quality Final Sample Set: 146 high-quality samples from individuals of African or African-admixed ancestry were retained for downstream analyses See PMID: 39764002 for further analysis detailsDiagnosis#SamplesControl155Table: Diagnostic Summary.Note: The data derived from HBCC resources were removed from dbGAP and are now available in the NIMH Data Archive (NDA). They include genotypes, short read whole genome sequencing (WGS), epigenetics (DNA methylation, ChIP-seq for histones), RNA expression (qPCR, microarray, RNA-seq, single nucleus RNA-seq) of various brain regions in cases with schizophrenia, bipolar disorder, major depression, substance use disorders and normative controls. Please access our NDA collection (https://nda.nih.gov/edit_collection.html?id=3151) for further detail.

  Study phs000979

• Gene Expression and Epigenetic Analyses of Human Myocytes From Different Muscles

  The study contains expression and DNA methylation data of in vitro cultured myoblasts derived from biopsies of control, FSHD1 and FSHD2 patients from the tibialis anterior, quadricep, bicep and deltoid. Expression data is from bulk RNA-seq using the SmartSeq2 protocol for days 0 and 5 of in vitro differentiation of primary myocytes from the bicep and deltoid of FSHD1 patients. DNA methylation data was produced using the TruSeq Methyl Capture EPIC kit (Illumina) for days 0, 3 and 12 of in vitro differentiation of primary myocytes from the tibialis anterior and quadricep of healthy individuals and FSHD2 patients.

  Study phs002554

• BBMRI – BIOS – Freeze 2 – RNA-seq Counts

  Read counts determined using HTSeq-count for the BBMRI BIOS Freeze 2 RNAseq data

  Dataset EGAD00010001420

• Single-Cell Sequencing Reveals Distinct Microenvironment Cell Types Associated with Response to High Dose Melphalan and Autologous Stem Cell Transplant in Multiple Myeloma

  The aim of this study is to understand the transcriptome of microenvironment cells in pre- and post- autologous stem cell transplantation (ASCT) samples between patients with complete response and partial response to transplant. Here, we studied immune cells from 40 multiple myeloma patients who have undergone ASCT. Samples were collected from 40 multiple myeloma patients before and after ASCT. Samples were sorted using magnetic activated cell sorting (MACS) and the non-tumor CD138- fraction underwent 3' single cell RNA-sequencing (scRNA-seq) or 5' scRNA-seq + 5' T cell receptor sequencing (TCRseq), to determine the scRNA transcriptome and TCR repertoire. This study includes 24 samples with 3' scRNA-seq, 56 samples with 5' scRNA-seq, and 56 samples with 5' TCRseq data.

  Study phs003219

• Gabriella Miller Kids First Pediatric Research Program in Pediatric T-Cell Acute Lymphoblastic Leukemia

  The outcome for patients with relapsed T-ALL is dismal with 3-year event free survival of AALL0434 was a Children's Oncology Group-initiated phase 3 randomized clinical trial comparing Capizzi-style escalating methotrexate plus pegaspargase (CMTX) vs. high dose methotrexate (HDMTX), with/without six 5-day courses of nelarabine. Survival on this study was superior to any prior trial for de novo T-ALL, changing the standard of care. Yet, a substantial minority (~15%) of patients had relapsed or refractory (r/r) disease. Through the TARGET initiative, RNA sequencing (RNA-Seq), DNA copy number analysis, and whole-exome sequencing (WES) were performed on 264 T-ALL patients treated on AALL0434, demonstrating recurrent alterations could be grouped into 10 different potentially targetable functional pathways. This analysis was not powered to examine associations between genetic lesions with outcome, because too few patients with r/r disease were included. This project is dedicated to testing the hypothesis that comprehensive genomic profiling of the entire AALL0434 cohort will identify recurrent genetic alterations that can be segregated into biologically relevant deregulated pathways that can be combined with MRD to identify patients at risk for poor outcomes before they relapse and provide rationale for treatment with alternative therapies. In addition, a number of small recent studies demonstrated that many of the biologically relevant alterations in T-ALL occur in non-coding regions of the genome, but no large studies have performed whole genome sequencing (WGS) in T-ALL. This project also tests the hypothesis that WGS of a large cohort of patients with T-ALL will identify novel lesions in coding and non-coding regions that will be highly impactful in the understanding of T-ALL pathogenesis.These hypotheses are tested by performing comprehensive genomic profiling (WGS, WES, RNA-Seq, and copy number analysis) of the entire AALL0434 cohort with available samples with the following specific aims: (1) identify recurrent genetic alterations that predict poor outcome in T-ALL; (2) identify novel alterations, including non-coding alterations in T-ALL; and (3) identify germline genetic variants that predispose to T-ALL and to increased toxicity to chemotherapy.

  Study phs002276

• Spatial Transcriptomics on prostate cancer heterogeneity

  Intratumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.

  Study EGAS00001003001

• Single-cell RNA sequencing of control and Notch inhibitor treated HCC PDX model

  We generated single-cell RNA-seq data for anti-Notch2 (n=3), anti-JAG1 (n=1) and anti-gD (n=4) treated LIV78 tumors. NCR nude mice bearing similarly sized LIV78 tumors (volumes between 300-900mm3) were injected intravenously with 30mg/kg body weight of either anti-Notch2, anti-Jag1 or anti-gD control antibody 72hrs prior to tumor harvest and tumor cell isolation. Following the depletion of CD45+ and Ter119+ cells, the samples were processed for single-cell RNA-seq (scRNAseq) as described previously (Long et al., 2019) using the Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual. cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq 2500 (Illumina) following the manufacturer’s sequencing specification (10X Genomics) to produce the resulting FASTQ files.

  Dataset EGAD50000000738

• Phenotype information

  This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n=171) derived from a DLBCL PDTX model in-cluding 27 humanized (HIS) PDTX, 8 HIS non-PDTX and 21 non-HIS PDTX non-obese diabetic (NOD)-scid IL2Rgnull (NSG) mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either rituximab, cyclophosphamide, doxorubicin, vincris-tine, and prednisone (R-CHOP), CD20-targeted human IFNα2-based AcTaferon combined with CHOP (huCD20-Fc-AFN-CHOP), or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform using the using the SMARTer Stranded Total RNA-Seq Kit v3.

  Dataset EGAD50000000806

• Single cell RNA-seq of 24 samples from 13 individual human embryonic meninges of PCW 5.0-13.0 using 10X chromium technology

  A total of 24 samples of meninges from 13 normal human embryos of post-conceptional week (PCW) 5.0-13.0 were dissected and subject to 10Xgenomics chromium single cell RNA sequencing with the purpose of identifying cell types and gene expression programs for normal meninges development. All libraries were sequenced on an Illumina NovaSeq 6000 using S4 to a target sequencing depth of 100,000 reads/cell. Final data after processing with STARSolo 2.7.10a, using human genome GRCh38.p12 and transcript annotations from ENSEMBL release 93 from reference package GRCh38-3.0.0 as available from 10Xgenomics, consists of 24 BAM files.

  Dataset EGAD50000001434

• Adult-type Granulosa Cell Tumour of the Ovary

  A recurrent mutation in FOXL2 (c.402C>G; p.C134W) is present in over 95% of adult-type granulosa cell tumours (AGCTs). In contrast, various loss-of-function mutations in FOXL2 lead to the development of blepharophimosis, ptosis and epicanthus inversus syndrome (BPES). BPES is characterized by an eyelid malformation often accompanied with primary ovarian insufficiency but not granulosa cell tumours. Two recent studies suggest that FOXL2 C402G is a gain or change-of-function mutation with altered DNA-binding specificity. Another study proposes that FOXL2 C402G is selectively targeted for degradation inducing somatic haploinsufficiency suggesting its role as a tumour suppressor. The latter study relies on data indicative of an FOXL2 allelic imbalance in AGCTs. Here we present RNA-seq data as genetic evidence that no real allelic imbalance is observed at the transcriptomic level in AGCTs. Additionally, there is no loss of protein expression in tumours harboring the mutated allele. These data and other features of this mutation as compared to other oncogenes and tumour suppressor genes argue strongly against FOXL2 being a tumour suppressor in this context. Given the likelihood that FOXL2 C402G is oncogenic, targeting the variant protein or its downstream consequences is the most viable path forward to identifying an effective treatment for this cancer.

  Study EGAS00001005414

• Transcriptomic Profiling of Oropharyngeal Squamous Cell Carcinoma

  The study is a retrospective transcriptomic profiling of oropharyngeal squamous cell carcinoma. The pathologic database was queried for squamous cell carcinoma tumors originating from the anatomic oropharynx (tonsil or tongue base) with available samples from surgical archives. This retrospective RNA sequencing cohort included cases dating prior to the routine implementation of p16 immunohistochemistry (IHC) testing at our institution, therefore, p16 status was not required for inclusion in this study. Formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center (LCCC) Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer's protocol (Promega 9FB167). After a pathology review of a hematoxylin and eosin (H&E) stained slides to identify tumor area, RNA was extracted from unstained slides using macrodissection. Total RNA quality was measured using a NanoDrop spectrophotometer (Thermo Scientific ND-2000C) and a TapeStation 4200 (Agilent G2991AA). Total RNA concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies Q33216). Libraries were prepared with Illumina TruSeq Stranded Total RNA with Ribo-Zero protocol. Libraries were sequenced on an Illumina HiSeq2500 sequencer. Paired end read data, with read lengths of 75 were collected.

  Study phs002935

• Characterization of a New Case of XMLV (Bxv1) Contamination in the Human Cell Line Hep2 (Clone 2B) Using High-Throughput DNA- and RNA-Seq

  We have sequenced DNA and RNA from the Hep2 (clone 2B) cell line (Sigma-Aldrich catalog number: 85011412-1VL) using short read Illumina sequencing. We show that this cell line is indistinguishable from the HeLa cell line (as mentioned on the Sigma-Aldrich website) by mapping integrations of the human papillomavirus 18. We also show that the cell line is contaminated by the Bxv1 xenotropic murine leukemia virus. This contamination has to be taken into account when using the cell line in future experiments.

  Study phs001944

• Identification_of_cardiovascular_biomarkers_through_an_integrative_omics_approach

  Recent GWAS studies have made extensive use of large eQTL data sets to functionallyannotate index SNPs. With a large number of association signals located outside codingregions there has been an intense search among sequence variants affecting geneexpression at the transcriptional level. However, little progress has been made in mappingregulatory variants that affect protein levels at the translational or post-translational level. It isnow possible to undertake a protein QTL scan for focused sets of e.g. oxidized proteins bymass spectrometry. We have established a collaboration with a longitudinal, family-basedstudy in France, the Stanislas cohort, which comprises circa 1000 nuclear families (4,295individuals) and has follow up data for 10 years (three visits). We have undertaken a pilotstudy in a focus set of 257 subjects from 79 families with the aim to integrate GWAS,transcriptomic and DNA methylation data with proteomic data on a set of 100 proteinsmeasured in PBMCs. We have already generated GWAS data using Illumina's core-exomechip as well as DNA methylation profiles with the 450K array. We propose to use RNA seq togenerate transcriptomic data of the corresponding PBMCs.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000711

• Breast Cancer Genome Guided Therapy Study (BEAUTY)

  The Breast Cancer Genome Guided Therapy Study (BEAUTY) is a prospective neoadjuvant clinical study enrolling 140 women with Stage I-III breast cancer. The goals of this study were to 1) perform comprehensive sequencing of germline and tumor tissues (exome and RNA seq), 2) identify genomic alterations and perturbed pathways associated with response/resistance to standard chemotherapy, and 3) develop patient-derived xenograft (PDX) for testing of therapeutic regimens chosen on the basis of alterations identified by genetic sequencing.

  Study phs001050

• Identification of potential blood biomarkers for early diagnosis of Alzheimer���s disease through immune landscape analysis

  Mild cognitive impairment (MCI) is a clinical precursor of Alzheimer���s disease (AD). Recent genetic studies have reported on associations between AD risk genes and immunity. Here, we obtained samples and data from 317 AD, 432 MCI, and 107 cognitively normal (CN) subjects and investigated immune-cell type composition and immune clonal diversity of T-cell receptor (TRA, TRB, TRG, and TRD) and B-cell receptor (IGH, IGK, and IGL) repertoires through bulk RNA sequencing. Our prognosis prediction model using the potential blood-based biomarkers for early AD diagnosis, which combined two immune repertoires (IGK and TRA), WDR37, and clinical information, successfully classified MCI patients into two groups, low and high, in terms of risk of MCI-to-AD conversion.

  Study JGAS000532

• Single-Cell ATAC and RNA Sequencing of Human Breast Cancer Reveals Salient Cancer-Specific Enhancers

  Matched single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq) were performed for 12 human breast tumor samples, 4 normal human mammary reduction samples, and 4 human breast cancer cell lines (HCC1143, SUM149PT, MCF7, and T47D). Both scATAC-seq and scRNA-seq assays resolved the underlying cellular heterogeneity in chromatin accessibility and transcriptional output for each patient sample. In this work, we quantitatively linked variation in chromatin accessibility to gene expression across malignant and non-malignant cell types from patient samples. We then showed that our findings were recapitulated in the breast cancer cell line samples. These data will serve as an important resource for the single-cell genomics and breast cancer research communities.

  Study phs003253

• FAM50A_Disruption_in_TOV21G_Cells___RNAseq

  In this project we aimed to assess the transcriptional consequences of disrupting FAM50A in TOV21G cells in vivo. To do this we generated a dox inducible FAM50A gRNA allele such that we could conditionally inactivate FAM50A by feeding mice a diet containing doxycycline. Tumour masses were harvested from mice when they reached the ethical limit and RNA was extracted for RNA-Seq analysis.

  Study EGAS00001004156

• TenK10K Phase 1:  Single Cell

  Understanding the genetic basis of gene expression can shed light on the regulatory mechanisms underlying complex traits and diseases. Single-cell resolved measures of RNA levels and single-cell expression quantitative trait loci (sc-eQTLs) have revealed genetic regulation that drives sub-tissue cell states and types across diverse human tissues. Here, we describe the first phase of TenK10K, the largest- to-date dataset of matched whole-genome sequencing (WGS) and single-cell RNA-sequencing (scRNA-seq). We leverage scRNA-seq data from over 5 million cells across 28 immune cell types and matched WGS from 1,925 individuals. This provides power to detect associations between rare and low-frequency genetic variants that have largely been uncharacterised in their impact on cell-specific gene expression. We map the effects of both common and rare variants in a cell type specific manner using SAIGE-QTL.

  Study EGAS50000001653

• RNA-Seq of Myeloid Cells in Dendritic Cell Therapy Response

  RNA libraries were prepared from 100 ng of total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, then sequenced (2×150 bp) on the Illumina NextSeq550. Transcript-level quantification was done with kallisto, followed by gene-level summarization (tximport) and differential expression analysis (DESeq2). Quality control included PCA, hierarchical clustering, and deconvolution with CIBERSORTx to exclude non-myeloid genes. Final analyses identified transcriptomic differences among healthy donors and three patient subgroups based on response to dendritic cell therapy.

  Dataset EGAD50000001681

• RNA-Seq Profiles from the CheckMate-577 Clinical Trial

  The dataset contains RNAseq profiles of 386 patients from the CheckMate-577 (CA209-577) clinical trial whose ICF allows data deposition into a public repository. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNA was analyzed using the Illumina TruSeq RNA Access method for library preparation, followed by sequencing on the Illumina NovaSeq platform with a 50bp paired-end strategy and a target read depth of 50M per sample. Fastq files are included.

  Dataset EGAD50000002394

• RNA Sequencing Analysis of Patient-Derived Xenograft Tissue PIM-084 Treated with L-NMMA+Alpelisib vs Vehicle Control

  This dataset contains RNA-seq analysis of vehicle control compared to L-NMMA+alpelisib treated metaplastic breast cancer PDX PIM084 tumors (RNA sequencing and analysis performed by Novogene). The submitted data contains the gene ID, gene name, normalized read counts from all samples from control group and combination treatment group, log2-fold change derived from DESeq2 R/EdgeR package, p-value, adjusted p-value, read counts from each group, and gene FPKM from the each sample in the group. Due to patient privacy, we are submitting only the processed and desensitized RNA sequencing analysis to this repository.

  Study phs003814

• The characterization of gene expression pattern of anticancer agent-resistant cancer stem cells using RNA sequencing analysis.

  Slow cycling cancer stem cells persist and contribute to tumor regrowth after chemotherapy.To investigate this mechanism, we developed stemness- and cell cycle-visualized colon cancer organoids from patient tissues, and perfomed comparative transcriptome analysis using sorted rapid cycling stem cells (LGR5+p27-) and slow cycling stem cells (LGR5+p27+). In addition, we analyzed the changes in the gene expression patterns in the slow cycling stem cells and all of tumor cells after chemotherapy (camptothecin) treatment. Gene ontology analysis and gene set enrichment analysis using these transcriptome data revealed cell adhesion signal and YAP siganling pathway were important to maintain the dormancy and resume propagation after chemotherapy. In each experiments, total RNA was extracted from organoids and sequenced with HiSeq X Ten (Illumina).

  Study JGAS000350

• CGP CORE CELL LINES - RNA-seq

  Genomic characterisation of a large series of cancer cell lines.

  Dataset EGAD00001001357

• FOXM1 is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer that is detectable using metabolic imaging (RNA-seq data)

  PIK3CA, encoding the PI3Kα isoform, is the most frequently mutated oncogene in estrogen receptor-positive breast cancer. Isoform-selective PI3K inhibitors are used clinically but intrinsic and acquired resistance limits their utility. Improved selection of patients that will benefit from these drugs requires novel predictive biomarkers. We show here that persistent FOXM1 expression following drug treatment is a biomarker of resistance to PI3Kα inhibition in ER+ breast cancer. Since the transcription factor drives expression of lactate dehydrogenase (LDH) but not hexokinase 2 (HK-II), changes in FOXM1 expression can be detected using magnetic resonance imaging of LDH-catalyzed hyperpolarized 13C label exchange between pyruvate and lactate but not by PET measurements of HK-II-mediated trapping of the glucose analog 2-deoxy-2-[18F]fluorodeoxyglucose.

  Study EGAS00001004452

• Dataset for cancer_of_unknown_primary-RNA

  Rare cancer sequencing data of 58 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008857

• Covacta RNAseq counts

  RNA-seq data from PAXgene extracted whole blood of patients enrolled in the COVACTA trial. This dataset includes read counts per gene. Read counts were generated for the Gencode v27 annotation using the summarize Overlaps method from bioC in mode “IntersectionStrict”

  Dataset EGAD00001011164

• 99 Cases of Small Cell Lung Cancer Study

  Small cell lung cancer (SCLC) is an aggressive disease with poor survival. A few sequencing studies performed on limited number of samples have revealed potential disease-driving genes in SCLC, however, much still remains unknown, particularly in the Asian patient population. Here we conducted whole exome sequencing (WES) and transcriptomic sequencing of primary tumors from 99 Chinese SCLC patients. Dysregulation of tumor suppressor genes TP53 and RB1 was observed in 82% and 62% of SCLC patients, respectively, and more than half of the SCLC patients (62%) harbored TP53 and RB1 mutation and/or copy number loss. Additionally, Serine/Arginine Splicing Factor 1 (SRSF1) DNA copy number gain and mRNA over-expression was strongly associated with poor survival using both discovery and validation patient cohorts. Functional studies in vitro and in vivo demonstrate that SRSF1 is important for tumorigenicity of SCLC and may play a key role in DNA repair and chemo-sensitivity. These results strongly support SRSF1 as a prognostic biomarker in SCLC and provide a rationale for personalized therapy in SCLC. The manuscript has been accepted by Plos Genetics.

  Study phs001083

• Assessment of candidate high-grade serous ovarian carcinoma predisposition genes through integrated germline and tumour sequencing

  High-grade serous ovarian carcinoma (HGSOC) has a significant hereditary component, only half of which is explained. Previously, we performed germline exome sequencing on BRCA1 and BRCA2-negative HGSOC patients, revealing three proposed and 43 novel candidate genes enriched with rare loss-of-function variants. For validation, we undertook case-control analyses using genomic data from disease-free controls. This confirms enrichment for nearly all previously identified genes. Additionally, one-hundred-and-eleven HGSOC tumours from variant carriers were sequenced alongside other complementary studies, seeking evidence of biallelic inactivation as supportive evidence. PALB2 and ATM validate as HGSOC predisposition genes, with 6/8 germline carrier tumours exhibiting biallelic inactivation accompanied by characteristic mutational signatures. Among candidate genes, only LLGL2 consistently shows biallelic inactivation and protein expression loss, supporting it as a novel HGSOC susceptibility gene. The remaining candidate genes fail to validate. Integrating case-control analyses with tumour sequencing is thus crucial for accurate gene discovery in familial cancer studies.

  Study EGAS50000000770

• Effects of Metformin on Transcriptomic and Metabolomic Profiles in Breast Cancer Survivors Enrolled in the Randomized Placebo-Controlled MetBreCS Trial

  RNA from snap-frozen breast tissue biopsies were purified after lysing by tissuelyser (Qiagen) and using RNA Purification Plus Kit (Norgen biotek CORP, 47700) with additional on-column DNase-I treatment (Qiagen, 79254) at 27 °C. RNA purity and integrity (RIN) were quantified using RNA 6000 Nano kit (Agilent Technologies, 5067-1511) on the 4200 TapeStation (Agilent, Santa Clara, USA). Library preparation and 2x75bp paired-end of 160 ng total RNA input was performed using Illumina Stranded Total RNA Prep Ligation kit and Illumina HiSeq4000 system (Illumina, Sand Diego, CA, USA). RNA sequencing data from HiSeq4000 were quality checked and aligned to GRCh38 (GCA_000001405.15) reference genome using HISAT2 2.0.5 and submitted to subread v.1.5.2 for feature counts calculation. Finally, 36 paired biopsies samples (metformin n=26 and placebo n=12) were sequenced and included in the final analyses.

  Dataset EGAD50000001274

• RNA-Seq profiles from the CheckMate-649 Clinical Trial

  This dataset contains RNA sequencing (RNAseq) data of 814 patients from the CheckMate 649 clinical trial whose ICF allows data deposition into a public repository. Gene expression profiling was performed retrospectively using RNAseq on a subset of baseline tumor samples. Paired-end FASTQ files were processed on Seven Bridges platform (Seven Bridges Genomics).

  Dataset EGAD50000001105

• Characterizing Immune Profiles in Extrapulmonary Tuberculosis via RNA Sequencing

  This dataset provides insight into the immune response in extrapulmonary tuberculosis (EPTB), using bulk RNA-seq data to analyze different disease severities. Hierarchical clustering identified three distinct levels of severity, revealing disease progression driven by interferon and IL-1β-mediated signaling. Additionally, the dataset helped develop a diagnostic gene expression signature for both EPTB and pulmonary TB.

  Dataset EGAD50000000943

• SCLC study MGH - RNAseq dataset

  RNA-seq analyses were performed on cDNA libraries prepared from PolyA+ RNA using the Illumina TruSeq protocol for mRNA. The final libraries were sequenced with a paired-end 2×75 bp protocol aiming at 8.5 Gb per sample for a 30x mean coverage of the annotated transcriptome. All sequencing reactions were conducted on an Illumina HiSeq instrument (Illumina, San Diego, CA, USA).

  Dataset EGAD00001003969

• LongRNA_Monocytes

  This dataset consists of bulk RNA sequencing profiles generated from monocytes isolated from peripheral blood mononuclear cells (PBMCs) collected from 315 patients enrolled in the ImmunAID consortium. Each sample corresponds to a unique patient, providing a resource to investigate transcriptional variation in circulating monocytes across the cohort. PBMCs were isolated from whole blood, and monocytes were subsequently enriched using standard immunological protocols. Total RNA was extracted and libraries were prepared using the SMART-Seq mRNA Library Preparation Kit with Unique Molecular Identifiers (UMIs). Sequencing was performed on an Illumina NovaSeq 6000 platform following manufacturer-recommended protocols.

  Dataset EGAD50000002341

• Raw RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the raw RNA-seq data.

  Dataset EGAD00001006205

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

  Genotyping by array and Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001000880

• RNA-Seq of kidney cancer organoid biobank

  Dataset EGAD00001005318

• 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

• SU2C-MARK Lung Cancer Consortium - Checkpoint Blockade Response Project

  Immune checkpoint inhibitors have become a critical part of the armamentarium against advanced Non-Small Cell Lung Cancer (NSCLC). While early studies have identified Tumor Mutation Burden (TMB) and PD-L1 staining as important biomarkers of response, they remain imperfect predictors. Here we describe a multi-institutional effort as part of the SU2C-MARK Lung Cancer Consortium in which Whole Exome Sequencing (WES) - and in select cases, RNA sequencing – was performed on a large collection of NSCLC samples prior to immune checkpoint blockade therapy, along with matched clinical response data following therapy. (Profiling of a small number of on- or post-treatment samples was also performed.) We anticipate this dataset to be of high value for the development of a deep understanding of the molecular determinants of immune checkpoint blockade response as well as the discovery of novel biomarkers.

  Study phs002822

• Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis

  The role of non-coding variants in polygenic skin disease and their connection to homeostatic transcription factors (TFs) in epidermis was investigated. Homeostatic TFs were identified by perturb-seq in differentiating keratinocytes, using either 10x or split-pool approaches to sequencing, with follow-up validation by siRNA and RNA-seq. TF binding events were profiled by population sampling Cleavage Under Targets & Release Using Nuclease (CUT&RUN), in which a random population of neonatal foreskin keratinocytes were assayed by CUT&RUN for homeostatic TFs under progenitor growth and differentiation conditions. Heterozygous alleles were identified from the TF binding data and examined for allele specific binding events (ASBs). ASBs were then compared with non-coding variants linked to skin disease. Variants with potentially pathogenic effects were identified. Promoters and high TF occupancy genomic regions were found to be "buffered" against variants causing ASBs.

  Study phs003977

• Genomic and Transcriptomic Data from Advanced Rare Cancer Patients Treated with Pembrolizumab

  This dataset comprises whole exome sequencing data and RNA-seq data of advanced rare cancer patients.

  Dataset EGAD50000002182

• 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

• Detection and characterization of lung cancer using cell-free DNA fragmentomes

  Lung cancer remains the leading cause of cancer death world-wide, largely due to its late diagnosis. Non-invasive approaches for assessment of cell-free DNA (cfDNA) provide an opportunity for detection and intervention that may have broader accessibility than current imaging approaches. Using a machine learning model for detecting tumor-derived cfDNA through genome-wide analyses of cfDNA fragmentation, we examined a prospective study of 365 individuals at risk for lung cancer (Lung Cancer Diagnostic Study, LUCAS), including 129 individuals ultimately diagnosed with lung cancer and 236 individuals determined to not have lung cancer. We externally validated the cancer detection model using an independent cohort of 385 non-cancer individuals and 46 predominantly early stage lung cancer patients. Combining fragmentation features with clinical risk factors and CEA levels followed by CT imaging detected 94% of patients with cancer across stages and subtypes, including 91% of stage I/II and 96% of stage III/IV, at 80% specificity. Genome-wide fragmentation profiles across ~13,000 ASCL1 transcription factor binding sites could be used to distinguish individuals with small cell lung cancer (SCLC) from those with non-small cell lung cancer (NSCLC) with high accuracy (AUC=0.98). Among individuals with lung cancer, a higher cfDNA fragmentation score was associated with tumor size and invasion, and represented an independent prognostic indicator of survival. These studies provide a facile approach for non-invasive detection of lung cancer and clinical management of this disease.

  Study EGAS00001005340

• Hyperdiploid Acute Lymphoblastic Leukemia RNA-Seq

  Few genetic drivers of children with hyperdiploid precursor B-cell acute lymphoblastic leukemia (ALL) have been identified to date. In an effort to detect novel genomic rearrangements that could be promoting leukemogenesis in this subset of patients, we sequenced ribosomal RNA-depleted transcriptomes isolated from 5 hyperdiploid acute lymphoblastic leukemia samples. In addition to looking for novel genomic rearrangements, we also sought to identify transcripts that could be created as a result of a novel posttranscriptional process. Surprisingly, we identified transcripts created as the result of exon circularization. The results of our studies are present in the paper "Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types" published in PLoS ONE (PMID: 22319583).

  Study phs000522

• Ghana Breast Health Study

  The Ghana Breast Health Study (GBHS) was a multi-disciplinary, population-based case-control study conducted in Accra and Kumasi, Ghana that was designed to investigate breast cancer etiology in the West Africa region. The study enrolled 1,126 invasive breast cancer cases and 2,106 frequency matched population-based controls using census-based sampling. GHBS participants were between the ages of 18 to 74 years of age. Breast cancer cases were recruited at the time they presented with lesions suspicious of breast cancer at three hospitals: Korle Bu Teaching Hospital (Accra), Komfo Anoyke Teaching Hospital (Kumasi) and Peace and Love Hospital (Kumasi). These hospitals are the primary providers of treatment for breast cancer in Ghana, allowing for cases in our study to represent most breast cancers diagnosed in these areas during the study period. The following publications describe the GBHS in detail: 1) Brinton LA et al. Design considerations for identifying breast cancer risk factors in a population-based study in Africa. Int J Cancer 2017;140:2667-2677 (PMID:28295287). 2) Nyante SJ et al. Recruiting population controls for case-control studies in sub-Saharan Africa: The Ghana Breast Health Study. PloS one 2019;14:e0215347 (PMID:30990841)Among subjects with an available source of germline DNA genotyping was performed using the Infinium Global Screening Array-24 per the manufacturer’s guidelines using the Infinium automated protocol. We excluded probable duplicates and close relatives, and samples with a call rate < 95% or samples with extreme heterozygosity. Female sex was verified by Identifiler using X chromosome heterozygosity and the X chromosome inbreeding coefficient F statistics. The GLU genetics’ ld.tagzilla module was used to confirm African ancestry. To resolve more detailed population substructure, principal components analysis was conducted among all unrelated subjects using the EIGENSOFT v7.2.1. Imputation was performed using the Michigan imputation server Minimac3 with 1K genomes phase3 as reference panel.

  Study phs002387

• The Natural History of Human Prostate Cancer

  Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of 3 men. For each of three different prostates, multiple tumour samples (4, 5, and 3 depending on the case) and one normal tissue sample were whole genome sequenced with a matched blood sample using the Illumiuna HiSeq platform. Tumour samples were sequenced to a target depth of 50X and normals and blood to a target depth of 30X. As of September 2020, some of the studies using these data include: Cooper et al, Nature Genetics 2015 (PMID: 25730763) Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)

  Dataset EGAD00001000689

• 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

• Single-Cell Transcriptomic Characterization of Microscopic Colitis

  Patients with microscopic colitis (MC), chronic diarrhea without histological signs of MC, or unaffected controls were profiled using single-cell RNA sequencing (scRNA-seq; inDrops and 10X Genomics were used). One profiled patient without clinical symptoms was found to have histological signs of MC (asymptomatic MC). Some of the subjects from dbGaP study phs003418 are controls in this study. T-Cell Receptor sequencing (TCR-Seq) was also performed on a subset of patients. Individual transcriptomes were analyzed to characterize the cellular profile associated with MC and search for mediators of disease pathology. Raw reads and processed count matrices will be available through dbGaP.

  Study phs003876

• RNA sequencing in primary human macrophages overexpressing ETS2

  This dataset consists of RNA sequencing data from an ETS2 overexpression experiment in M0 macrophages. Controlled overexpression of ETS2 mRNA or control mRNA (an equivalent amount of mRNA encoding the reverse complement of ETS2 – thereby controlling for the quantity, length and purine/pyrimidine composition of the transfected RNA but with a transcript that would not be translated) was induced in resting, non-activated (M0) macrophages by transfecting predefined amounts of in vitro transcribed mRNA. To minimise non-specific activation due to the transfected RNA, in vitro transcription was performed using co-transcriptional capping (to minimise uncapped products), and incorporating modified, minimally immunogenic nucleotides (replacing uridine with N1-methyl-pseudouridine and cytidine with methylcytidine). After 18 hours, transfected cells were were activated with low dose LPS and harvested for RNA-sequencing 6 hours later. Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NovaSeq6000. Raw data are provided as 100 bp paired-end Illumina reads from n = 8 donors.

  Dataset EGAD00001011341