12004 results for "cancer rna-seq"

in 21.05 milliseconds.

• Dynamics of sequence and structural cell-free DNA landscapes in small-cell lung cancer

  The dataset for the study “Dynamics of sequence and structural cell-free DNA landscapes in small-cell lung cancer” includes 171 bam files from targeted next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 33 individuals with small cell lung cancer, alongside 10 bam files from whole exome sequencing of tumor and matched normal DNA for 5 individuals with small cell lung cancer.

  Dataset EGAD00001009860

• Mutation of FOXL2 in granulosa cell tumors of the ovary

  We generated paired-end RNA-Seq data using the Illumina Genome Analyzer II platform for four adult granulosa cell tumours (GCTs) of the ovary (1 primary, 3 recurrent). We screened this data for the presence of GCT specific sequence variants and detected a non-synonymous mutation in the FOXL2 gene that was found to be recurrent in 97% of 89 additional GCTs. To measure genomic stability of the four index cases, we generated Affmetrix SNP 6.0 data and analysed these data for copy number changes. Raw sequence reads as well as Affymetrix CEL files are available to applicants.

  Study EGAS00000000040

• Genomic Features of Lung Adenocarcinoma from Individuals with <= 10 Pack-Year Smoking History

  Actionable oncogenic alterations are identified in a subset of lung adenocarcinomas. Many of these driver alterations are enriched in lung adenocarcinomas from individuals with minimal smoking history and are generally mutually exclusive of one another. We generated whole-exome and RNA-seq data from lung adenocarcinomas obtained from individuals with &#8804;10 pack-year smoking history. Most of these tumors harbored an established oncogenic alteration. We identified a novel OCLN-RASGRF1 fusion from one tumor that lacked a known oncogenic driver. Functional studies demonstrated this fusion activates RAS signaling and promotes tumorigenesis in cell models.

  Study phs002556

• 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

• Genetic and Epigenetic Determinants of Pediatric Obesity-Associated Asthma

  Fifty-nine obese and sixty-one normal-weight asthmatic children of African American or Hispanic background, age 7-11 years, with well controlled asthma, were recruited from clinics affiliated with Children&#39;s Hospital at Montefiore, Bronx, New York, USA. We isolated CD4+ T cells (Th cells) from a fasting sample of peripheral blood and conducted genome-wide assays of gene expression by Directional Transcriptome Sequencing (RNA-seq), DNA methylation by HELP-tagging, and examined genetic polymorphisms and single nucleotide polymorphisms (SNPs), informative about ancestry, by array-based genotyping using Multi-Ethnic Genotyping Array.

  Study phs001812

• Multi-Omic Investigation of Beckwith-Wiedemann Syndrome Wilms Tumor

  Wilms&#8217; Tumor (WT), also known as nephroblastoma, is one of the most common malignant kidney tumors diagnosed in children. One of the most common WT predisposition syndromes is Beckwith-Wiedemann Syndrome (BWS, OMIM: 130650), which affects approximately 1/10,000 live births. In this study, we perform Whole Exome Sequencing (WES), DNA methylation array, and messenger RNA-Sequencing (mRNA-Seq), to examine the genomic, methylomic, and transcriptomic signature of BWS WT. We analyzed six tumor-normal paired samples, three BWS tumor only samples, and four non-BWS control samples to identify BWS WT drivers.

  Study phs002769

• EWS-WT1 Fusion Isoforms Establish Oncogenic Programs and Therapeutic Vulnerabilities in Desmoplastic Small Round Cell Tumors

  Desmoplastic Small Round Cell Tumor (DSRCT) is an aggressive mesenchymal tumor driven by fusions between the disordered domain of the Ewing sarcoma RNA binding protein 1 (EWSR1) and the developmental transcription factor Wilms tumor 1 (WT1). We used genome-wide chromatin profiling to identify EWSR1-WT1-dependent gene regulatory networks and target genes. Our studies show that EWS-WT1 is a powerful activator of distal regulatory elements and controls an oncogenic gene expression program that characterizes primary DSRCTs. ChIP-seq profiles for histone marks in primary DSRCT samples are available through dbGaP.

  Study phs003682

• ABHD11 inhibition drives sterol metabolism to modulate T cell effector function and alleviate autoimmunity

  Chronic inflammation in autoimmunity is driven by hyperactive T cells with dysregulated metabolism. ABHD11 is a mitochondrial hydrolase that supports alpha-ketoglutarate dehydrogenase function and has been associated with remission in rheumatoid arthritis. To explore its role in T cell function, we used CRISPR/Cas9 to knock down ABHD11 in Jurkat T cells and performed RNA-Seq analysis. Differential gene expression revealed widespread transcriptional changes, with sterol-related pathways among the most significantly enriched. These findings highlight ABHD11 as a potential regulator of metabolic programming in T cells with implications for autoimmunity.

  Study EGAS50000001297

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the regulation of B cell recptor repertoire in B cell subsets and its contribution to autoimmune diseases, B cell subsets from 36 Systemic Lupus Erythematosus(SLE), 90 Systemic Sclerosis(SSc), 85 Myositis(IIM), 21 Mixed Connective Tissue Disease(MCTD), 18 Sjogren's syndrome(SjS), 27 Rheumatoid Arthritis(RA), 23 Behcet's disease(BD), 18 Adult Onset Still���s Disease(AOSD), 24 ANCA-associated Vasculitis(AAV), 16 Takayasu���s Arteritis(TAK) and 137 healthy controls(HC) were collected (Naive_B, USM_B, SM_B, DN_B, Plasmablast. RNA-seq and BCR-mapping was performed with each B cell subset samples.

  Study JGAS000485

• Transcriptomic profiling of skin biopsies from psoriasis patients following treatment with Zasocitinib

  The objective of this study is the exploratory analysis and characterization of psoriasis using RNA-seq-based profiling. Specifically, the cutaneous and serum biomarker profiles associated with the molecular, histological and clinical effects of Zasocitinib treatment in patients with moderate-to-severe plaque psoriasis were characterized. To evaluate differences between the transcriptomic profiles of Zasocitinib- and placebo-treated patients, exploratory biomarker endpoints included quantification of skin biomarkers, such as immune cell infiltration and mRNA expression levels in lesional and non-lesional skin, as well as quantification of circulating cytokines and other inflammatory biomarkers.

  Study EGAS50000001548

• An Integrated Approach to Patient Stratification and Therapy Selection in Acute Myeloid Leukemia

  As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we developed and validated a clinical transcriptome-based assay for stratification of acute myeloid leukemia (AML). Comparison of RNA-Seq to whole genome and exome sequencing revealed that as a standalone assay, RNA-Seq offered the greatest diagnostic return, enabling identification of expressed gene fusions, single nucleotide and short insertion/deletion variants, and whole-transcriptome expression information. Expression data were used to develop a novel risk score which, when combined with molecular risk guidelines, allowed for the re-stratification of 22.1 to 25.3% of AML patients from three independent cohorts into correct risk groups. Within the adverse-risk subgroup, we identified a subset of patients characterized by dysregulated integrin signaling and RUNX1 or TP53 mutation. We show that these patients may benefit from therapy with inhibitors of focal adhesion kinase (PTK2), demonstrating additional utility of transcriptome-based testing for therapy selection in myeloid malignancy.

  Dataset EGAD00001006701

• RNA-seq data

  RNA-seq FASTQ files from 296 bulk pre-treatment tumors from IMblaze370

  Dataset EGAD00001008553

• HiDEF-seq single-molecule sequencing of single-strand mismatches and damage

  Our study sought to resolve, with single-molecule fidelity, the mismatches and damage events that precede DNA mutations. Using a novel single-molecule, long-read sequencing method (HiDEF-seq) we detect base substitutions when present in either one or both DNA strands. We also detect cytosine deamination, a common type of DNA damage, with single-molecule fidelity. This study profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes. These samples revealed single-strand mismatch and damage signatures. Since double-strand DNA mutations are only the endpoint of the mutation process, our approach enables new studies of how mutations arise in a variety of contexts, especially in cancer and aging.

  Dataset EGAD50000000460

• RNA sequencing

  RNAseq of 45 high-grade serous ovarian cancer tumour samples. Libraries were generated using the NEB Ultra II Directional RNA library Prep kit with polyA enrichment. Libraries were sequenced as paired-end 50 or 100bp on an Illumina NextSeq or NovaSeq.

  Dataset EGAD00001009844

• CCMA-RNA

  This dataset has the raw RNA sequencing data for the cancer models in CCMA.

  Dataset EGAD00001010034

• Cell and Circuit-Specific Exploration of HIV Neurogenomics in Context of Opiate and Cocaine Misuse

  Utilizing frozen postmortem brain tissue from the Manhattan HIV Brain Bank, we performed cell-type-specific, genome-wide sequencing of three different types: 1) single-nucleus RNA-sequencing (snRNA-seq), 2) in situ Hi-C, and 3) HIV integration site sequencing (IS-seq). We assayed tissue from three different donor types: 1) HIV-uninfected control (HIV-), HIV-infected (HIV+), and HIV-infected with HIV encephalitis (HIVE), who served as a positive control for active CNS viral infection. The diagnosis of HIVE was made by a board-certified neuropathologist on routine histopathology, based on the presence of a microglial nodule encephalitis with characteristic multinucleated syncytial cells and staining for HIV p24 antigen. Other HIV-infected individuals (the HIV+ group) did not have this histologic evidence of active HIV brain replication, and were variable with regard to cART status and virologic control prior to death. Donor characteristics, including ante-mortem plasma HIV loads, CD4 counts, and cART status, were documented. Quality controls were used for each assay: For snRNA-seq we applied filters to remove low quality nuclei from analysis and performed experiments in which mouse tissue was mixed with human tissue to determine a reliable HIV read count threshold. For Hi-C, we used paired HIV- and HIVE samples and processed all samples in parallel, at the same time. Correlation analysis was used to ensure biological replicates were aligned. For IS-seq, each time the assay was run, a positive and negative control were included. This allowed us to ensure a lack of contamination in IS-seq libraries and that, when a particular sample failed to yield library, this was due to low levels of HIV rather than a failure of the assay. Altogether, we built an integrative dataset from 79 sequencing files, including snRNA-seq, and cell type specific Hi-C, IS-seq, and ChIP-seq datasets. Human autopsy brain samples were collected by the Manhattan HIV Brain Bank (MHBB, U24MH100931), using protocols under the supervision of the Icahn School of Medicine at Mount Sinai (ISMMS) Institutional Review Board. Written informed consent was obtained either from decedents or their primary next of kin. Major Findings: Reorganization of open/repressive (A/B) compartment structures in HIVE microglia encompassing 6.4% of the genome was linked to transcriptional activation of interferon (IFN) signaling and cell migratory pathways and was partially recapitulated by IFN-gamma stimulation of cultured microglia. In contrast, decreased expression and repressive compartmentalization of genes regulating neuronal health and signaling was seen in both HIVE and HIV+ microglia. IS-seq recovered 1,221 integration sites in the brain that displayed distinct genomic patterns as compared to peripheral lymphocyte integration and were enriched for chromosomal domains newly mobilized into a permissive chromatin environment in HIVE microglia. Viral transcription occurred in a subset of highly activated microglia comprising 0.003% of all nuclei in HIVE brain. Our findings point to a disruption of microglia-neuronal interactions in the HIV infected brain and an interrelation of retroviral integration and expression with interferon-associated remodeling of the microglial 3D genome during progression to HIVE. Search terms: HIV, postmortem brain, microglia, substance abuse, viral integration, chromosomal conformation capture, Hi-C, chromatin, single nuclei RNA-seq, Irf8, NeuN, HIV encephalitis, neuron-microglia interaction, cytokine

  Study phs003080

• Childhood Cancer Data Initiative (CCDI): Molecular Characterization across Pediatric Brain Tumors and Other Solid and Hematologic Malignancies for Research, Diagnostic, and Precision Medicine

  This study contains tumor and germline WGS, RNA-Seq, Clinical Panel Sequencing, and other omics and molecular data for patients with pediatric brain tumors and other solid and hematologic malignancies. This data has been collected from multiple organizations including the multi-institute Children's Brain Tumor Network (CBTN), the Pacific Pediatric Neuro-Oncology Consortium (PNOC), and the Children's Hospital of Philadelphia Division for Genomic Diagnostics (CHOP DGD). In addition to being available pre-publication and without embargo via dbGaP and the NCI Cancer Research Data Commons, this data is made available via Cavatica, PedcBioPortal and the Kids First Data Resource Portal. Collectively, this availability strives to accelerate the research process and enable members of the scientific and patient communities to partner and make discoveries faster than ever before.In 2019, the CBTN launched the Pediatric Brain Tumor Atlas, which now comprises the largest collection of childhood brain tumor data in the world. This resource is helping accelerate not only brain tumor research, but is also empowering discovery for other rare childhood conditions. Brain tumors are the most common form of cancer in children aged 0-19 in the United States, and are the largest cause of cancer-related deaths. The estimated number of new cases in 2019 is nearly 3,800, and thus brain tumors are a rare disease. Despite their relative rarity, the years of potential life lost due to brain tumors in 2009 was estimated at 47,631 years for children and adolescents aged 0-19 in the United States; this is a disproportionate amount of life lost compared to adult cancers and represents an unrecognized societal threat. There is an urgent need to improve therapies for these children. This sequencing cohort defines the largest, clinically annotated pediatric brain tumor cohort study to date and seeks to define the intersection of germline and somatic underpinnings of pediatric brain tumors across a shared developmental context of cancer and structural birth defects.

  Study phs002517

• RNA sequencing data of 66 matched primary and recurrent high grade serous ovarian cancer

  Gene expression profiles of matched primary and recurrent fresh frozen tumor tissues from 66 HGSOC patients were obtained by RNA sequencing. RNA libraries were created using the Illumina TruSeq RNA sample preparation kit V2 according to the manufacturer’s instructions and sequenced on a HiSeq2000 (Illumina, California, USA) using a V3 flowcell generating 1 x 50 bp reads. Raw sequencing reads were mapped to the transcriptome and the human reference genome (NCBI37/hg19) using TopHat 2.0 and Bowtie 2.0.

  Study EGAS00001002660

• Single cell ATAC seq component of ATAC-RNA multiome analysis of a four weeks post conception embryo head

  Four single-cell ATAC libraries were generated from an unbiased sample of cells of a human four weeks post conception embryo using the 10X Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC+Gene Expression kit (10X Genomics) according to the manufacturer’s protocol.

  Dataset EGAD50000001502

• ResolveCRPS study - Transcriptomics

  Transcriptome profiling of CRPS-affected skin using low-input total RNA-seq (paired-end mode with 54 and 68 nt read length for R1 and R2 respectively, Illumination NextSeq2000). 42 snap-frozen skin biopsies were analyzed together with longitudinal clinical data. The dataset contains FASTQ files, the processed read count matrix, and the corresponding clinical metadata.

  Dataset EGAD50000001545

• Dataset of Master Samples submitted to other HIPO projects

  RNA-Seq, WES and WGS data of 5 rare tumor/control pairs which were submitted to other HIPO projects, not MASTER. The sequencing was always paired.

  Dataset EGAD00001008905

• Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

  RNA seq of iPSC-derived cardiomyocytes cultured in lipid-enriched maturation medium (MM), in MM on nanopattern-surfaces (NP) and under the influence of MM, NP and electrical Stimulation (ES, 2Hz, 14 days). 9 Samples from 3 Independent batches/differentiations of cardiomyocytes from 2 different iPSC-lines (iWTD2.1 and isWT7.22).

  Dataset EGAD00001011289

• Human tumor single-cell

  We profiled 11 patient tumor samples by single-cell and single-nuclei RNA-seq using 10X Chromium 3'. These include samples from the following entities: WNT-subtype medulloblastoma (N=3), embryonal tumors with multilayered rosettes (N=3), and atypical teratoid-rhabdoid tumors (N=5). The BAM files are provided.

  Dataset EGAD00001005129

• Sequencing Data for Sample 51_Hf01_BlCM_Ct

  Sequencing Data for DEEP Paper: "reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T-Cells" Sample: 51_Hf01_BlCM_Ct (human, female, Blood, CD4+ central memory cell, normal control) Sequencing types are: total RNA, Whole Genome Bisulfite, ChipSeq (H3K27ac, H3K9me3, H3k36me3, H3K4me1, H3k27me3, H3K4me3, Input), reChipSeq (H3K27me3, H3K4me3)

  Dataset EGAD00001002255

• RNA-seq of T-ALL patient-derived xenograft (PDX) samples

  This dataset includes 4 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Human patient T-ALL samples were serially propagated as xenografts in immunodeficient mice. The samples were collected after development of frank leukemia in recipient mice.

  Dataset EGAD00001009749

• Bulk RNA Seq in FAP Adenoma

  Bulk RNASeq data of Duodenal organoids, sorted ILC3 and duodenal tissue

  Dataset EGAD00001015488

• RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

  Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples (n=374) for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs (n=96) for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect. 18 of 36 participants developed a replicative SARS-CoV-2 infection as evidenced by consecutive PCR-positive swabs for the virus. For every participant, blood RNA from selected days were extracted and depleted for genomic DNA and globin mRNA, before cDNA libraries were constructed using KAPA RNA HyperPrep with RiboErase kits. Libraries were sequenced on the Illumina NovaSeq 6000 platform using NovaSeq 6000 S4 Reagent Kits (200 cycles). Nose swab RNA samples were extracted and depleted for genomic DNA before cDNA libraries were constructed using KAPA mRNA HyperPrep Kits. Libraries were sequenced on the Illumina NextSeq platform the using the NextSeq 500/550 High Output Kit (75 cycles).

  Dataset EGAD50000000942

• Healthy control cfMeDIP-seq

  This dataset comprises 46 raw fastq files derived from 23 plasma cfDNA samples from 23 healthy (CTL) cancer-free donors. For each sample, 10ng of cfDNA was used for library preparation utilizing the cfMeDIP-seq technology based on the 5mC antibody-immunoprecipitation strategy. Libraries were validated via Bioanalyzer trace analysis and sequenced on the Illumina NovaSeq 6000 platform with paired-end 150-bp model for ~100 million reads per sample.

  Dataset EGAD50000000652

• Chromatin accessibility of clear cell renal cell carcinoma

  To investigate chromatin accessibility in ccRCC, we performed ATAC-seq in 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001325

• scRNA sequencing of in vitro generated suppressive myeloid cells using parental and Sialidase expressing A549 cancer cell lines

  Fresh peripheral blood mononuclear cells of four human donors were cultured together with either lung adenocarcinoma A549 cancer cells or A549-expressing H1N1 Sialidase cancer cells. These treatments induced the differentiation of donor cells into immunosuppressive MDSC-like cells, which were further subjected to single-cell RNA sequencing.

  Dataset EGAD50000000351

• Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

  Droplet-based single-cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While these approaches offer the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective, reliable, and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we have developed a microfluidic control instrument that can be easily assembled from 3D printed parts and commercially available components costing approximately $575. We adapted this instrument for massively parallel scRNA-seq and deployed it in a clinical environment to perform single-cell transcriptome profiling of disaggregated synovial tissue from 5 rheumatoid arthritis patients. We sequenced 20,387 single cells from synovectomies, revealing 13 transcriptomically distinct clusters. These encompass a comprehensive and unbiased characterization of the autoimmune infiltrate, including inflammatory T and NK subsets that contribute to disease biology. Additionally, we identified fibroblast subpopulations that are demarcated via THY1 (CD90) and CD55 expression. Further experiments confirm that these represent synovial fibroblasts residing within the synovial intimal lining and subintimal lining, respectively, each under the influence of differing microenvironments. We envision that this instrument will have broad utility in basic and clinical settings, enabling low-cost and routine application of microfluidic techniques, and in particular single-cell transcriptome profiling. Reprinted from [Stephenson et al., Nature Communications, 2018], with permission from the Nature Publishing Group.

  Study phs001529

• 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

• Single-cell transcriptomic analyses of peripheral blood mononuclear cells, peritoneal fluid, and peritoneal metastases from patients with colorectal cancer

  The data published here contains single-cell RNA- sequencing (scRNAseq) on peripheral blood mononuclear cells (PBMC), peritoneal fluid (PF), and peritoneal metastases (PM). PBMC, PF and, where possible, PM was acquired from patients with colorectal cancer (CRC) and subjected to 3' scRNAseq using the 10X Genomics (Chromium Single Cell 3’ Reagent). Sequencing was performed in a paired-ended fashion on either the HiSeq4000 or the NovaSeq6000.

  Study EGAS50000000173

• Efficacy of dual KRAS G12D–EGFR blockade versus triple combinations in patient-derived models of KRAS G12D-mutant colorectal cancer

  RNA sequencing was performed on patient-derived xenograft (PDX)-derived organoid models of metastatic colorectal cancer (mCRC). The aim of this study was to characterize the transcriptional landscape of KRAS-mutant mCRC cells in response to therapeutic strategies targeting the EGFR and KRAS signaling pathways. Transcriptomic profiling was conducted following drug treatments to investigate molecular changes associated with single and combination therapies. A total of 24 samples were analyzed.

  Study EGAS50000001700

• Gene expression profile of mesothelial-derived carcinoma-associated fibroblasts

  RNA-sequencing was carried out on ascetic fluid-isolated mesothelial cells from low-grade serous ovarian cancer patients, high-grade serous ovarian cancer patients, chemotherapy-treated high-grade serous ovarian cancer patients and control mesothelial cells obtained from non-oncologic patients to identify differentially expressed genes associated to mesothelial-to-mesenchymal transition process. The dataset contains 18 samples: - Control mesothelial cells: 4 samples - Group 1, high-grade serous ovarian cancer patients: 3 samples - Group 2, chemotherapy-treated high-grade serous ovarian cancer patients: 5 samples - Group 3, low-grade serous ovarian cancer patients: 6 samples

  Dataset EGAD00001005133

• RNA sequencing data of 257 samples from 106 patients with HR+/HER2- breast cancer treated with AC plus paclitaxel or letrozole plus ribociclib (SOLTI-1402 CORALLEEN trial)

  Early-stage Luminal B breast cancer is frequent and is a major cause of breast cancer death due to its poor prognosis. Our proposal aims to study the biology behind the sensitivity and resistance of Luminal B breast cancer to chemotherapy (CHT) or a non-CHT regimen composed of hormone therapy in combination with ribociclib, a CDK4/6 inhibitor. To accomplish this, we first completed the SOLTI-1402 CORALLEEN phase II trial, a study where 106 patients with early-stage Luminal B breast cancer were randomized to standard neoadjuvant CHT for 6 months, or neoadjuvant letrozole and ribociclib for 6 months. After treatment, patients underwent surgery. The primary results of the study, which showed that the response rate to letrozole+ribociclib was similar to CHT, was reported (Prat et al; Lancet Oncol). Tumor biopsies were available at baseline, week 3 and surgery. A total of 257 samples were analyzed using the Illumina TruSeq Stranded Total RNA w/Ribo Zero Gold with MiSeq in TGL (Sequencer NovaSeq S4/PE/100x).

  Study EGAS00001007060

• RNAseq dataset of ovarian cancer patients

  Dataset of transcriptomics data from a cohort of individuals diagnosed with ovarian cancer. This dataset includes RNAseq sequencing data from 68 individuals. A total of 109 tumor samples were sequenced. Samples were prepared with the Illumina TruSeq Stranded RNA library. Sequencing data are paired end.

  Dataset EGAD50000001556

• Mechanisms of Extreme Genomic Instability at Large Transcribed Genes

  Inhibiting DNA replication leads to copy number variant (CNV) formation throughout the genome, especially at chromosome fragile sites (CFSs). We previously showed that these hotspots for genome instability reside in late-replicating domains associated with large transcribed genes. In this study, we compared aphidicolin (APH)-induced CNV and CFS frequency between wild-type cells and isogenic cells in which FHIT gene transcription was ablated. We further examined the impact of altering RNase H1 expression on CNV or CFS induction frequency and analyzed R-loop formation genome-wide in a human fibroblast cell line. Data sets include Bru-seq nascent RNA transcription, whole genome sequencing for replication timing, SNP microarray analysis, and DRIP-seq. Results suggest that large gene transcription is a determining factor in replication stress-induced genomic instability and that CFSs mainly result from transcription-dependent passage of unreplicated DNA into mitosis with low R-loop levels observed at these loci.

  Study phs002066

• Interpreting molecular role of DNA variants associated with Crohn's Disease through integrative analysis of open chromatin, epigenome and transcriptome data in diverse and relevant tissues and cells

  Crohn&#39;s disease (CD), one of the two major inflammatory bowel diseases (IBD), results from an inappropriately directed inflammatory response to the enteric microbiota in a genetically susceptible host. Genome wide association studies (GWAS) have linked &gt;200 specific single nucleotide polymorphisms (SNPs) to CD disease pathogenesis. Within these regions, there are over 5600 additional SNPs that are in linkage disequilibrium (LD) with the tag SNPs, and it is not known which of these contribute to CD. Most of these SNPs map to non-coding regions of the genome, suggesting that causal variants contribute to CD by modifying gene regulatory element activity. In ths study, we have generated genotype, open chromatin (FAIRE-seq), and transcriptome (RNA-seq) data from macroscopically uninflamed regions of colon tissue for 21 CD patients and 11 non-IBD controls. All patients are adults (&gt;18 years old).

  Study phs001418

• Human CD4+ T cells regulate peripheral immune responses in rheumatoid arthritis via IGFL2

  To elucidate the role of the immunoregulatory mechanisms of human CD4+ T cells, we analyzed CD4+ T cells in PBMC, synovium and synovial fluid using single-cell RNA sequencing (scRNA-seq). We identified insulin-like growth factor (IGF) like family member 2 (IGFL2), an evolutionary novel paralogous inflammatory factor found exclusively in primates. ScRNA-seq of RA synovium showed that IGFL2 is specifically expressed by CD4+ T cells, predominantly within peripheral helper T (Tph) cells, with upregulation correlating to disease severity. IGFL2 promotes TGF-��-induced CXCL13 production in CD4+ T cells. In addition, IGFL2 activates NF-��B signaling and induces monocyte gene signatures associated with pathogenic macrophages from RA synovial tissue, including CXCL10 and CXCL9. Notably, blood IGFL2 protein levels significantly correlate with RA disease severity and effectively discriminate RA patients. These findings highlight the substantial involvement of IGFL2 in RA pathogenesis, emphasizing how human CD4+ T cells exert pleiotropic regulation of local immune responses via this novel primate-specific soluble factor.

  Study JGAS000727

• Integrative understanding of human immune system by functional genomics and development of intervention strategies for the prevention of autoimmune diseases

  To elucidate the regulation of gene expression in immune cell subsets and its contribution to autoimmune diseases, Whole blood and various immune cell subsets from 119 Systemic Lupus Erythematosus (SLE), 65 Dermatomyositis & Polymyositis, 67 Systemic Sclerosis, 19 Mixed Connective Tissue Disease, 18 Sjogren's syndrome, 24 Rheumatoid Arthritis, 23 Behcet's disease, 18 Adult Onset Still���s Disease, 25 ANCA-associated Vasculitis, 16 Takayasu���s Arteritis and 141 healthy controls (C) were collected (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu). Whole genome sequencing was performed with whole blood samples. RNA-seq was performed with each immune cell subset samples. After filtering and normalization of the gene expression data, eQTL analysis was performed in each immune cell type. 15 immune cell subsets ATAC-seq was also performed in 8 SLE and HCs, each.

  Study JGAS000220

• 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

• 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 atlas of large B-cell lymphoma

  The dataset comprises multi-omics profiles from 232 biopsies, including 217 from patients with large B-cell lymphoma (114 newly diagnosed and 103 relapsed/refractory) and 15 benign control samples. Specifically: single-nucleus RNA sequencing (snRNA-seq) was performed on all 232 biopsies; single-nucleus ATAC sequencing was conducted on 96 biopsies; bulk RNA sequencing was generated for 208 biopsies; whole-exome sequencing (WES) was performed on 174 tumor biopsies with 118 matched germline samples; Low-pass whole-genome sequencing (lpWGS) was performed on 174 tumor biopsies with 41 matched germline samples. All raw data files are provided in FASTQ format.

  Dataset EGAD50000001491

• 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

• RNA seq of intestinal biopsies and blood cells from patients with celiac disease and controls

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Dataset EGAD50000001597

• Single-cell RNA-seq of human kidney tumors

  Fresh nephrectomy samples were collected from a total of 5 untreated ccRCC patients. Out of these 5 patients, 7 samples were obtained. Two samples consisted of fresh versus frozen single cells from the primary tumor site of one patient. Two other samples consisted of matched primary and distant thrombus sites (the vena cava) of a second patient. The three remaining samples came from the primary tumor sites of three distinct ccRCC patients. Single-cells were captured into 10x barcoded gel beads and RNA-sequencing library preparation was done using Chromium Single Cell 3' v2 chemistry. Sequencing was performed on a Illumina HiSeq 4000 sequencer.

  Dataset EGAD00001009306

• Bulk RNA-seq dataset of Single cell RNA sequencing reveals induced bifurcated differentiation after RUNX1::RUNX1T1 depletion in patient-derived leukemic blasts

  In this study, we demonstrate that primary AML cells harboring the chromosomal translocation t(8;21) are critically dependent on the corresponding fusion gene, RUNX1::RUNX1T1, to suppress differentiation and maintain stemness. Silencing RUNX1::RUNX1T1 expression using siRNA-loaded lipid nanoparticles induces significant changes in chromatin accessibility, redirecting the leukemia-associated transcriptional network towards a myeloid differentiation program. Single-cell analyses reveal that this transcriptional reprogramming is associated with the depletion of immature stem and progenitor-like cell populations, accompanied by an expansion of granulocytic and eosinophilic/mast cell-like populations with impaired self-renewal capacity.

  Dataset EGAD00001015508

• Using Genomics to Reduce Breast Cancer Disparities in the African Diaspora

  Differences in breast cancer incidence and mortality rates between North American Caucasian and African American women are well-described and transcend socioeconomic issues. Black women are diagnosed with breast cancer at a younger median age; have more clinically aggressive disease and stage-for-stage; and have higher mortality rates than age-matched Caucasian women. Black women in West Africa, the origin of the slave trade in the US in the 19th century and thus the founder population for most African Americans, have even higher rates of early-onset, poor-prognosis breast cancer than African American women. Racial difference in the distribution of intrinsic molecular subtypes has been well characterized in the US and throughout the African Diaspora as well. Despite the large efforts on characterizing racial/ethnic differences, however, the reasons women of African ancestry are disproportionately affected by breast cancer incidence and mortality remain poorly understood - largely due to paucity of data on inherent genomic differences that contribute to the disparities in incidence and progression of breast cancer across populations. West Africa Breast Cancer Study (WABCS) is an initiative that aims to comprehensively understand the genetic architecture of breast cancer in West Africans, the founder population of a large proportion of black women in the United States. The objective of the study was to provide a better understanding of the molecular genetic factors that influence prognosis in Nigerian breast cancer patients, and determine which of these alterations may be amenable to available therapy. To that end, we examined the molecular features of breast cancers of indigenous African women using a combination of whole-genome, whole-exome, and transcriptome sequencing (WGS, WES, and RNA-seq) on 194 tumors from Nigerian patients. The goal of this project was to obtain answers to two related research questions using an unscreened population without genetic admixture in Nigeria: 1) why are women of African ancestry more likely to develop aggressive young onset breast cancer? 2) What are the associated genomic and non-genomic risk factors? We hypothesize that the genomic determinants of breast cancer molecular subtypes in women of African ancestry are also molecular drivers of tumor progression and represent targets for interventions to improve clinical outcomes and close the mortality gap. By identifying causal links between genetic variants that promote aggressive tumor progression in Nigerian women in comparison to women from different population found in TCGA and ICGC, the present dataset will have significant public health impact on millions of women in the African Diaspora. The potential to identify novel pathways for interventions to reduce the increasing mortality gap between women of African and European ancestry is huge

  Study phs001687

• RNA sequencing of untreated head and neck cancer patient-derived xenografts (PDXs) and matched patient tumor tissue.

  RNA sequencing was performed on untreated patient tumor tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC). The aim of this analysis was to characterize the transcriptional landscape of the tumors in the in vivo setting.

  Study EGAS50000001595