7188 results for "({!join from=dataset_studies to=id v=$q1}) OR ("transcriptome" OR "RNA-seq" OR "rna sequencing" OR "rna-sequencing")"

in 39.29 milliseconds.

• RNA-seq, WGS and WES of Hepatocellular carcinomas, enriched in fibrolamellar carcinomas

  Dataset EGAD00001005308

• Myeloma XI trial data

  The dataset contains WGS and RNA-seq from Myeloma XI trial

  Dataset EGAD00001005491

• bulkRNA

  Bulk RNA-seq for cALL patient-derived PDX samples

  Dataset EGAD00001006133

• RNAseq data

  RNA-seq data from PAXgene extracted whole blood of patients enrolled in the COVACTA trial. This dataset includes raw FASTQ files.

  Dataset EGAD00001011168

• Gene expression of transduced human primary germinal centre B-cells

  RNA-seq sequencing data of human germinal centre B-cells (42 samples)

  Dataset EGAD00001005281

• Berlin Neuroblastoma Dataset

  Paired tumor/normal WGS and RNA-seq of primary neuroblastoma.

  Dataset EGAD00001005488

• GEP-NEN Bulk-RNA-seq dataset

  This dataset entails 40 Bulk-RNA sequenced patient-derived gastro-intestinal neuroendocrine (GEP-NEN) neoplasms.

  Dataset EGAD00001006657

• Single-cell transcriptomic analyses of peripheral blood mononuclear cells from patients with colorectal cancer metastasized to the peritoneum

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peripheral blood mononuclear cells (PBMC) from patients with colorectal cancer (CRC) and peritoneal metastases (PM). Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000247

• INTEGRATIVE MOLECULAR ANALYSIS OF SKIN TUMORS FROM CYLD CUTANEOUS SYNDROME PATIENTS

  CYLD cutaneous syndrome (CCS) is a rare autosomal dominant disorder characterized by germline CYLD mutations and by multiple benign skin tumors dependent on NF-kB pathway. We assembled a large cohort of CCS rare skin tumors that was profiled with whole exome or genome sequencing, RNA sequencing and methylation arrays to better understand genetic mechanisms of CCS tumorogenesis.

  Dataset EGAD50000000362

• Ischemia Reperfusion Responses in Human Lung Transplants at the Single Cell Resolution

  Ischemia reperfusion is an unavoidable step of organ transplantation. Development of therapeutics for lung injury during transplantation has proved challenging; understanding lung injury from human data at the single cell resolution is required to accelerate the development of therapeutics. Donor lung biopsies from six human lung transplant cases were collected at the end of cold preservation and 2-hour reperfusion and underwent single cell RNA sequencing.

  Dataset EGAD50000000704

• TIRE-seq_PDN

  TIRE-seq is a novel RNA sequencing method that integrates mRNA purification directly into library preparation, eliminating separate RNA extraction. The technique demonstrated utility across three biological applications, including capturing transcriptional changes in human T cells, identifying genes driving murine dendritic cell differentiation, and analyzing the dose-response effects of temozolomide on patient-derived neurospheres. With its simplified approach and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies.

  Dataset EGAD50000001261

• scRNAseq of co-culture of human organoids with polarized pro-inflammatory or anti-inflammatory macrophages

  In order to know if the mechanisms we identified in mice – demonstrating that macrophages are able to orchestrate the intestinal regenerative process – are conserved in humans we develop a co-culture system with human intestinal organoids and human polarized macrophages. We co-culture human organoids with pro-inflammatory or anti-inflammatory macrophages for 48h. On day 3 cells were collected to perform single cell RNA sequencing.

  Dataset EGAD50000000675

• Comparison clinical recommendation MASTER and panel sequencing: RNA data

  This dataset contains 19 case/control samples of RNA sequencing data. Sequencing was performed on Illumina HiSeq 4000 and NovaSeq 6000 using TruSeq Stranded mRNA Kit. The sequencing was always paired.

  Dataset EGAD50000000625

• scRNA and V(D)J sequencing of WM under ibrutinib

  Single-cell RNA sequencing (5′ gene expression) and single-cell V(D)J sequencing (B-cell receptor and T-cell receptor) were performed on bone marrow mononuclear cells from patients with Waldenström macroglobulinemia treated with ibrutinib monotherapy. Sequential bone marrow aspirate samples were collected at baseline and after treatment. A total of 222 BAM files are included in this dataset.

  Dataset EGAD50000002279

• Bulk RNASeq of metastatic colorectal cancer organoids treated with crenigacestat alone or in combination with cetuximab

  Bulk RNA sequencing was performed on mCRC organoids cultured under untreated conditions or treated with crenigacestat alone or in combination with cetuximab. This dataset was generated to investigate the transcriptional changes associated with combination therapy and to compare these profiles with the adaptive responses observed following cetuximab monotherapy in the corresponding ATOH1 wild-type and knockout organoid models.

  Dataset EGAD50000002061

• Data for the study "Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer"

  Sequencing data from patients with bladder cancer. BAM files from targeted DNA sequencing of bladder cancer driver genes in 344 circulating tumor DNA and tumor tissue samples. BAM files from whole exome sequencing of 49 circulating tumor DNA and tumor tissue samples. Paired FASTQ files from RNA sequencing of 86 tumor tissue samples.

  Dataset EGAD00001006362

• NCCS-NSCLC-ITH2-WES

  NCCS-NSCLC-ITH2 dataset of 185 sectors from 48 patients with early-stage non-small cell lung cancer diagnosed in National Cancer Centre Singapore; these are paired-end, whole-exome and bulk RNA sequencing data, sequenced by Illumina HiSeq 4000/2000.

  Dataset EGAD00001010158

• RNA sequencing of NK cells in human lung

  The dataset contains RNAseq data from 5 subsets of NK cells isolated from human lung: 1) CD69+CD49a+CD103+CD16-CD56bright NK cells 2) CD69+CD49a+CD103-CD16-CD56bright NK cells 3) CD69+CD49a-CD103-CD16-CD56bright NK cells 4) CD69-CD49a-CD103-CD16-CD56bright NK cells 5) CD56dimCD16+NKG2A+CD57- NK cells The dataset contains paired data for the subsets from 2 donors with 2 biological replicates/donor and subset.

  Dataset EGAD00001004850

• Human Biofluid RNA Atlas

  This dataset contains small RNA sequencing data and mRNA capture sequencing data from 20 different human biofluids (amniotic fluid, aqueous humor, ascites, bile, bronchial lavage fluid, breast milk, cerebrospinal fluid, colostrum, gastric fluid, pancreatic cyst fluid, plasma, saliva, seminal fluid, serum, sputum, stool, synovial fluid, sweat, tear fluid and urine). In total, 180 samples were sequenced. Files are provided in fastQ format. Samples were sequenced on a NextSeq 500.

  Dataset EGAD00001005439

• Single-cell RNA sequencing of cytokine-induced T cell responses

  Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated condition, as well as in the presence of Th2, iTreg and Th17 polarizing cocktail. To characterize the efficacy of cytokine induced porization and subpopulation specific response, we profiled single cell transcriptome five days following polarization using 10x platform (3' v2).

  Dataset EGAD00001005290

• TRACERx NSCLC - Multiregion RNA sequencing data from the 421 cohort

  RNAseq data from the TRACERx 421 cohort

  Dataset EGAD00001009862

• Exome and RNA-sequencing data from a relapsed t(1;19) acute lymphoblastic leukemia

  Sequence data is from 4 samples from an adult patient with TCF3-PBX1 t(1;19)-positive acute lymphoblastic leukemia. Exome sequencing was performed on a skin biopsy (normal tissue control) and leukemic bone marrow biopsies taken at diagnosis and at two relapse time points. RNA-sequence data is from leukemic bone marrow from two relapse biopsies.

  Dataset EGAD00001002203

• Smartseq2 data of single immune cells in hepatocellular carcinoma

  The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This dataset is part of Smartseq2 data

  Dataset EGAD00001005960

• Prognostic and immunomodulatory consequences of ERV expression in ovarian cancer

  The dataset contains transcriptional data obtained using total RNA sequencing on a Illumina machin. 59 samples are from the Hammersmith Hospital (HH) cohort of human primary ovarian tumours and 20 samples are from ovarian cancer cell lines Kuramochi (3 replicates) and Ovsaho (2 replicates) treated with 1 uM DNMTi guadecitabine or vehicle, at an early (day 5) or late (day 8) timepoint.

  Dataset EGAD00001006589

• The BNT162b2 mRNA COVID-19 vaccine induces long-term effects on both adaptive and innate immune responses

  This dataset contains bulk RNA sequencing at different timepoints post-BNT162b2 mRNA COVID-19 vaccination. Stimulation experiments were performed at each of the timepoints (RPMI, Influenza, R848 and Influenza stimuli), resulting in 242 libraries distributed over 4 stimulations and 4 timepoints. Libraries were sequenced on the DBNSEQ platform.

  Dataset EGAD00001011042

• Genomics of enteropathy-associated T cell lymphoma (EATL)

  Whole exome sequencing of enteropathy-associated T cell lymphoma (EATL) tumors and paired normals, as well as RNA-sequencing of EATL tumors: including (1) 69 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples, (2) 36 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL paired normal samples, and (3) 32 RNAseq, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples.

  Dataset EGAD00001003284

• SCA1 and control cerebral organoids

  3' RNA-sequencing data of cerebral organoids from controls and individuals with SCA1 was performed at day 31 and day 60 of organoid formation. Matched case-control cerebral organoids were used (Ctrl A+SCA1 A and Ctrl B+SCA1 B) as well as isogenic cerebral organoids, CRISPR/Cas9 gene-edited from Ctrl A (SCA1-/CAG and SCA1CAG/CAG). Biological triplicates were assessed for all lines at both time points.

  Dataset EGAD50000002473

• mRNA profiling of CAFs and cancer cells in response to TGF-β and BMP signaling

  TGF-β and BMP signalings are important signaling pathways in the tumor microenvironment during cancer progression. This RNA-sequencing (62 fastq pairs) analysis explored how cancer-associated fibroblasts (CAFs) from human (19TT) and mice (Balbc A/B) respond to TGF-β, BMP2, or Gremlin antibody, as well as how cancer cells (66cl4) respond to Gremlin antibodies.

  Dataset EGAD50000001351

• Analysis of chromosomal background of cancerous mutations using a long-read sequencer

  In our previous study detecting cancerous complex SVs, we performed whole-genome sequencing of lung cancer clinical samples using PromethION. In this study, its depth and quality was substantially enriched and we conducted the phasing analysis in human lung cancer genomes. In addition, long read and short read RNA-seq was performed for transcriptome analysis.

  Study JGAS000349

• RNA-Seq data of hepatoma (Huh7 derived) and Ph5CH cells and primary hepatocytes

  The innate immune response of cells of hepatic origin (Huh7, Huh7.5, PH5CH and primary human hepatocytes (PHH), 66 samples) was analyzed by transcriptome analysis (RNAseq) upon supernatant delivery or transfection of synthetic dsRNA (poly(I:C)). Expression of TLR3 and RIG-I was reconstituted by lentiviral transduction in Huh7 and Huh7.5 cells. The sequencing is single RNA-Seq on an Illumina HiSeq 4000 with the Illumina TruSeq stranded mRNA kit.

  Dataset EGAD00001007083

• Controlling cell differentiation with precision through understanding the structure and dynamics of gene regulatory networks

  We established a set of transgenic human ES cell lines that carry inducible expression gene cassette for singe transcriptional factor induction with Tet-ON system. Transcriptome data was obtained 48h after transgene induction by Microarray. We established inducible human ES lines about more than 700 genes, and achieved microarray analysis on 115 genes. Our data set has multiple characteristic properties; 1) the same platform across data set, 2) analyzed with dynamic cell status, 3) pre-determined initiation point on gene perturbation, 4)inducible in different cell status. In parallele, we also performed RNA sequenncig analysis on 435 transgene induced ES lines as well. 32 transgene induced transcriptome data were obtained from both Microarray and RNA sequencing, normalizing technical gaps between them. We hope those systematic data set to reveal transcriptional network structure and molecular mechanisms of cell differentiation.

  Study JGAS000121

• Cell-type, allelic and genetic signatures in the human pancreatic beta cell transcriptome

  Pancreatic beta cells within the islets of Langerhans are centrally involved in the pathogenesis of both type 1 and type 2 diabetes. Describing the differentiated state of the human beta cell has been hampered so far by technical (low resolution microarrays) and biological limitations (whole islet preparations rather than isolated beta cells). We circumvent these by deep RNA sequencing of purified beta cells from 11 individuals, presenting here the first characterization of the human beta cell transcriptome. Additionally, we perform the first comparison of gene expression profiles between beta cells, whole islets (N=7) and beta cell depleted islet preparations (N=5), revealing thus beta cell specific expression signatures. Finally, we combine this with whole-genome sequencing data for 7 of our donors, describing here the first set of genetic variants controlling inter-individual variability in beta cell gene expression.

  Study EGAS00001000442

• G&T-seq: parallel sequencing of the genomes and transcriptomes of single cells

  The ability to simultaneously sequence the genome and transcriptome of the same single cell offersa powerful means to dissect functional genetic heterogeneity at the cellular level. Here we describeG&T-seq, a method for separating and sequencing genomic DNA and full-length mRNA from singlecells. By applying G&T-seq to over 220 single cells we reveal cellular properties that cannot beinferred from DNA or RNA sequencing alone, including associations between DNA copy numbervariation and gene expression dosage. We further demonstrate the detection of coding interchromosomalfusions and single nucleotide variants in both the genomes and transcriptomes ofindividual cells. G&T-seq enables the study of genotype-phenotype associations in single cells, andthe investigation of DNA cell lineage trees of healthy and diseased tissues with transcriptome inferredcell types and states.

  Study EGAS00001001204

• Identifying the role of ID3 in DNA repair and maintenance of genome integrity (RNA-seq)

  Dataset EGAD00001008198

• RNA-Seq of kidney cancer organoid biobank

  Dataset EGAD00001005318

• scRNA PDX

  Single cell RNA-seq for PT1-derived PDX samples

  Dataset EGAD00001006134

• JMS dataset

  Juntendo Muscle Study (JMS) dataset comprises 23 samples of paired-end RNA-Seq sequences in fastq format.

  Dataset EGAD00001008983

• RNA-seq data of LMS tumors

  This dataset contains paired fastq files for LMS tumor samples

  Dataset EGAD00001003828

• RNA sequencing of undifferentiated sarcomas

  Dac EGAC00001001055

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

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

  Study phs003304

• Djerroudi et al., E-cadherin inactivation shapes tumor microenvironment specificities in invasive lobular carcinoma

  Invasive lobular breast carcinoma (ILC) shows specific stromal features, T lymphocyte infiltration (TIL) being associated with poor prognosis. Here, we reveal the involved mechanism by performing single cell RNA sequencing, combined immunohistochemistry, deconvolution of bulk RNA sequencing from large retrospective ILC series, and functional assays using primary cells. We show that ILC accumulate FAP+ inflammatory cancer-associated fibroblasts (iCAF) through a previously undescribed mechanism mediated by E-cadherin/CDH1 on CAF plasticity. Indeed, CDH1 inactivation in ILC cancer cells prevents differentiation of iCAF into myofibroblastic CAF (myCAF), leading to iCAF accumulation. In turn, iCAF increase TIL infiltration and shape their spatial organization in ILC. Subsequently, CDH1-inactivated ILC cancer cells promote immune escape by lack of retention and activation of ITGAE-expressing resident memory CD8+ T lymphocytes (TRM). Hence, our study uncovers reciprocal interactions between CDH1-inactivated cancer cells, iCAF and CD8+ TRM, revealing why and how TILs have a poor prognosis in ILC patients, a mechanism extrapolated to other CDH1-mutated cancer types.

  Study EGAS50000000761

• Transcriptome and TCR Sequencing of T Cells from Metastectomies

  T cells were sorted from metastatic tumors (colon, rectal, breast, anal, melanoma primary histologies) following tumor dissociation and single-cell sequencing was performed (RNAseq and TCRseq). For samples from tumors that had been previously studied, cells were analyzed comparing known neoantigen-reactive TCR-expressing cells to other T cells. For samples without previously identified neoantigen reactivity, TCRs were predicted on the basis of T cell transcriptomic states. To determine candidate neoantigen screening, exome and RNA sequencing were performed on fragments of matched tumors from which T cells were sequenced   

  Study phs002748

• Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [time-course bulkRNAseq]

  Time-course bulk-RNA sequencing of brain organoids grown in four distinct growth protocols designed to generate dorsal (D) and ventral (V) forebrain, midbrain (M) and striatum (S) tissue at days 13 (for dorsal and ventral)/16 (for midbrain and striatum), 25, 40, 80 and 120. Per per cell line-protocol-timepoint combination three organoids (biological replicates) were grown. For reference, also three samples of the pluripotent stem cells across cell lines, not yet exposed to any protocol, were sequenced (day 0, pluripotent).

  Study EGAS50000000663

• The single plasma-cell transcriptional landscape in POEMS syndrome

  POEMS syndrome is a rare monoclonal plasma cell disorder that shows unique symptoms distinct from other plasma cell neoplasms, including high levels of serum VEGF; however, none of the previous studies have succeeded in direct identification of plasma cell clones in POEMS syndrome, leaving their real nature obscure.���We herein performed single-cell RNA sequencing (scRNA-Seq) of bone marrow (BM) plasma cells from patients with POEMS syndrome. These data unveil unique features of POEMS clones among plasma cell neoplasms and enhance our understanding of the pathogenesis of POEMS syndrome.

  Study JGAS000289

• Differential Transcription Start Site Usage in Brain-related Samples

  RNA-Seq is an effective method to study the transcriptome, but specialized methods are required to identify 5' ends of transcripts. Several published strategies exist for this specific purpose, but their relative merits have not been systematically analyzed. Here, we directly compare the performance of six such methods - testing five with cellular RNA as well as a novel spike-in RNA assay that helps address interpretation challenges that arise from uncertainties in annotation or RNA processing. Using a single human RNA sample, we constructed and sequenced 18 libraries with these methods and one standard, control RNA-Seq library. We find that the CAGE method performed best for mRNA and that most of its unannotated peaks are supported by evidence from other genomic methods. We then applied CAGE to eight brain-related samples and revealed sample-specific transcription start site (TSS) usage as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.

  Study phs001463

• Comparison of good PDX responders and bad PDX responders

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

  Dataset EGAD50000000876

• RNA-seq data from 9 patients with peri-implantitis

  Fastq files + patients' characteristics

  Dataset EGAD50000000544

• RNA-seq of murine osteosarcoma cell line genetically modified for CYR61

  Transcriptomic analysis of K7M2 murine osteosarcoma cells stably modified to overexpress or repress CYR61

  Dataset EGAD50000000747

• RNA-Seq of SMARCB1 re-expression and HDAC+mTOR inhibition experiments in malignant rhabdoid tumor organoids

  Dataset EGAD00001006574

• RNASEQ_TALL_t_14_16_translocation

  RNA-seq results of sequenced data of patients with t(14;16) translocated T-ALL.

  Dataset EGAD50000001781

• MSAT dataset

  Muscle SATellite cell study (MSAT) dataset comprises 39 samples of paired-end RNA-Seq sequences in fastq format.

  Dataset EGAD00001008984

• Transcriptomic profiling of patient-derived xenografts and organoids in prostate cancer

  Dataset contains RNA-seq of 30 samples (normal prostate tissue, human prostate cancer, PDX and organoids).

  Dataset EGAD00001006404

• Single-cell RNA-seq of cervix and placenta

  Placental trophoblasts have been detected in cervical smears early in gestation, creating opportunities for non-invasive prenatal diagnosis. However, trophoblast isolation is limited by the lack of a cell catalogue and molecular profile of cervical smears. To establish an atlas and to explore the potential of single-cell RNA-sequencing to detect cervical trophoblasts, 10,539 single-cell transcriptomes from 12 non-invasive exocervical smears from pregnant women were profiled. In addition, we characterized 34,565 cells from six placental biopsies. We uncovered a novel extravillous trophoblast cell subtype characterized by epithelial marker genes and reduced HLA-G expression. Integration of both cell atlases demonstrated surprisingly similar expression profiles between maternal epithelial cells and placental extravillous trophoblasts, indicating that these trophoblasts retained epithelial properties without an invasive mesenchymal phenotype. Additionally, differential expression analysis identified novel markers discriminating cervical and placental cell types. Those analyses may contribute to trophoblast discovery and isolation from cervical smears.

  Study EGAS00001007044

• Arriba: accurate and efficient detection of gene fusions from RNA-Seq (H021)

  The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the availability of many computational tools, fusion detection remains challenging. Existing methods suffer from poor prediction accuracy and are computationally demanding. We developed Arriba, a novel fusion detection algorithm with high sensitivity and short runtime. When applied to a large collection of published pancreatic cancer samples (n=803), Arriba identified a variety of driver fusions, many of which affected druggable proteins, including ALK, BRAF, FGFR2, NRG1, NTRK1, NTRK3, RET, and ROS1. The fusions were significantly associated with KRAS wild-type tumors and involved proteins stimulating the MAPK signaling pathway, suggesting that they substitute for activating mutations in KRAS. In addition, we confirmed the transforming potential of two novel fusions, RRBP1-RAF1 and RASGRP1-ATP1A1, in cellular assays. These results demonstrate Arriba’s utility in both basic cancer research and clinical translation.

  Study EGAS00001003554

• Impact of cryopreservation on transcriptome analysis of peripheral blood mononuclear cells

  To investigate the effect of cryopreservation on PBMCs, we conducted an experiment using samples from three healthy donors under four conditions: fresh PBMCs, PBMCs subjected to a single freeze–thaw cycle, PBMCs refrozen in freezing mix, and PBMCs refrozen in TRIzol. This resulted in a total of 12 samples (three replicates per condition). RNA was extracted from all PBMC samples using the Qiagen miRNeasy Mini Kit, followed by polyA RNA sequencing on the Illumina NovaSeq 6000 platform. Blood was collected from one male and two female adult donors. Sequencing yielded high-quality data, with an average of 27.8 million reads per sample and over 94% of bases exceeding a Q30 quality score.

  Study EGAS50000001196

• Whole blood RNAseq from a large ALS case-control study at Univ of Michigan

  Patients with amyotrophic lateral sclerosis (ALS), a rare fatal neurodegenerative disease, face a lengthy diagnostic process, and, although most survive only 2 to 4 years from diagnosis, lack information regarding their specific anticipated disease course due to a lack of prognostic tools. Although ALS is a heterogeneous disease of varied etiology, peripheral immune system dysfunction is ubiquitous, reflected in altered whole blood transcriptome. Herein, we profiled whole blood gene expression by RNA sequencing in a large cohort of ALS cases versus controls. Several machine learning classifiers trained on our gene expression dataset predicted case-control status and survival, and integration analysis with external cohorts led to the identification of drug candidates.

  Study EGAS50000001019

• Dual RNA-seq data of chlamydia infected M2 macrophages

  This dataset contains 8 unpaired fastq files sequenced with Ilumina NextSeq 2000. The files contain transcriptome data of host and pathogen from infected and uninfected samples from extracted total RNA at 30 hours post infection.

  Dataset EGAD50000001398

• Whole Transcriptome Sequencing

  RNA-seq data of 15 snap-frozen tissue of peritoneal mesothelioma. The strand specific RNA library prepared using TruSeq (Illumina) and pair-end sequencing performed in Illumina HiSeq 4000. The datasets contains paired fastq files for each of 15 tumor samples.

  Dataset EGAD00001004504

• Whole exome sequencing and RNA sequencing of lineage-switched acute myeloid leukemia with KMT2A-AFF1 rearrangement

  We performed whole exome sequencing and RNA sequencing of lineage-switched acute myeloid leukemia (LS AML) with KMT2A-AFF1 rearrangement to elucidate the feature and potential treatment targets. Notably, LS AML possessed gene expression signatures of monocytic myeloid derived suppressor cells (M-MDSCs). Several known genes related to MDSCs were highly expressed in LS AML, which could be novel treatment targets.

  Study JGAS000631

• Single-cell RNA sequencing on single CD45+ immune cells isolated from peripheral blood, lymphnode, ascites, tumour and adjacent normal tissues from six hepatocellular carcinoma patients.

  Single-cell RNA sequencing on single CD45+ immune cells isolated from peripheral blood, lymphnode, ascites, tumour and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional properties of these individual cells, were used to delineate the molecular subtypes, lineage, and functional properties of each cell group

  Study EGAS00001003449

• RNA-Seq data from tumor samples collected from 12 UTSW translocation renal cell carcinoma (tRCC) patients.

  This study investigates differentially expressed genes associated with the progression of translocation renal cell carcinoma (tRCC) by analyzing RNA-Seq data from 23 tumor samples obtained from 12 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. RNA isolated from tumor samples was sequenced using the Illumina platform.

  Dataset EGAD50000000172

• Single-cell RNA-seq of immune cell subsets isolated from human tumors (Kaptein et al., 2024)

  Single-cell RNA-seq profiling of effector (KLRG1+ PD1-), transitional (KLRG1+ PD1-intermediate), dysfunctional (CD39+ PD1+) and memory (IL7Rα+) CD8 T cells isolated from 4 human tumors (1 melanoma, 1 renal carcinoma and 2 ovarian carcinoma). Respective cell populations were identified and isolated using FACS. FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on individual CD8 T cell subsets across the 4 different samples.

  Dataset EGAD50000000376

• RNA-seq of 2D cell culture and 3D muscle bundles generated by primary myoblast cell lines and the human iPSCs derived from mosaic FSHD patients, respectively.

  The dataset includes the RNA-seq on the 2D cell culture of primary myoblast cell lines derived from FSHD patients and healthy donors (n=3 in each condition) and on the 3D muscle bundles generated by the human iPSCs derived from healthy and FSHD-affected cells of mosaic FSHD patients (n=3 in each condition)

  Dataset EGAD50000000717

• RNA-seq libraries from FFPE samples using Illumina Ribo-Zero Plus kit

  RNA was extracted from FFPE human tissue samples and used to prepare RNA-seq libraries with the Illumina Stranded Total RNA Prep Ligation kit with Ribo-Zero Plus. cDNA synthesis was performed starting from 100 ng of DNA-free RNA. Libraries were amplified with 16 PCR cycles and sequenced in paired-end mode (2×150 bp) on the Illumina NextSeq 550 platform. Library quality was assessed with Bioanalyzer and Qubit.

  Dataset EGAD50000001553

• Small RNA-Seq of MicroRNA's in extracellular vesicles of Ushers Syndrome patients

  Small RNA-Seq dataset of MicroRNA's found in tear extracellular vesicles (EVs) and hiPSC-derived retinal pigment epithelium (RPE) cells of Ushers Syndrome patients and control samples. 14 samples were isolated and assessed for quality before preparing libraries using the miReasy and TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired end FASTQ files.

  Dataset EGAD50000001709

• Phase II clinical trial of adult Philadelphia chromosome-negative precursor B-cell acute lymphocytic leukemia with combination chemotherapy

  Adults with B-ALL showed extremely inferior outcomes when compared to children. Genetic basis undelying adult B-ALL is largely unknown. We performed integrated analysis of RNA-seq and target DNA-seq for the patients enrolled in BALL213 study.

  Study JGAS000278

• BLUEPRINT release August 2016, RNA-Seq for Acute Myeloid Leukemia - SAHA, on genome GRCh38

  RNA-Seq data for 2 Acute Myeloid Leukemia - SAHA sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002343

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2884, on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002352

• BLUEPRINT release August 2016, RNA-Seq for T-cell Prolymphocytic Leukemia, on genome GRCh38

  RNA-Seq data for 3 T-cell Prolymphocytic Leukemia sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002426

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2884 (24h), on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (24h) sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002461

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - CTR, on genome GRCh38

  RNA-Seq data for 3 Acute Promyelocytic Leukemia - CTR sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002353

• BLUEPRINT release August 2016, RNA-Seq for neutrophilic metamyelocyte, on genome GRCh38

  RNA-Seq data for 3 neutrophilic metamyelocyte sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002366

• 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

• BLUEPRINT release August 2016, RNA-Seq for Mantle Cell Lymphoma, on genome GRCh38

  RNA-Seq data for 5 Mantle Cell Lymphoma sample(s). 5 run(s), 5 experiment(s), 5 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002336

• BLUEPRINT release August 2016, RNA-Seq for Acute Myeloid Leukemia, on genome GRCh38

  RNA-Seq data for 27 Acute Myeloid Leukemia sample(s). 27 run(s), 27 experiment(s), 27 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002465

• BLUEPRINT release August 2016, RNA-Seq for macrophage, on genome GRCh38

  RNA-Seq data for 6 macrophage sample(s). 7 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002507

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2884 (4h), on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (4h) sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002513

• RNA-seq data from primary AML samples with t(3;8)

  RNA-seq was generated to investigate differences in gene expression between t(3;8) AML and other primary AMLs. Briefly, sample libraries were prepared using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina

  Dataset EGAD00001006819

• RNA-seq of endometrial organoids from MRKH patients and controls grown under expansion medium or hormonal treatment

  Raw, unfiltered fastq files obtained through RNA-seq of endometrial organoids from MRKH patients and controls. The dataset divides into three parts, depending on the growth conditions of the organoids, ie expansion medium or treated with hormones. Each sample consists of two paired-end fastq files.

  Dataset EGAD00001008453

• BLUEPRINT release August 2016, RNA-Seq for band form neutrophil, on genome GRCh38

  RNA-Seq data for 3 band form neutrophil sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002446

• BLUEPRINT release August 2016, RNA-Seq for Multiple Myeloma, on genome GRCh38

  RNA-Seq data for 14 Multiple Myeloma sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002401

• BLUEPRINT release August 2016, RNA-Seq for Acute Lymphocytic Leukemia - CTR, on genome GRCh38

  RNA-Seq data for 1 Acute Lymphocytic Leukemia - CTR sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002332

• BLUEPRINT release August 2016, RNA-Seq for Chronic Lymphocytic Leukemia, on genome GRCh38

  RNA-Seq data for 7 Chronic Lymphocytic Leukemia sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002518

• BLUEPRINT release August 2016, RNA-Seq for neutrophilic myelocyte, on genome GRCh38

  RNA-Seq data for 3 neutrophilic myelocyte sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002288

• BLUEPRINT release August 2016, RNA-Seq for monocyte, on genome GRCh38

  RNA-Seq data for 2 monocyte sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002375

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - MC2392, on genome GRCh38

  RNA-Seq data for 1 Acute Promyelocytic Leukemia - MC2392 sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002359

• BLUEPRINT release August 2016, RNA-Seq for T-cell Acute Lymphocytic Leukemia, on genome GRCh38

  RNA-Seq data for 1 T-cell Acute Lymphocytic Leukemia sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002287

• BLUEPRINT release August 2016, RNA-Seq for Acute Promyelocytic Leukemia - ATRA, on genome GRCh38

  RNA-Seq data for 3 Acute Promyelocytic Leukemia - ATRA sample(s). 3 run(s), 3 experiment(s), 3 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002356

• BLUEPRINT release August 2016, RNA-Seq for mature eosinophil, on genome GRCh38

  RNA-Seq data for 2 mature eosinophil sample(s). 3 run(s), 3 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002326

• BLUEPRINT release August 2016, RNA-Seq for Acute Myeloid Leukemia - CTR, on genome GRCh38

  RNA-Seq data for 7 Acute Myeloid Leukemia - CTR sample(s). 7 run(s), 7 experiment(s), 7 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002443

• BLUEPRINT release August 2016, RNA-Seq for osteoclast, on genome GRCh38

  RNA-Seq data for 2 osteoclast sample(s). 2 run(s), 2 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002479

• BLUEPRINT release January 2015, RNA-Seq for regulatory T cell

  RNA-Seq data for 1 regulatory T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001174

• BLUEPRINT release August 2015, RNA-Seq for neutrophilic metamyelocyte, on genome GRCh38

  RNA-Seq data for 2 neutrophilic metamyelocyte sample(s). 2 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001566

• BLUEPRINT release August 2014, RNA-Seq for mature neutrophil

  RNA-Seq data for 7 mature neutrophil sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000904

• BLUEPRINT release August 2015, RNA-Seq for T-cell acute leukemia, on genome GRCh38

  RNA-Seq data for 1 T-cell acute leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001469

• BLUEPRINT release August 2014, RNA-Seq for alternatively activated macrophage

  RNA-Seq data for 1 alternatively activated macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000937

• BLUEPRINT release August 2014, RNA-Seq for inflammatory macrophage

  RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000908

• BLUEPRINT release January 2015, RNA-Seq for mature neutrophil

  RNA-Seq data for 10 mature neutrophil sample(s). 10 run(s), 10 experiment(s), 10 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001129

• BLUEPRINT release January 2015, RNA-Seq for memory B cell

  RNA-Seq data for 1 memory B cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001171

• BLUEPRINT release August 2015, RNA-Seq for band form neutrophil, on genome GRCh38

  RNA-Seq data for 3 band form neutrophil sample(s). 3 run(s), 3 experiment(s), 3 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001504