3883 results for "RNA AND sequencing OR transcriptome"

in 20.56 milliseconds.

• Dataset for identification of the dismal subtype of B-ALL with dysregulation of CDX2 and UBTF

  WGS (tumor and germline samples) was performed to identify structural variants in the UBTF/CDX2 subgroup. RNA-seq was performed to detect gene fusion in the UBTF/CDX2 subgroup. HiChIP was performed to investigate 3D chromatin architecture and enhancer landscapes of representative patient samples and cell lines harboring Type I and II FLT3-PAN3 deletions and amplifications.

  Dataset EGAD00001008416

• Vumc_organoids

  Organoid cultures derived from normal colon and/or colorectal adenomas and/or colorectal carcinomas. RNA and DNA was isolated from these cultures for genome wide profiling.

  Dataset EGAD00001008479

• WES and RNA-seq data of 11 cancer patients with multiple cancer types

  This dataset includes WES and RNAseq from 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy samples, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems. Paired-end reads are provided in fastq format.

  Dataset EGAD00001010169

• TK-EPN862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - RNAseq

  In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. RNAseq data (paired end) provided here correspond to Primary tumour, two metastatic lesions (one spinal, one cranial), and a patient-derived xenograft derived from the patient.

  Dataset EGAD00001009870

• scMultiome

  This dataset gather scMultiomic data including RNA-seq and ATAC-seq in MM.1S in control and dex condition at 1h and 4h

  Dataset EGAD00001011140

• Leiomyosarcoma Cancer Transcriptome Sequencing

  RNA-Seq data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 75bp paired-end protocol to a minimum mean reads of 50 million.

  Dataset EGAD00001003192

• RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL)

  RNA-sequencing (RNA-seq) efforts in acute lymphoblastic leukaemia (ALL) have identified numerous prognostically significant genomic alterations which can guide diagnostic risk stratification and treatment choices when detected early. However, a full RNA-seq Bioinformatics workflow is time-consuming and costly in a clinical setting where rapid detection and accurate reporting of clinically relevant alterations are essential. To accelerate the identification of ALL-specific alterations (including gene fusions, single nucleotide variants and focal gene deletions), we developed the rapid screening tool RaScALL, capable of identifying more than 100 prognostically significant lesions directly from raw sequencing reads. RaScALL uses the k-mer based targeted detection tool km and known ALL variant information to achieve a high degree of accuracy for reporting subtype defining genomic alterations compared to standard alignment-based pipelines. Gene fusions, including difficult to detect fusions involving EPOR and DUX4, were accurately identified in 98% (164 samples) of reported cases in a 180-patient Australian study cohort and 95% (n=63) of samples in a North American validation cohort. Pathogenic sequence variants were correctly identified in 75% of tested samples, including all cases involving subtype defining variants PAX5 p.P80R (n=12) and IKZF1 p.N159Y (n=4). Accurate detection of intragenic IKZF1 deletions resulting in aberrant transcript isoforms was also detectable with 98% accuracy. Importantly, the median analysis time for detection of all targeted alterations averaged 22 minutes per sample, significantly shorter than standard alignment-based approaches, ensuring accelerated risk-stratification and therapeutic triage.

  Dataset EGAD00001009087

• HuBMAP: KULMAP - Human Kidney, Urinary Tract, and Lung Mapping Center

  The major goal of the Human Kidney, Urinary Tract, and Lung Mapping Center (KULMAP) is to generate multi-omic and spatially resolved molecular anatomical maps of the human bladder, ureter and kidneys (BUKMAP) and the lung airways and parenchyma (LAPMAP) at a single cell resolution. This entails sequencing of the transcriptomes and epigenomes of dissociated single cells in a massively parallel manner. These profiles will then inform on highly multiplexed RNA in situ imaging for spatial mapping of hundreds of molecular targets in the tissue sections, at a subcellular resolution. These spatial molecular maps will serve as scaffolds for computational registration of cell types and the associated transcriptome/chromatin maps to the tissue space. The combination of sequencing single dissociated cells and multiplexed in situ mapping will allow the construction of detailed spatial maps for these large organs.

  Study phs002249

• PRO-SPeCT: PROstate cancer heterogeneity deconvolution through Single cell Profiling of Chromatin accessibility and Transcriptomic output

  38 prostate cancer specimens derived from five human patients with ISUP ≥ 3 pathology who underwent radical prostatectomy and pelvic lymph node dissection at surgery as part of the International Cancer Genome Consortium (ICGC) late-onset cohort. Using single-cell multiome (expression and chromatin accessibility from RNA and ATAC, respectively) sequencing assay, we characterized 282,956 nuclei/cells, with a median of 6 primary tumor foci from the prostate gland and 3 locoregional lymph node metastases across all patients.

  Dataset EGAD50000000745

• Sequencing data for oesophageal and related samples - Ogden et al (WGS, RNA)

  Data supporting: "Widespread reorganisation of the regulatory chromatin landscape facilitates resistance to inhibition of oncogenic ERBB2 signalling" Ogden et al. WGS for tumour and normal samples. RNAseq for tumour samples.

  Dataset EGAD00001007496

• Dataset for Ewing_sarcoma_PNET-RNA

  Rare cancer sequencing data of 28 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008845

• Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models: validation cohort

  While cell-free DNA (cfDNA) in liquid biopsies is widely being used and investigated, free circulating RNA (extracellular RNA, exRNA) has the potential to improve therapy response monitoring and cancer detection due to its dynamic nature. A fundamental open question hampering the initiation of large-scale liquid biopsy collections for tumour exRNA analysis is that it remains unclear in which blood subcompartment tumour-derived exRNAs primarily reside. We set out to develop a host-xenograft deconvolution framework, exRNAxeno, with cDNA mapping strategies to either a combined human-mouse reference genome or both species genomes in parallel, that can be applied to exRNA sequencing data from liquid biopsies of human xenograft mouse models, enabling to distinguish (human) tumoural RNA from (murine) host RNA, and as such to specifically analyse tumour-derived exRNA. Subsequently, the preferred exRNAxeno combination pipeline was applied to total exRNA sequencing data from blood platelets and three plasma fractions from a breast cancer patient-derived and neuroblastoma cell line-derived xenograft mouse model. We show that tumoural exRNA concentrations are not determined by plasma platelet levels, while host exRNA concentrations increase with platelet content. Furthermore, a large variability in exRNA levels and gene content across individual mice is observed. In general, the tumoural gene detectability in plasma is correlated with the RNA expression levels in the tumour tissue or cancer cell line. Our results unravel new aspects of tumour-derived exRNA biology in xenograft mouse models.

  Study EGAS00001006582

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

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

  Dataset EGAD00001006576

• Adipose transcriptome response after a 6-day very-low energy fast in obesity, in the single-arm feeding trial FASTOMICS-6

  Background: Fasting and ketogenic diets have gained popularity due to potential health benefits, in part via autophagy and other protective processes. However, although the basic physiology of fasting is well-established, we lack a deeper understanding of mechanisms on the tissue level and associated metabolome changes, particularly in humans. Method: 4 males and 9 females with severe obesity underwent a very-low-energy in-hospital feeding study (600 kcal/day). Plasma (n=13) and subcutaneous adipose tissue samples (n=12) were collected in the morning before and after 6 days and analyzed by GC-MS/MS and RNA-sequencing, respectively. Gene set enrichment analysis (GSEA) and weighted gene co-expression network analysis were used to identify biological pathways and modules of affected genes and their correlation with plasma ketones and metabolites.

  Dataset EGAD50000001484

• Transcriptional and DNA binding profiling of CEBPE in REH acute lymphoblastic leukaemia cells using shRNA RNA-Seq and ChIP-Seq

  ChIP-Seq - CEBPE - REH. The ETV6/RUNX1 translocated acute lymphoblastic leukaemia cell line. REH was used to perform ChIP-Seq using a CEBPE antibody. Cells were fixed in 1% formaldehyde for 10mins, prior to preparation of chromatin using Active Motif Express ChIP-IT. 2ug of antibody (anti CEBPE Atlas Antibodies HPA002928)was added to 25ug of chromatin O/N at 4C with rotation. Duplicate reactions were pooled and purified. 10ng of ChIP’d and input DNA used for Illumina NGS preparation (NEBNext ChIP-Seq Library kit; New England Biolabs), CEBPE and Input DNA ChIP samples were sequenced on a MiSeq using 150bp Kit v3 paired end and a HiSeq 2500 using 2x101 version 4 paired end (Illumina) respectively. Reactions performed in duplicate. shCEBPE RNA-Seq - REH. REH cells were lentivirally transduced with a pTRIPZ shRNA vector for transcriptional profiling of CEBPE. Two controls (empty and non-targeting) and two CEBPE shRNAs (V3THS_150517(A13), V3THS_404312(G3) Dharmacon, GE) were transduced into REH cells. Cells were treated with 1ug/ml doxycyclin for 144hrs and total RNA purified using Qiagen RNeasy. Knock down of CEBPE was validated by qRT. RNA integrity >7.7 for all samples. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illuimna HiSeq 2500 using 2x101 version 4 paired end chemistry. 3 biological replicates of each samples were prepared.

  Dataset EGAD00001004084

• Sequencing data associated with Smith et al, Acta Neuropathologica, 2020 (PMID: 32519082)

  The dataset includes 144 BAM files of WGS, WES, and RNA-seq data from primary and PDOX samples analyzed in Smith et al, Acta Neuropathologica, 2020 (PMID: 32519082).

  Dataset EGAD00001007980

• Unraveling the heterogeneity of multiple myeloma identifies therapy resistant subpopulation with vulnerability to the splicing pathway intervention

  Intra-tumor heterogeneity underlies the therapy resistance of multiple myeloma (MM). However, its details remain unknown. Here, we performed single-cell RNA sequencing coupled with VDJ targeted sequencing on highly purified bone marrow lineage marker-negative CD38+ MM cells from patients at diagnosis and in remission. This approach successfully subdivided MM cells into distinct clusters, unraveling their heterogeneity and plasticity on the axis of cell surface CD138 expression. Notably, unique clusters were identified in the minor CD138-negative population that resisted therapies. CRISPR/Cas9 screening of upregulated genes in the resistant population identified their vulnerability to the splicing pathway inhibition, among which RNA-binding protein 39 (RBM39) appeared to be overexpressed in the resistant population and involved in aberrant splicing. Genetic and pharmacological inhibition of RBM39 exerted a profound synthetic lethal effect on them. Our results unveil an uncharacterized subpopulation associated with therapy resistance and provide a novel therapeutic strategy targeting the splicing pathway in MM.

  Study JGAS000723

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

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

  Study phs001451

• RNA Sequencing of Pulmonary Arterial Endothelial Cells in Pulmonary Hypertensive Patients and Controls

  The transcriptome of pulmonary arterial endothelial cells from healthy lungs and from lungs of patients with idiopathic pulmonary arterial hypertension have been analyzed and specific differences in disease-relevant pathways were identified. The genes identified as altered in these patients have direct effects on pulmonary arterial endothelial cell function. This finding may underlie the inability of the pulmonary vasculature to respond to and repair the damage observed in pulmonary hypertension.

  Study phs000998

• RNA sequencing of NK cells in human lung

  Human lung tissue-resident NK cells (trNK cells) are likely to play important roles in viral infections, inflammation and cancer. However, knowledge about lung trNK cells is lacking but is fundamental for exploiting these cells in therapeutic approaches. Here we analysed the transcriptome of CD69+CD49a+CD103+CD16-CD56bright, CD69+CD49a+CD103-CD16-CD56bright, CD69+CD49a-CD103-CD16-CD56bright, CD69-CD49a-CD103-CD16-CD56bright, and CD56dimCD16+NKG2A+CD57- NK cells isolated from human lung.

  Study EGAS00001003544

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model - WT, APP KI, Abeta-treated, Abeta/Aducanumab-treated

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model. Samples include distinct conditions (each as biological duplicates): - wild-type cells from cultures after 1 month (WT_1mo, cell lines: A18, KOLF) and 3 months (WT_3mo, cell lines: SA2, KOLF, A18) of culturing - knock-in cells from cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (KI_3mo, cell lines: SA2, A18) - subset of WT 1 month-old samples were exposed to 500nM synthetic Abeta42 for 2 consecutive feeds, and a subset of these subsequently treated with 1µg/ml Aducanumab antibody for 14 days

  Dataset EGAD50000002031

• RNA-seq of non-LPS treated (N), non-tolerized (NT), and tolerized (T) IFNg-primed macrophages pretreated with or without HDAC3i

  In this experiment we investigated the effect of HDAC3 inhibition on the transcriptome of IFNg-primed macrophages under different tolerization conditions. Peripheral blood mononuclear cells (PBMCs) were isolated from 3 healthy donors. PBMCs were isolated from whole blood of healthy donors using Ficoll gradient (Invitrogen). Monocytes (CD14+ cells) were positively selected from PBMCs using CD14 Microbeads according to the manufacturer’s instructions (Miltenyi Biotec). Monocytes were subsequently treated with or without 500 nM HDAC3i (ITF3100) for 30 minutes prior to overnight IFNg priming (50 ng/mL). Cells were then kept without LPS (non-LPS; N), treated with 10 ng/mL LPS once (non-tolerized; NT), or treated with LPS twice (tolerized; T; second LPS concentration: 100 ng/mL). In total, there were 18 samples included.

  Dataset EGAD00001005959

• FASTQ files of total RNA-Seq data from the POPS SGA (Small for Gestational Age) samples

  All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003507

• FASTQ files of total RNA-Seq data from the POPS PET (pre-eclamptic) samples

  All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003508

• 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

• RNA-sequencing of ex vivo exhausted human antigen-specific T cells

  Tumor-specific T cells are frequently exhausted by chronic antigenic stimulation. To explore new pathways for reinvigoration of anti-tumor immune functions, we developed a human ex vivo exhaustion model by repetitive antigenic stimulation of primary CD8 T cells. This results in T cells that resemble patient-derived T cells in tumors on a phenotypic and transcriptional level. Four human healhy donor CD8+ T cells were isolated, transduced with an NY-ESO-1 TCR lentivirus construct, stimulated in four different conditions (Trested, Ttumor, Tex, Teff) with T2 tumor cells and specific peptides over 12 days. Cells were then sorted for TCR Vbeta 13.1+ (NY-ESO-1 TCR) CD8+ CD3+ CD56- CD4- DAPI- cells. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode (2x51bp) on 2 lanes of an Illumina NovaSeq 6000 flow-cell. FASTQ sequence files were generated with the Illumina RTA version 3.4.4 and Base-calling Version bcl2fastq-2.20.0.422.

  Dataset EGAD00001009754

• scRNA-seq of a 3D human cortical tissue model from human iPSCs exploring 2D versus 3D co-culturing

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions as described in the Study section. The dataset was generated using the BD Rhapsody technology and sequenced paired-end with Illumina NovaSeq2000. Information on the multiplexing of samples is reported in the Analyses section.

  Dataset EGAD50000002021

• De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

  Dataset EGAD50000001673

• Whole scRNA-seq from pre frontal cortex patient biopsy

  The single- cell RNA-seq prefrontal cortex sample was selected from a cohort of patients with hydrocephalus ≥18 years of age planning to undergo CSF diversion surgery either with a ventriculoperitoneal shunt placement (VP) or ventriculocisternostomy (VCS). The tissue was dissociated followed by red cell and debris removal and counting of the cells to be sequenced with (scRNA-seq; 10x Genomics kit v2). After dissociation only non neuronal cells were retrieved.

  Dataset EGAD50000001542

• Evaluating potential drug candidates for the treament of Henamgiopericytoma on patient derived cell line models

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1. Potential drug candidates that could be repurposed for the treatment of SFT/HPC were screened. Screening was performed through RNA-Seq

  Dataset EGAD50000000039

• Gene expression in CSF and whole blood of adults with proven bacterial meningitis in Malawi

  Dataset of BAM files from patients with proven bacterial meningitis in Malawi. Samples consist of BAM files from PolyA RNA seq runs from patients classifed as admission whole blood or CSF on admission (pre-antibiotics) in the Emergency Department. Subsequent BAM files are identical runs from whole blood from the same patients, taken at either day 10 or day 40 post admission to hospital. All patients have disease, they are divided into survivors and non-survivors at the day 40 time point.

  Dataset EGAD00001004488

• RNAseq from PDAC samples

  BAM files from RNA-seq of PDAC samples used in the COMPASS hENT1 study

  Dataset EGAD00001009409

• Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma - Ribo-Seq

  This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.

  Dataset EGAD00001011193

• RNA-seq dataset of A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study describing the differentiation trajectory of atypical teratoid rhabdoid tumors (ATRTs) at single-cell level. This study describes how the differentiation trajectory differs per subtype of ATRTs, and how those findings could contribute to develop so-called "maturation therapy" tailored towards ATRTs.

  Dataset EGAD00001015544

• Adipose transcriptome and plasma metabolome responses after a 6-day very-low energy fast in obesity: a single-arm feeding trial (FASTOMICS-6)

  Background: Fasting and ketogenic diets have gained popularity due to potential health benefits, in part via autophagy and other protective processes. However, although the basic physiology of fasting is well-established, we lack a deeper understanding of mechanisms on the tissue level and associated metabolome changes, particularly in humans. Method: 4 males and 9 females with severe obesity underwent a very-low-energy in-hospital feeding study (600 kcal/day). Plasma (n=13) and subcutaneous adipose tissue (sAT) samples (n=12) were collected in the morning before and after 6 days and analysed by GC-MS/MS and RNA-sequencing, respectively. Gene set enrichment analysis (GSEA) and weighted gene co-expression network analysis were used to identify biological pathways and modules of affected genes and their correlation with plasma ketones and metabolites.

  Study EGAS50000001015

• Single cell and plasma RNA sequencing

  Single cell and plasma RNA sequencing for RNA liquid biopsy for hepatocellular carcinoma

  Study EGAS00001005194

• Spatiotemporal single-cell analysis reveals a time-dependent immunological modulation by multi-fractionated radiotherapy in esophageal cancer

  Description Here, by integrative spatial and single-cell analyses using spatial transcriptome (VISIUM) and single-cell RNA sequencing (scRNA-seq), we examined the spatiotemporal dynamics of immune-response in the tumor microenvironment of esophageal squamous cell carcinoma (ESCC) before, during and after RT. The comprehensive single-cell analyses demonstrated the infiltration of immune cells into tumor with the dynamic change of immune-stimulatory and -suppressive gene expression after RT. ScRNA-seq analysis uncovered the time- and cell-type-dependent alteration of gene expression profile from during to after RT. This datasets in the present study will provide the information of RT-induced gene signature to seek an appropriate target of personalized immunotherapy combined with radiotherapy and of determining the timing of the combination therapy.

  Study JGAS000712

• Pathogenic variants damage cell compositions and single cell transcription in cardiomyopathies

  Pathogenic variants in genes that cause dilated (DCM) and arrhythmogenic cardiomyopathies (ACM) convey high risks for the development of heart failure (HF) through unknown mechanisms. Using single nucleus RNA sequencing (snRNAseq), we characterized the transcriptome of 880,000 nuclei from 18 control and 61 failing, non-ischemic human hearts with pathogenic variants in DCM and ACM genes or idiopathic disease. We performed genotype-stratified analyses of the ventricular cell lineages and transcriptional states. The resultant DCM and ACM ventricular cell atlas demonstrated distinct right and left ventricular responses, highlighting genotype-associated pathways, intercellular interactions, and differential gene expression at single cell resolution. Together these data illuminate both shared and distinct cellular and molecular architectures of human HF and suggest novel candidate therapeutic targets.

  Study EGAS00001006374

• Risk Factors for Asymptomatic Diverticulosis

  Data for this analysis came from a prospective study of colonic diverticulosis at the University of North Carolina Hospital in Chapel Hill, North Carolina (NIH R01DK094738). This is a case-control genetic and transcriptomic study to identify the genetic and cellular determinants underlying colonic diverticulosis and the relationship with other gastrointestinal disorders. The study inclusion and exclusion are described below. DNA and RNA sequencing were performed on colonic tissue from 404 patients with (N=172) and without (N=232) diverticulosis. We assessed variation in the transcriptome associated with diverticulosis and integrated this variation with human intestine single-cell RNA-seq data. We integrated our expression quantitative trait loci with GWAS using Mendelian Randomization. A polygenic risk score analysis examined associations between severity of diverticulosis and other gastrointestinal disorders. We identified 38 genes with differential expression and 17 genes with varied transcript usage linked to diverticulosis. Our results suggest tissue remodeling as a primary mechanism for diverticula formation. The presence of diverticulosis was linked to stromal and epithelial cells in the colon including endothelial cells, myofibroblasts, fibroblasts, goblet, tuft, enterocytes, neurons, and glia. MR highlighted five genes including CCN3, CRISPLD2, ENTPD7, PHGR1, and TNFSF13. In diverticulosis cases, ENTPD7 upregulation was confirmed. A greater burden of diverticula was positively correlated with genetic predisposition to diverticulitis. The data related to the study including total RNA-Seq, SNP array and imputed genotypes will be available through dbGaP.

  Study phs003556

• Genomic and immune signatures predict clinical outcome in newly diagnosed multiple myeloma treated with immunotherapy regimens

  In this study we performed whole genome sequencing on matched tumor-normal CD138+ bone marrow mononuclear cells from 60 patients with newly diagnosed multiple myeloma treated with daratumumab, carfilzomib, lenalidomide, and dexamethasone (NCT03290950-MANHATTAN trial). In addition, we performed 5’-single-cell RNA-sequencing (10X Genomics) coupled with V(D)J sequencing and capture of the surface protein markers (TotalSeq-C, Biolegend) of the CD138- bone marrow mononuclear cells to interrogate the composition of the immune microenvironment at baseline and after eight cycles of induction therapy in 22 patients with newly diagnosed multiple myeloma. Samples were multiplexed using hashtag oligo.

  Dataset EGAD00001011132

• Single-nuclei multiomic analysis of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  Datasets consists of 12 samples of nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. 6 single nuclei (RNA-ATAC) samples of XMAS protocol with cells collected at days 0,11,16,28,42 and 56 after differentiation. 3 snRNA-seq samples from AMS protocol of cells collected at days 14,16 and 28 after differentiation and 3 snRNA-seq samples with AMS protocol until day 14 grafted and grafts processed after 5 months grafting.

  Dataset EGAD50000002054

• Sequencing data for oesophageal and related samples - OACs release 4 (RNA)

  Dataset EGAD00001004021

• 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

• RNA-seq of cells after injection into immunodeficient mice

  This dataset includes 73 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Normal human CD34+ cord blood (CB), bone marrow (BM), or post-natal thymus (PNT) cells were transduced with various combinations of T-ALL oncogenes, cultured in vitro on OP9-DL1 feeders for up to 25 days, and then transplanted into immunodeficient NSG or NRG mice. The samples were collected after development of frank leukemia in recipient mice.

  Dataset EGAD00001009751

• Systematic Analysis of Transcription Program Regulation by Transcription Factor EB (TFEB)

  In order to evaluate the effects of TFEB, a master regulator of autophagy and lysosomal biogenesis, CRISPR-Cas9 TFEB knock out cell lines were generated and reconstituted with wild-type TFEB (TFEB-WT), a vector control (TFEB-KO) or TFEB engineered to remain localized to the cytosol (TFEB-cyto) or to the nucleus (TFEB-nuc). RNA sequencing was performed on engineered cell lines at steady-state or following exogenous stimulation with autophagy inducer (Torin1 or Salmonella bacterial infection). Comparative analyses were performed to identify TFEB-dependent transcriptional response to subcellular localization at steady-state or to exogenous stimuli.

  Study phs002099

• Multiomic analysis of CD4+ T cells from blood, lymph node and tumor of NSCLC patients

  This dataset contains data derived from FACS-sorted CD4+ T cells. This dataset contains FASTQ files for: - paired blood, lymph node, and tumor single-cell RNA-seq (scRNA-seq) samples from 5 patients with NSCLC (including scRNA-seq coupled to scTCR-seq for 3 patients), - paired blood, lymph node, and tumor single-cell ATAC-seq (scATAC-seq) samples from 2 patients with NSCLC, - lymph node and tumor bulk RNA-seq and TCR-seq data from CD4+ T cell subsets (Treg-Tfr, Treg-Trm, Treg-Naive, Tconv-Tfh, Tconv-CXCL13, and Tconv-Naive) from 5 patients (one patient has lymph node samples only). In addition, this dataset includes processed analysis files: - Seurat object for scRNA-seq data, - fragment files generated by Cell Ranger for scATAC-seq samples, - contig annotations generated by Cell Ranger for scTCR-seq samples. Sequencing was performed using Illumina NovaSeq, MiSeq, or HiSeq Rapid Run platforms.

  Dataset EGAD50000000424

• WGS, RNAseq and ATACseq data for the validation of an iPSC model of MPNST progression

  WGS, RNA-seq and ATAC-seq data for the validation of an iPSC model of MPNST progression. It includes the cells of the model (1KO, 2KO and 3KO) at various differentiation stages plus primary human tumors of the peripheral nervous system associated to NF1 (plexiform neurofibromas (PNFs), Atypical Neurofibromas (ANFs) and Malignant Peripheral Nerve Sheath Tumors (MPNSTs). Data linked to paper iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities by Uriarte-Arrazola et. al. 2026

  Dataset EGAD50000002533

• Single cell and whole tissue transcriptomes investigating Barrett's oesophagus

  Data consists of 4,640 RNA-sequencing sample libraries. These libraries were sequenced from four sites of the upper gastro-intestinal tract (Barrett’s oesophagus, proximal normal oesophagus, proximal normal stomach, and duodenum) in two experiments. 4,587 libraries were produced in the first experiment in which whole transcriptomes were isolated single cells dissociated from endoscopic biopsy tissue obtained from the four previously mentioned tissues. The other 53 libraries were produced in the second experiment in which whole transcriptomes were isolated from whole tissue from endoscopic biopsies of the four previously mentioned tissues. The data found here are stored in the raw fastq file format from paired end sequencing.

  Dataset EGAD00001004344

• Osteosarcoma mate-pair and RNA-sequencing

  DNA mate pair and RNA sequencing data of conventional osteosarcomas. Mate pair libraries, with average insert sizes of 2-4 kb, were prepared for sequencing using the Nextera Mate Pair Library Preparation Kit. Paired-end 76 base pair reads were generated using an Illumina NextSeq 500 sequencing instrument. Total RNA was enriched for polyadenylated RNA using magnetic oligo(dT) beads. Enriched RNA was prepared for sequencing using the TruSeq RNA Sample Preparation Kit v2 and paired-end 151 base pair reads were generated from the cDNA libraries using an Illumina NextSeq 500 instrument.

  Study EGAS00001003842

• Plasma RNA sequencing

  Plasma RNA sequencing

  Study EGAS00001000731