4984 results for "*oma"

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• RNA sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  RNA-seq for 26 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study, and 32 samples from a previously uploaded dataset.

  Dataset EGAD50000001365

• Whole genome sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Whole genome sequencing for 10 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study, and 6 samples from a previously uploaded dataset.

  Dataset EGAD50000001366

• Low pass WGS from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Low pass whole genome sequencing from 46 samples from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Dataset EGAD50000001367

• Bulk RNA sequencing data of high-grade serous ovarian cancer samples (set 7-17)

  The dataset contains RNA sequencing data of 272 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000, MGISEQ or Hiseq X Ten. The 814 samples are fresh frozen tissue samples that have been collected from different tissues and time points before and during treatment. The files provided are paired fastq files.

  Dataset EGAD50000001370

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0187_002

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0167_003 for Diffuse large B-cell lymphoma patient sample TFRIPAIR10

  Dataset EGAD50000001372

• 10x Genomics BCR Sequencing

  BCR sequencing done with 10x Genomics V(D)J kit + platform for the paper: Integrated single cell analysis reveals co-evolution of malignant B cells and tumor micro-environment in transformed follicular lymphoma. Dataset contains paired FASTQ files for 35 samples, each was processed with the 10x Genomics V(D)J kit to obtain the sequence of the B-cell receptor sequence.

  Dataset EGAD50000001373

• scRNA-seq for 4 reactive lymph node and 12 high grade B cell lymphoma samples

  Dataset includes count matrices, barcode tsvs, and features tsv for each sample, generated using Cell Ranger.

  Dataset EGAD50000001386

• Nanopore whole-genome sequencing of human bone and soft-tissue sarcomas

  We performed single and multi-region nanopore whole-genome sequencing on human bone and soft-tissue sarcoma samples. We also performed nanopore whole-genome sequencing on matched whole blood samples.

  Dataset EGAD50000001392

• (RNA-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  Raw and processed RNA-seq data from a patient-derived xenograft (yielding 18 samples) and the VOA1066 undifferentiated endometrial carcinoma cell-line (yielding 15 samples). PDX samples were treater with either compound-14, dBRD9, or were untreated. VOA1066 samples were treated with either compound-12, dBRD9, or were untreated. Samples were sequenced on an Illumina NextSeq 500 using 37-bp single-end sequencing. Raw fastq files and gene count tables are included for each sample.

  Dataset EGAD50000001471

• (ATAC-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  Raw and processed ATAC-seq data from the VOA1066 undifferentiated endometrial carcinoma cell-line (10 samples). Samples were treated with DMSO, dBRD9, or compound 12, without doxycycline; some samples instead received doxycycline-induced ARID1A treatment, or doxycycline alone. Samples were sequenced on Illumina NextSeq 500 using 37 bp paired-end sequencing parameters. Raw fastq fastq files, bigwig files giving normalized genomic coverage per region, and called broad peaks are included for each sample.

  Dataset EGAD50000001472

• (ChIP-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  ChIP-seq data of 18 samples from the VOA1066 undifferentiated endometrial carcinoma cell-line with various pulldowns: BRG1 (abcam, ab110642, GR3255117-11), BRD9 (CST, E4Q3F, Lot 1), ARID1A (CST, D2A8U, Lot 4), SS18 (CST, D6I4Z, Lot 1), PBRM1 (CST, D3F70, Lot 3), GLTSCR1 (CST, E6I3A, Lot 1), H3K27ac (CST, C36B11, Lot 16), or none. Sample were either untreated or received doxycycline-induced ARID1A treatment. Samples were sequenced on Illumina NextSeq 500 using 37 bp single-end sequencing parameters. Raw fastq files, along with processed bigwig files containing normalized genomic coverage, and called narrow peaks, are included for each sample.

  Dataset EGAD50000001473

• Common origin and somatic mutation patterns of composite lymphomas and leukemias

  The dataset contains six composite lymphomas and leukemias cases (four composite B-cell lymphomas (case 1-4), and two combinations of B-cell and T-cell lymphoma (case 5+6)). Two tumor and one non-tumor (NTC) sample were sequenced from each case after library prep with NEBNext Ultra DNA Library Prep Kit, Exome capturing was done with NimbleGen SeqCap EZ Choice kit, and sequenced on a Illumina HiSeq 2000 HO and given as fastq files. WGA (Qiagen REPLI-g kit) was used for case 2 and 3. Case 1-4 were microdisected, case 5+6 were flow-sorted.

  Dataset EGAD50000001486

• 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

• shallow whole genome sequencing BAM files aligned to the human reference genome GRCh38

  We profiled large B-cell lymphoma (LBCL) patient plasma samples with ultra-low-pass (shallow) whole genome sequencing. The DNA sequencing was performed on pre-capture genomic libraries, with an intended mean coverage of at least 0.1X, FASTQ files were cleaned by fastp and mapped to the reference human genome (GRCh38) with bwa.

  Dataset EGAD50000001497

• Human glioblastoma single cell RNA-seq from two patient, sampled at different positions within as well as outside tumor

  We performed deep single-cell RNA sequencing of two rare glioblastoma cases where tissue could be sampled from tumor core to macroscopically normal cortex. We processed two to three replicates per sample with the 10X Genomics V3.1 kits. Deep sequencing was performed to about 100,000 reads per cell on the Illumina NovaSeq 6000 platform, resulting in a total of 37 BAM files.

  Dataset EGAD50000001500

• Visium Spatial transcriptomics

  This study consists of the spatial transcriptomics data generated by : Visium CytAssist Spatial Gene Expression for FFPE (10x) for steatotic liver disease-associated hepatocellular carcinoma (SLD-HCC) (n=7) and non-SLD-HCC (n=5) The goal of this data is to compare SLD-HCC vs non-SLD-HCC as well as response to immunotherapy

  Dataset EGAD50000001506

• singel cell RNAseq dataset for the study "Composition and functional status of T and NK cells in Extramedullary myeloma tumor microenvironment""

  Dataset contains all newly generated single cell RNAseq data generated for the study. It includes 5 EMM soft tissue samples, 5 EMM bone marrow samples (EMM_BM) and 6 RRMM BM samples without EMM (RRMM_BM). Samples that are sequenced twice are marked by _1 or _2 in the sample name. The sample name mentioned corresponds to the sample name used in the publication. The rest of the EMM single cell RNAseq samples mentioned int the publication, EMM_03_1, EMM_11, EMM_14_1, EMM_14_2, EMM_16, and EMM_15_1 are already uploaded in EGA archive – dataset id EGAD50000000053.

  Dataset EGAD50000001511

• Single-cell G&T sequencing - Genomic data

  Single-cell G&T seq from an untreated PDX mouse with neuroblastoma (MYCN amplified).

  Dataset EGAD50000001513

• Single-cell G&T sequencing - Transcriptomic data

  Single-cell G&T seq from an untreated PDX mouse with neuroblastoma (MYCN amplified).

  Dataset EGAD50000001514

• Single Cell Multiome ATAC + Gene Expression sequencing

  The SHH medulloblastoma tumor 7316-178 was received through the Childhood Brain Tumor Network (CBTN). From the patient tumor, disassociated cryopreserved cells stored in 10% DMSO/FBS were used. At least 50 mg of tissue (1 M cells) was used for both samples. Disassociated cells were prepared for Single Cell Multiome ATAC + Gene Expression sequencing (10× Genomics) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq S4 200 to a depth of at least 250 M reads for snATAC-seq and 200 M reads for snRNA-seq.

  Dataset EGAD50000001515

• Whole exome sequencing of Human High-Grade-B-Cell-Lymphomas, classified according to IGH status

  HGBCL-DH-BCL2(-BCL6) lymphoma cases, classified according to IGH status in IGH+ or IGH-undetectable

  Dataset EGAD50000001527

• Whole genome sequencing of metachronous FL-High-Grade-B-Cell-Lymphomas, classified according to IGH status

  FL-HGBCL-DH-BCL2(-BCL6) metachronous lymphoma pairs, classified according to IGH status in IGH+ or IGH-undetectable

  Dataset EGAD50000001528

• T cell and Antibody Responses in Rituximab-Treated Lymphoma Patients After SARS-CoV-2 Vaccination

  This dataset contains T cell receptor (TCR) sequencing data from 51 RNA samples, each processed into three independent libraries (tot 153 FASTQ files). Sequencing was performed on an Illumina NextSeq 500 platform using the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles), generating paired-end FASTQ files with dual 10 bp barcodes and 5% PhiX as internal control. Libraries were quantified with the Qubit HS dsDNA kit and assessed for fragment size distribution using the Agilent Tapestation D1000 system before isochoric pooling to 4 nM and sequencing in two independent runs. The resulting dataset enables analysis of TCR β-chain CDR3 sequences for clonal expansion and diversity studies.

  Dataset EGAD50000001714

• Somatic L1 retrotransposition mapping in high-grade serous ovarian carcinoma using LDI-PCR/Nanopore-sequencing

  Somatic L1 retrotransposition was mapped in high-grade serous carcinoma (HGSC) tumors using LDI-PCR/Nanopore-seq method. This method identifies somatic L1 insertions originating from two active L1 loci at chr22q12.1 and chrXp22.2. Multiple tumors from the same patient were utilised to understand L1-mediated intrapatient heterogeneity. Long-read data generated by LDI-Nanopore sequencing was aligned to the reference genome (GRCh38).

  Dataset EGAD50000001707

• MOSAIC Window Mesothelioma Data

  This dataset will include Spatial Transcriptomics from the 10x Genomics Visium SD technology, Single-Cell RNA-Seq from the 10x Genomics Chromium Flex protocol, Bulk RNA-Seq (sequenced on Illumina), WES (sequenced on Illumina), H&E, and Clinical data from 10 Mesothelioma patients. For Visium and Chromium data we are sharing the outputs of respectively Space Ranger and Cell Ranger. For Bulk RNA-Seq we are including processed files such as counts.tsv, FPKM.tsv, fusion_genes.tsv, TPM count matrix.tsv, DESeq2 count matrix.tsv, multiqc_report. For WES, we are sharing the presence or absence of single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variants (CNVs).* Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001706

• The dataset for "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”

  The dataset for the study “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma” includes 169 bam files from whole genome sequencing on the Illumina NovaSeq6000 platform. The samples analyzed include tumor (n=28) and normal (n=28) DNA samples, and serial plasma cfDNA (n=113) samples from 28 individuals with resectable diffuse pleural mesothelioma, treated with nivolumab or nivolumab plus ipilimumab on the NCT03918252 trial.

  Dataset EGAD50000001701

• Human Paraganglioma

  This dataset comprises single-nucleus transcriptomic profiles from 9 human paraganglioma samples. Nuclei were isolated and processed using the SMART-Seq2 protocol to enable full-length, high-resolution RNA sequencing at the single-nucleus level. cDNA libraries were generated and sequenced on the Illumina HiSeq 2500 platform. The resulting raw sequencing data are provided as .fastq files for downstream analysis.

  Dataset EGAD50000001689

• 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 genome sequencing of UM with MSI

  Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 1 case of melanoma uveal with MSI

  Dataset EGAD50000001337

• WGBS of melanoma patients

  This dataset contains WGBS of seven melanoma patients and one cultured primary melanocyte sample.

  Dataset EGAD50000001319

• WGBS of patients from six tumor types

  This dataset contains healthy and tumor samples from patients covering breast adenocarcinoma, colon adenocarcinoma, kidney renal clear cell carcinoma, hepatocellular carcinoma, lung adenocarcinoma and pancreas adenocarcinoma.

  Dataset EGAD50000001318

• WGBS of stepwise-edited melanoma model

  This dataset contains WGBS of a stepwise-edited, human melanoma model including in vitro samples and corresponding xenografts.

  Dataset EGAD50000001317

• Targeted panel DNA sequencing of melanomas, nevi and melanocytic tumors

  This dataset was derived from 360 formalin-fixed paraffin-embedded (FFPE) samples distributed across (i) 118 primary melanomas, (ii) 132 nevi and (iii) 110 melanocytic tumors. Next generation sequencing (NGS) libraries were prepared following the FFPE DNA Archer VariantPlex Somatic Protocol for Illumina. Input DNA was determined by the PreSeq DNA QC assay, with 100 ng of DNA used for samples with high quality scores, 200 ng for low quality scores and 300 ng for samples with bad quality scores as defined by the PreSeq DNA QC assay. NGS libraries were quantified using the KAPA Library Quantification Kit for Illumina (KK4824) and sequencing performed on the Nextseq 500/2000 without custom primers using paired-end sequencing (151bp for Read 1 and Read 2) with index reads (8bp for Index Read 1 and Index Read 2). For each sample, resulting paired-end fastq files are available as part of this dataset. Prefix for each sample name is associated with the the type of sample: NAE: nevi samples. MEL: Melanoma samples. BL: melanocytic tumor.

  Dataset EGAD50000001297

• Tumor Profiler Project - OV scDNA data additional samples

  The dataset contains 10x Chromium single-cell DNA sequencing data from 6 samples from 5 different patients with ovarian cancer. 4 samples were collected from the tumor, and 2 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. This dataset contains additional samples from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001294

• Tumor Profiler Project - OV scRNA data additional samples

  The dataset contains 10x Chromium single-cell transcriptomics data from 6 samples from 4 different patients with ovarian cancer. 3 samples were collected from the tumor, 3 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. This dataset contains additional samples from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001293

• Sequencing data for filanesib-treated hepatoblastoma samples

  This dataset contains RNA sequencing data of two hepatoblastoma PDX cell models. Cells were either treated with KSP inhibitor filanesib or with DMSO (controls).

  Dataset EGAD50000001314

• Spatial transcriptomics reveals immune and tissue remodeling, highlighting diverse host responses across mycobacterial granuloma types

  Granulomas are the hallmark of Mycobacterium infections, forming structured immune environments that drive disease persistence. However, their spatial and functional organization remains unclear. Using spatial RNA sequencing on 33 patient explants, we try to reveal the detailed gene expression and cell composition landscape of granulomas.

  Dataset EGAD50000001462

• Fragmentomics profiling and quantification of plasma Epstein-Barr virus DNA enhance prediction of future nasopharyngeal carcinoma.

  This dataset included human plasma EBV DNA target-capture sequencing data. The capture probes were designed to cover the entire EBV genome and selected human autosomal regions. After enrichment, the products were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19) in BAM format. A total of 558 cases were analyzed, including seven subjects who developed NPC in the second-round screening, 431 non-NPC subjects with first-round transiently positive EBV, and 120 non-NPC subjects with first-round persistently positive EBV.

  Dataset EGAD50000001449

• Whole-exome and RNA sequencing data from a uveal melanoma patient with multi-regional sampling

  This dataset includes whole-exome sequencing (WES) and RNA sequencing (RNA-seq) data from a uveal melanoma patient. Tumor samples were obtained from three distinct regions, each with matched RNA-seq and WES data. Additionally, WES data from the patient’s peripheral blood mononuclear cells (PBMCs) is provided as a germline reference.

  Dataset EGAD50000001422

• Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

  Bulk RNA Sequencing of 33 epithelioid sarcomas (EpS) and 3 extracranial extra-renal rhabdoid tumors (EERT) Whole-exome sequencing of 30 EpS and 3 EERT Single-cell RNA Sequencing of 8 EpS Visium Spatial Transcriptomics of 3 EpS

  Dataset EGAD50000001419

• SCANDARE TNBC transcriptomics data

  SCANDARE (NCT03017573) is a multicentric biobanking study, enrolling adult patients with newly diagnosed head and neck squamous cell carcinoma (HNSCC), triple negative breast cancer (TNBC), ovarian and cervical cancer. Tumor tissue and blood samples are collected at several time points during patient's journey, including at diagnosis, post-neoadjuvant chemotherapy in case of neoadjuvant treatment, at surgery, at recurrence and at disease progression following treatment initiated at recurrence. Since its launch in 2017 at Institut Curie, SCANDARE has enabled the longitudinal collection and preservation of samples for in-depth analyses. Here, we describe molecular alterations in 124 frozen samples (n=84 at baseline and n=40 paired at post-NAC surgery) from 91 TNBC patients using total RNAseq technology, with FASTQ files deposited in the dataset.

  Dataset EGAD50000001416

• Tumor Profiler Project - OV cell-free DNA data additional samples

  The dataset contains amplicon sequencing data from 7 samples from 7 different patients with ovarian cancers. Cell free DNA was collected from plasma. Sequencing was performed on an Ion Torrent platform and the sequencing data is provided in bam format. These samples are from patients not classified as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001412

• Tumor Profiler Project - OV bulk transcriptomics data additional samples

  The dataset contains bulk transcriptomics data from 4 samples from 3 different patients with ovarian cancer. 3 samples were collected from the tumor, 1 sample from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format. These samples are from patients not classified as as having high-grade serous adenocarcinoma.

  Dataset EGAD50000001411

• PCR-Free Shallow Whole Genome Sequencing for Chromosomal Copy Number Detection

  Archival peripheral blood or bone marrow plasma samples from non small-cell lung cancer, B-cell lymphoma and acute myeloid leukemia patients, and healthy donors. Shallow whole genome sequencing of 100 Samples by two distinct library preparation methods (PCR = 45, PCR-Free = 55). sWGS done for Chromosomal CN detection.

  Dataset EGAD50000001404

• Spatial transcriptomic analysis of renal cell carcinoma

  Spatial transcriptomic analysis of two Japanese ELOC-mutated renal cell carcinoma

  Dataset EGAD50000001400

• Human Neuroblastoma

  This dataset comprises single-nucleus transcriptomic profiles from 10 human neuroblastoma samples. Nuclei were isolated and processed using the SMART-Seq2 protocol to enable full-length, high-resolution RNA sequencing at the single-nucleus level. cDNA libraries were generated and sequenced on the Illumina HiSeq 2500 platform. The resulting raw sequencing data are provided as .fastq files for downstream analysis.

  Dataset EGAD50000001596

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 226 patients with mUC

  Targeted tissue (n=210), cfDNA (n=402), and WBC (n=245) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000001571

• Whole genome sequencing data of cfDNA and WBC from 5 patients with mUC

  Whole genome Illunima sequencing of cfDNA of 5 metastatic urothelial carcinoma patients. White blood cell (WBC) samples are used as patient matched germline samples (n=5). All files are in paired-end fastq format.

  Dataset EGAD50000001570

• Melanoma transcriptomic data from patients undergoing immunotherapy

  This dataset contains raw RNA sequencing data from melanoma patient tumor samples collected before and during immunotherapy. The data support investigation of treatment-related changes in tumor cell populations. Samples were analyzed as part of a study exploring cellular responses to immune-based therapies.

  Dataset EGAD50000001569

• Hybrid Capture of PyBKV integration in Urothelial Carcinoma from Kidney Transplant

  Hybrid Capture of PyBKV integration in Urothelial Carcinoma from Kidney Transplant. The Panel was designed using Agilent SureDesign on SureSelect XTHS Hybrid Capture Panel. Sequencing was done on Illumina NovaSeq 6000

  Dataset EGAD50000001548