9182 results for "cancer rna-seq"

in 30.92 milliseconds.

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX057_SA535X5XB02887_001

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq

  Dataset EGAD00001005174

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX057_SA535X5XB02887_002

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq

  Dataset EGAD00001005175

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX049_SA928_001

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq

  Dataset EGAD00001005176

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX049_SA928_002

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq

  Dataset EGAD00001005177

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX049_SA928_003

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq

  Dataset EGAD00001005178

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX067_VOA12024_001

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq

  Dataset EGAD00001005179

• Sequencing data for study Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses for library TENX067_VOA12024_003

  Single-cell RNA-sequencing data generated using the 10X genomics chromium platform, comprising patient derived xenograft, cell line, and primary tumour data. This includes different digestion conditions (37C collagenase vs 6C cold protease) and FACS sorting for live, dying, and dead cells. 12 samples; filetype=fastq

  Dataset EGAD00001005180

• WGS,RNA data of patients with multiple myeloma (MM) refractory to immunomodulatory agents (IMiDs) and proteasome inhibitors (PIs)

  Paired WGS and RNA-Seq data of patients with multiple myeloma (MM) refractory to immunomodulatory agents (IMiDs) and proteasome inhibitors (PIs). We performed whole genome and transcriptome sequencing of 39 heavily pretreated RRMM patients with at least double refractoriness revealing complex structural changes and a high mutational load.

  Dataset EGAD00001006189

• Single-cell RNA-seq data of bronchoalveolar lavage (BAL) fluid in late severe COVID-19

  We performed single-cell RNA-sequencing of cells in the bronchoalveolar lavage (BAL) fluid of late severe COVID-19. This study provides detailed insights into the alveolar macrophage response to SARS-CoV-2 infection and reveals a profibrotic macrophage response in severe COVID-19 patients.

  Dataset EGAD00001008161

• Whole exome and RNA sequencing data from the OXIRI phase 1b clinical trial in Asian pancreatic ductal adenocarcinoma (PDAC) patients

  This dataset contains 8 samples, each of which has paired-end WXS fastq files for Tumour and Normal samples, as well as RNA-Seq fastq file.

  Dataset EGAD00001008632

• Transcriptome: chondrosarcoma

  Transcriptome sequencing of nine patients diagnosed with chondrosarcoma. cDNA was generated using the NuGEN Ovation RNA-Seq FFPE system. Total RNA was randomly primed and thermally sheared and the resulting cDNA fragment was amplified. The cDNA was then mechanically sheared using sonication to generate ~250 bp fragments. Sequencing libraries were generated using the NuGEN Ovation Ultralow System V2 library prep kit and sequenced on HiSeq2500 TruSeq v3.

  Dataset EGAD00001008699

• RNA-Seq of GM adipose tissue samples

  This dataset contains 210 fastq files (RNA sequencing was performed in two centers) from 105 individuals (106 files in subcutaneous tissue and 104 files in visceral tissue). Of the 210 fastq files, 129 files are in PEx100 mode (appeared in a single fastq file) and 81 files are in PEx49bp mode (appeared in two separate fastq files). Sequencing was done on the Illumina HiSeq2000 platform.

  Dataset EGAD00001010253

• Oxidative phosphorylation is a key ontogenetic feature of monocyte immunometabolism promoting myeloid differentiation after birth

  The dataset consists of 12 samples of monocytes, which were analyzed using RNA-sequencing (RNA-seq). These samples were categorized into four distinct groups, each comprising three samples. The dataset was designed to investigate the transcriptomic and metabolic profiles of monocytes across different age groups and stimulation conditions. 3 neonatal controls, 3 neonatal LPS stimulated, 3 adult controls and 3 adult LPS stimulated samples.

  Dataset EGAD00001011340

• RNA-seq of PBX1 knock-down or overexpressing cell lines

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains 44 samples derived from RNA-sequencing data of bile duct and CCA cell lines. Data was generated on Illumina NovaSeq 6000 device in paired-end mode and is stored in compressed FASTQ file format.

  Dataset EGAD00001011325

• Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks

  Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status – which distinguishes the two major subtypes of CLL – was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we discovered widespread heterogeneity in the chromatin landscape of CLL, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research.

  Dataset EGAD00001002110

• Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001227

• ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001235

• Fastq data for smRNA-Seq assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for smRNA-Seq assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001401

• BLUEPRINT: RNA-seq of progenitor cells

  Data supporting the paper Transcriptional diversity during lineage commitment of human blood progenitors

  Dataset EGAD00001000745

• NASH RNA-seq data

  This dataset includes transcriptome sequencing of 17 paired NAFLD-HCC samples and adjacent normal tissues. All the experiments were performed on Illumina HiSeq 2000 platform with raw reads stored in fastq format.

  Dataset EGAD00001004326

• RNA-seq TPM matrices

  Matrices of TPM-normalized counts from RNAseq data for the three phase II clinical trials (IMvigor210, POPLAR, IMmotion150) and the phase I clinical trial PCD4989g.

  Dataset EGAD00001006741

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities - RNA-Seq

  We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles

  Dataset EGAD00001009794

• Dataset for Stromal-induced epithelial-mesenchymal transition induces drug resistance in acute lymphoblastic leukemia

  RNA-seq was performed to compare gene expression profiles between 11 patient adherent ALL samples and nonadherent ALL samples.

  Dataset EGAD00001009056

• RNA sequencing of Korean ER positive breast cancer females aged under 35 years old.

  Corresponding data set is composed of RNA sequencing of Korean ER positive breast cancer under 35 years old. This set provides 50 alignment files of 50 tumor samples. This is a part of total project data set.

  Dataset EGAD00001003243

• Single cell RNAseq of PBMC from bladder cancer patients

  This dataset contains single cell RNA sequencing data of PBMC samples from 10 bladder cancer patients. cDNAs and single cell RNA libraries were prepared following manufacturer’s user guide (10x Genomics). Each library was sequenced in HiSeq4000 (Illumina) to achieve ~300 million reads following manufacturer’s sequencing specification.

  Dataset EGAD00001005481

• Single cell RNAseq of PBMC from bladder cancer patients

  This dataset contains single cell RNA sequencing data of PBMC samples from 20 bladder cancer patients. cDNAs and single cell RNA libraries were prepared following manufacturer’s user guide (10x Genomics). Each library was sequenced in HiSeq4000 (Illumina) to achieve ~300 million reads following manufacturer’s sequencing specification.

  Dataset EGAD00001006182

• small RNA next generation sequencing in head and neck cancer

  small RNA next generation sequencing in head and neck cancer

  Dataset EGAD00001008402

• FASTQ files of the small RNA-Seq dataset from the POPS cohort

  Placental biopsies were collected within 30 minutes of birth and flash frozen in RNAlater(ThermoFisher). For each biopsy,total placental RNA was extracted from approximately 5 mg of tissue using the “mirVana miRNA Isolation Kit” (Ambion) followed by DNase treatment (“DNA-free DNA Removal Kit”, Ambion). RNA quality was assessed with the Agilent Bioanalyzer and all the samples with RIN values ≥ 7.0 were used in the downstream experiments. Total RNA-libraries were prepared from 300-500ng of total placental RNA with the “TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat”(Illumina). Small RNA-libraries were prepared from 150ng of total placental RNA with the “NEBNext Multiplex Small RNA Library Prep Kit for Illumina”(New England Biolabs)and concentrated using the “QIAquick PCR purification kit”(Qiagen). Paired libraries were combined and size selected using the Pippin Prep and 3% Agarose Gel Cassette with marker F (Sage Science),pooled and sequenced (single-end, 50bp) using a Single End V4 cluster kit and HiSeq4000 instrument.

  Dataset EGAD00001004860

• The Effect of the Menstrual Cycle on DNA Expression in the Normal Human Breast Epithelium

  The Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center [www.komentissuebank.iu.edu] (KTB) was established expressly for the prospective collection of normal, healthy breast tissue from volunteer donors. Blood is also obtained from donors at the time of donation and is processed for serum, plasma and peripheral blood leukocyte DNA. Specimens are annotated and data includes age, race, ethnicity, personal health history, family cancer history, medication usage at the time of donation, and breast cancer risk factors. Premenopausal donors to the KTB were identified by a query of the Bank's database. Hematoxylin and eosin stained sections of the formalin-fixed paraffin-embedded tissue of the identified donors were reviewed and tissue was graded on the basis of the abundance of epithelium within the section. Only tissue containing abundant epithelium was considered for this study. Based on dates, the specimens of nine women in the follicular phase of the menstrual cycle and five in the luteal phase were chosen. Six donors using hormonal contraception at the time of donation were also included. Whole blood obtained from 19 of the 20 donors at the time of tissue donation was available and it was processed for serum. Estradiol, estriol, luteinizing hormone and progesterone concentrations were determined by the Indiana University Health Pathology Laboratory using a Beckman Unicel DxI 800 Immunoassay System. The phase of the menstrual cycle was verified by serum progesterone concentration. The epithelium of these 20 specimens was microdissected from multiple 8 micron frozen tissue sections. Total RNA extracted from the tissue was subsequently depleted of rRNA via locked nucleic acid probes. This enabled profiling of both poly-A and non-poly-A RNA species. Barcoded cDNA libraries from the 20 normal breast epithelia were prepared and sequenced on an Applied Biosystems (AB) SOLiD3 or SOLiD 4 platform. RNA-seq reads for each sample were then mapped to the human genome (hg19) using the LifeScope software version 2.5.1 (Life Technologies, Foster City, CA) and BAM (Binary Alignment/Map) files generated. Read counts for each gene were derived from the output BAM files using the RefSeq database (UCSC Genome Brower) as the gene model.

  Study phs000644

• Differential Gene Expression in Cryptorchid Testes

  Differential Gene Expression in Cryptorchid Testes Study uses whole-genome RNA profiling of testicular biopsies to determine a potential causative role of isolated congenital cryptorchidism in azoospermia and/or infertility in the context of our previously published GeneChip data. Cryptorchid patients, aged 7 months to 5 years and otherwise healthy, were enrolled in this prospective study. During surgery, testicular tissue biopsies were obtained for histological examination and RNA-sequencing (RNA-seq). Fifteen patients were selected based on the histological results and were divided into two groups. Seven were classified as belonging to the high infertility risk (HIR) and eight to the low infertility risk (LIR) group. Cryptorchid boys in the high infertility risk group lacked transformation of gonocytes into Ad spermatogonia due to impaired mini puberty. This group of patients will be infertile despite successful surgery.

  Study phs001275

• University of Pennsylvania CAR T Cell Responding and Non-responding Patients

  The adoptive transfer of autologous T cells genetically modified to express a CD19-specific, 4-1BB/CD3zeta-signaling chimeric antigen receptor (CAR; CTL019) has shown remarkable activity in patients with B acute lymphoblastic leukemia. Similar therapy can induce long-term remissions for relapsed/refractory chronic lymphocytic leukemia (CLL) patients, but in only a small subset of subjects. The determinants of response and resistance to CTL019 therapy of CLL are not fully understood. We employed next generation sequencing of RNA (RNA-seq) to identify predictive indicators of response to CTL019 treatment. We performed RNA-seq on leukapheresis and manufactured infusion product T cells from patients with heavily pre-treated and high-risk disease. To characterize potency, we also performed RNA-seq on the cellular infusion product after CAR-specific stimulation. Our findings indicate that durable remission in CLL is associated with gene expression signatures of early memory T cell differentiation (e.g., STAT3), while T cells from poorly- or non-responding patients exhibited elevated expression of key regulators of late memory as well as effector T cell differentiation, apoptosis, aerobic glycolysis, hypoxia and exhaustion. These gene expression signatures, along with additional immunological biomarkers, may be used to identify which patients are most likely to respond to cellular therapies and suggest manufacturing modifications that might potentiate the generation of maximally efficacious infusion products. In a follow-up study, we report multiplex CRISPR-Cas9 gene editing on T cells in humans to test the hypothesis that disrupting genes encoding the endogenous T cell receptor (TCR), TCRα (TRAC) and TCRβ (TRBC), as well as PD-1 (PDCD1) would enhance the efficacy of autologous T cells engineered to express a transgenic NY-ESO TCR. We used single cell RNA-seq to comprehensively characterize the transcriptomic phenotype of this T cell product and its evolution over time in a patient with sarcoma. Notably, this patient's transferred T cells that persisted in vivo demonstrated increases in expression of genes associated with a central memory state (IL7R, TCF7). These findings may guide future trials involving administration of genetically redirected, genome -edited T cells.In this follow-up study, we investigated whether CRISPR-Cas9-mediated disruption of PDCD1 and/or CTLA-4 could restore CART dysfunction in healthy donors and/or CLL patients. We show that depletion of CTLA-4 rescues the function of T cells from leukemia patients that previously failed CART cell treatment. We performed single-cell RNA sequencing and characterized the transcriptomic landscape of CTLA-4 KO CART19 cells that showed higher proliferation and anti-tumor efficacy by permitting unopposed CD28 signaling and maintenance of CAR expression on the T cell surface under stress-test conditions of chronic antigen exposure. Our findings reveal that selective disruption of CTLA-4 invigorates dysfunctional patient T cells, providing a strategy for increasing patient responses to CART cell therapy.

  Study phs001707

• PIK3CA SiMSen-Seq

  Simple, Multiplexed, PCR-based barcoding of DNA for Sensitive mutation detection using Sequencing (SiMSen-Seq) of 11 PIK3CA hotspot mutations in plasma DNA of breast cancer patients.ng

  Dataset EGAD00001006897

• GINS3 fibroblast RNAseq

  The eukaryotic CDC45/MCM2-7/GINS (CMG) DNA helicase unwinds the DNA double helix during DNA replication. We report the identification of individuals presenting with a Meier-Gorlin syndrome (MGS) like phenotype, secondary to hypomorphic variants in the GINS3 gene.  To verify whether the GINS3 variant affected the transcriptome, RNA-seq was performed from 3 fibroblast cultures derived from a patient with compound heterozygous GINS3 variants, and 1 replicate of fibroblasts derived from each of the two parents.

  Study EGAS00001006038

• Whole Transcriptome Sequencing of NXF1 or CRM1 depleted Cell

  mRNA exporters, NXF1 and CRM1 are known to function in mRNA export. However, since each target mRNA has not been identified genome-widely, it is not clear whether they export exclusive mRNA subsets. To reveal this point, we prepared the nuclear and the cytoplasmic RNAs under either exporter inhibited condition and carried out RNA-seq. In these experiments, we also focused in the export machinery of aberrant transcripts that usually retained and decayed in the nucleus.

  Study JGAS000294

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

  To elucidate the feature of age-associated helper T (ThA) cells and its contribution to autoimmune diseases, CD4+ T cell subsets from 19 rheumatoid arthritis (RA), 62 systemic lupus erythematosus (SLE), 40 idiopathic inflammatory myopathy (IIM) and 64 healthy controls (HC) were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA). RNA-seq was performed with each CD4+ T cell subset samples.

  Study JGAS000626

• The genomic landscape of follicular and diffuse large B-cell lymphoma

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing and RNA sequencing of follicular and diffuse large B-cell lymphoma. Follicular and diffuse large B-cell lymphomas are the most common B-cell lymphomas in adulthood. Analyses were performed in concordance with the guidelines of the ICGC. The results define the genomic landscape of structural variants, somatic single nucleotide variants and mutational signatures in these lymphomas

  Study EGAS00001002199

• Reference Profiles of ExRNAs in Normal Human Pregnancy

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

  Study phs003182

• Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2

  Single cell RNA sequencing (scRNA-seq) is widely used for profiling transcriptomes of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently-used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data by the two platforms from the same samples of CD45- cells, we systematically evaluated their features using a wide spectrum of analysis. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data better. For 10X-based data, we observed higher noise for mRNA in the low expression level. Despite the poly(A) enrichment, approximately 10-30% of all detected transcripts by both platforms were from non-coding genes, with lncRNA accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can better detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected different sets of differentially expressed genes between cell clusters, indicating the complementary nature of these technologies. Our comprehensive benchmark analysis offers the basis for selecting the optimal scRNA-seq strategy based on the objectives of each study.

  Dataset EGAD00001005448

• Poikiloderma_syndrome_RNAseq

  We will sequence the RNA of lymphoblast samples, transformed with EBV, which have poikiloderma syndrome with mutations in c16orf57. The aim of the experiment is to characterise RNA structural effects in this disease.

  Study EGAS00001000250

• RNA sequencing in primary inflammatory (TPP) macrophages following deletion of a disease-associated gene desert at chr21q22, disruption of ETS2, or treatment of ETS2-edited macrophages with a HIF1α stabiliser.

  This dataset comprises raw RNA sequencing data (FASTQs) from primary inflammatory (TPP) macrophages that were unedited (non-targeting control, NTC), edited to delete the disease-associated chr21q22 enhancer region (n=5), or edited to disrupt ETS2 with 1 of 2 independent gRNAs (n=9). We also performed RNA-sequencing in NTC or ETS2-edited TPP macrophages that were treated for 12 hours with vehicle (DMSO) or roxadustat (30 uM, n=3). Macrophages were detached using Accutase and lysed. RNA was extracted from cell lysates using an AllPrep DNA/RNA Mini Kit (Qiagen). Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NextSeq500. Raw data are provided as 50 bp paired-end Illumina reads.

  Dataset EGAD00001011338

• Genomic Analysis of Medullary Thyroid Carcinoma

  Sequence data from two medullary thyroid carcinoma patients: WGS datasets generated from tumors and matched normal tissues and RNA-Seq from tumors are included.

  Dataset EGAD00001001618

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

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

  Dataset EGAD00010001420

• RNA-Seq of primary pediatric kidney tumor controls for the soft tissue sarcoma tumoroid biobank

  Dataset EGAD00001008709

• PDAC organoid genomic heterogeneity

  Two primary tumor-derived PDAC organoids were subjected to SNP array, RNA-seq, and single-cell WGS.

  Dataset EGAD00001009741

• Characterization of a novel MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line RNA-Seq

  A novel in-house-made pediatric MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line was characterized

  Dataset EGAD00001009759

• Covacta RNAseq counts

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

  Dataset EGAD00001011164

• scRNA-seq and snRNA-seq of trophoblast stem cells (TSCs) differentiation into extravillous trophoblast organoids (EVTs)

  This dataset is part of a study that aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. This specific dataset includes scRNA-seq and snRNA-seq data from trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) together with EVT differentiation media. This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells. Data for primary trophoblast organoids is available under E-MTAB-12650.

  Dataset EGAD00001010017

• ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K27ac) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001229

• ChIP-Seq (H3K27me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K27me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001230

• ChIP-Seq (H3K36me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K36me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001231