14982 results for "cancer studies using rna-seq"

in 22.33 milliseconds.

• Enzymatic methylation sequencing of intestinal metaplasia

  We perform genome-wide EM-seq of 14 patients with concurrent matched normal, dysplasia and early gastric samples from South Korea. The dataset contains cram files from 38 samples.

  Dataset EGAD50000001538

• HiChIP for 2 samples

  This dataset contains H3K27ac HiChIP data from ta primary sample and a patient derived model (PDX) of the novel FOXF1/FENDRR ALL subtype. All the 2 samples are in bam file type.

  Dataset EGAD50000001787

• Paired-end Whole Exome-seq analysis of TERT promoter duplication in GBM

  Dataset contains paired-end Whole Exome sequencing data from 5 tumor samples and 1 single normal blood sample from a single primary GBM patient.

  Dataset EGAD00001008768

• RNA-Seq of PBMC's from rUTI Patients and Healthy Controls

  Recurrent urinary tract infections (rUTIs) are a major health burden worldwide, with history of infection being a significant risk factor. While the gut is a known reservoir for uropathogenic bacteria, the role of the microbiota in rUTI remains unclear. We conducted a year-long study of women with and without history of rUTIs, from whom we collected urine, blood and monthly fecal samples for multi-omic interrogation. The rUTI gut microbiome was significantly depleted in microbial richness and butyrate-producing bacteria compared to controls, reminiscent of other inflammatory conditions, though Escherichia coli gut and bladder dynamics were comparable between cohorts. Blood samples revealed signals of differential systemic immunity, leading us to hypothesize that rUTI susceptibility is in part mediated through a syndrome involving the gut-bladder axis, comprising gut dysbiosis and differential immune response to bacterial bladder colonization, manifesting in symptoms. This work highlights the potential for microbiome therapeutics to prevent and treat rUTIs.  (Reprinted from medrxiv.org ) 

  Study phs002728

• Rna-Seq Leiomyosarcoma subtypes

  Leiomyosarcomas (LMS) are genetically heterogeneous tumors differentiating along smooth muscle lines. Currently, LMS treatment is not informed by molecular subtyping and is associated with highly variable survival. While disease site continues to dictate clinical management, the contribution of genetic factors to LMS subtype, origins, and timing are unknown. Here we analyzed 70 genomes and 130 transcriptomes of LMS, including multiple tumor regions and paired metastases. Molecular profiling highlighted the extremely early origins of LMS. Three specific subtypes of LMS develop from distinct lineages of smooth muscle cells. Of these, dedifferentiated LMS with high immune infiltration and tumors primarily of gynaecological origin acquired the highest burden of genomic mutation and are associated with worse survival. Homologous recombination defects lead to genome-wide mutational signatures, and a corresponding sensitivity to PARP and other DNA damage response inhibitors, suggesting a novel therapeutic strategy for LMS. Finally, by phylogenetic reconstruction, we present evidence that clones seeding lethal metastases arise decades prior to LMS diagnosis.

  Study EGAS00001004783

• RNA-seq from human embryonic tissues (additional samples 2018)

  How the genome activates or silences transcriptional programmes governs organ formation. Little is known about this in human post-implantation embryos undermining our ability to benchmark the fidelity of in vitro stem cell differentiation or cell programming, or interpret noncoding variation as potential causes of disease. Here, by studying histone modification we identified genome-wide open chromatin states and active repression across thirteen tissues during human organogenesis. We integrated the data with transcription to build the first view of how promoter states from nearly 20,000 genes differentially regulate alternative organ fates, arguing against bivalency during human organogenesis. The data illustrate tissue-specific as well as complex patterns of enhancer activity functional in zebrafish and impute master transcription factors. Overlaying 739 noncoding de novo mutations in patients allowed phenotypic correlation of developmental disorders to unanticipated target genes. Taken together, the data provide a comprehensive genomic framework for understanding normal and abnormal human development.

  Study EGAS00001003738

• Single-cell RNA-seq and spatial transcriptomics data for the sarcoidosis baseline project

  Granulomas are lumps of immune cells that can form in various organs. Most granulomas appear unstructured, yet they have some resemblance to lymphoid organ formation. To better understand granuloma formation, we performed single-cell sequencing and spatial transcriptomics on granulomas from patients with sarcoidosis and bioinformatically reconstructed the underlying gene-regulatory networks. We discovered an immune stimulatory environment in granulomas that repurposed transcriptional programs associated with lymphoid organ development. Granuloma formation followed characteristic spatial patterns and involved genes linked to immunometabolism, cytokine and chemokine signaling, and extracellular matrix remodeling. Three cell types emerged as key players in granuloma formation: metabolically reprogrammed macrophages, cytokine-producing Th17.1 cells, and fibroblasts with inflammatory and tissue remodeling phenotypes. Pharmacological inhibition of one of the identified processes attenuated granuloma formation in a sarcoidosis mouse model. We show that human granulomas adopt characteristic aspects of normal lymphoid organ development in aberrant combinations, indicating that granulomas constitute aberrant lymphoid organs.

  Study EGAS00001006970

• DAC for BCP-LBL Kiel

  Whole exome sequencing and RNA sequencing of B-Cell Precursor Lymphoblastic Lymphoma tissue biopsies.

  Dac EGAC50000000181

• DupiAERD DAC

  DAC to regulate access to RNA sequencing data of NERD patients with dupilumab treatment before and after aspirin provocation.

  Dac EGAC50000000273

• resistance to FGFR inhibitor from RNA sequencing

  WTS performed on tissues from resistant patients

  Study EGAS50000000306

• Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA

  Study EGAS00001005740

• CGC_RNAseq

  RNA sequencing during time series

  Dataset EGAD00001006321

• RNAseq data

  Individual FASTQ files from RNA sequencing.

  Dataset EGAD00001008796

• WTCCC case-control study for Hypertension

  WTCCC genome-wide case-control association study for Hypertension (HT) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000009

• Exome Sequencing of Multiple Localised Spiradenoma and Spiradenocarcinoma

  Tumor samples were microdissected from formalin-fixed, paraffin-embedded tissue and genomic DNA was extracted. DNA libraries were generated using xGen ssDNA & Low-Input DNA Library Preparation Kit (IDT). The libraries were enriched for the exome using xGen Exome Hyb Panel (IDT) and sequenced on DNBSEQ G400RS.

  Dataset EGAD50000000788

• Elucidation of molecular mechanism of NAFLD-HCC

  We analysed the somatic mutation profile of 69 genes with recurrent genetic alterations reported in HCC using surgically-resected tumor tissues of non-viral HCC patients.

  Study JGAS000523

• Metabolome analysis of persons with type 2 diabetes with or without diabetic complications

  We profiled serum metabolites of persons with T2D with or without diabetic complications using a comprehensive non-targeted metabolomics approach with mass spectrometry.

  Study JGAS000572

• Flexible and rapid validation of structural variants using adaptive sampling

  This is the DAC that oversees the application and approval process for access to the Oxford Nanopore fastq files associated with the study, "Flexible and rapid validation of structural variants using adaptive sampling". The DAC members include Dr. Stephen W. Scherer (swscherer@sickkids.ca) and Dr. Lars Feuk (lars.feuk@igp.uu.se).

  Dac EGAC50000000748

• Clinical and serum metabolomics data for individuals with ACS

  Full clinical data for a cohort of 199 individuals with acute coronary syndrome. Untargeted serum metabolomics using the Metabolon platform for individuals with ACS (n=156). Serum metabolomics using the Nightingale Health (NMR) platform for individuals with ACS and controls (ACS, n=191; controls, n=961).

  Dataset EGAD00001007724

• Mutation analysis of 17 genes in plasma DNA of CRC patients using the AVENIO ctDNA Targeted Kit

  Mutation analysis of 17 genes (ALK, APC, BRAF, BRCA1, BRCA2, DPYD, EGFR, ERBB2, KIT, KRAS, MET, NRAS, PDGFRA, RET, ROS1, TP53, UGT1A1) in plasma DNA of CRC patients using the AVENIO ctDNA Targeted Kit.

  Dataset EGAD00001006103

• Whole genome sequence data from Illumina HiSeqX instruments

  This dataset includes bam files from 120 samples. These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner. All samples were processed with TruSeq DNA PCR-free sample preparation.

  Dataset EGAD00001003562

• SNF_CyTOFF_20

  Matrix of normal values from 39 marker CyTOF assay performed on baseline BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011146

• Single-nucleus APP Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for APP using custom designed primers.

  Dataset EGAD00001008284

• Single-nucleus BIN1 Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for BIN1 using custom designed primers.

  Dataset EGAD00001008288

• Single-nucleus SPP1 Isoforms in Down Syndrome Brains (long-read)

  16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for SPP1 using custom designed primers.

  Dataset EGAD00001008285

• Whole Exome Sequencing

  Whole exome sequencing data of 19 snap-frozen peritoneal mesothelioma (tumor) samples and 16 matched normal samples. Sequencing library was prepared using Ion AmpliSeq Exome RDY Library Preparation. Samples were sequenced on the Ion Proton System using the Ion PI Hi-Q Sequencing 200 Kit and Ion PI v3 chip.

  Dataset EGAD00001004503

• Exome sequencing in bipolar disorder families

  In the present study two large, multiply affected bipolar disorder families from Cuba were investigated using whole exome sequencing (Illumina HiSeq2500 v4). The variant calling files (VCFs) of 15 individuals provided here were generated using the Varbank exome pipeline from the Cologne Center for Genomics (CCG, https://varbank.ccg.uni-koeln.de).

  Dataset EGAD00001004276

• TXT_Cytof_15B

  Matrix of normal values from 39 marker CyTOF assay performed on longitudinal BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011143

• Single Cell Sperm sequencing try 2

  Sequence single cell sperm using a 10X Chromium. As a pilot test, we used samples from men who have had children with autism and normal controls.

  Study EGAS00001004035

• SNP array data for 140 individuals from 5 populations in Pakistan

  We have genotyped 140 individuals from 5 populations in Pakistan, using the OmniExpressExome-8 array, which includes approximately one million autosomal SNP markers.

  Study EGAS00001002965

• Covid19 WGS BAM files

  The Samples were collected from Saint James's Hospital, Dublin, and after informed consent Extracted Genomic DNA samples were prepared and sequenced using the Automated Illumina TruSeq PCR-free methodology.

  Study EGAS00001007048

• Mosaic structural variation sample

  Mosaic Normal-Tumor genomes are generated from real normal-tumor pairs with validated somatic variants. In this case, validated variants from the GRIDSS2 paper. Mosaic genomes were generated using GenomeMosaicMaker, an open-source software tool designed and implemented for this specific purpose. The variants provided in the VCF truth file for each mosaic tumor/normal pair were annotated using funnSV for SVs and VEP for SNVs and indels. All CRAM files are aligned to GRCh37. Please see https://github.com/EUCANCan/oncoliner and https://github.com/Computational-Genomics-BSC/GenomeMosaicMaker for more information.

  Study EGAS50000000460

• Copy Number Abnormalities of Chr1 in Multiple Myeloma at the Single Cell Level

  Single-cell whole genome sequencing (scWGS) provides a tool to gain deeper insights into the clonal relationships of Chr1 copy number changes. Here, we study Chr1 copy number alteration (CNA) using Direct library preparation plus (DLP+), a scalable scWGS platform implemented by image-based object recognition, and open-source computational methods. We report scWGS of 2,046 cells with 400-650 single-cells per patient from 5 Multiple Myeloma patients selected from our biobank with chr1q gains identified by iFISH using a CKS1B probe (IRB S21-01218 and I19-01384)

  Study phs004109

• Targeted Myeloid DNA-Panelsequencing, DKFZ

  Targeted myeloid DNA-Panelsequencing from purified bone marrow blasts of 104 treatment naive AML patients from the discovery cohort. For more details, we refere to Jayavelu, Wolf, Buettner et al. Libraries were prepared from 40 ng DNA using the QIASeq Human Myeloid Neoplasms Panel (Qiagen) according to the manufacturer’s protocol. Samples were tagged with the QIAseq 96-Unique Dual Index Set A for Illumina platforms (Qiagen) to yield unique combinations of i5 and i7 barcodes for each sample. Sample fragment size distribution and concentration was estimated using the Agilent High Sensitivity DNA kit on a 2100 Bioanalyzer (Agilent). Samples were pooled in an equimolar fashion, denatured, and diluted to 1.5 pM according to Illumina’s recommendations. The diluted library was sequenced on a NextSeq 500 benchtop sequencer (Illumina) using NextSeq High Output cartridges. Demultiplexing was performed using the BaseSpace cloud platform (Illumina).

  Dataset EGAD00001008501

• Mechanisms of patient response to Dabrafenib in Melanoma

  Samples will be from the BRF113683 (BREAK-3) study which is a Phase III Randomized, Open-label Study Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma (n=250 enrolled)*NGS [Agilent capture (Sanger V2 panel): 360 genes and 20 gene fusions; Illumina HiSEQ Sequencing]*CNV: [via NGS or Affy SNP 6.0 or Illumina Omni (TBD)]Bioinformatics: Analysis will be performed using core Sanger informatics pipelines similar to those previously described (Papaemmanuil E et al. (2013) Blood. 22:3616 -3627). Briefly, copy number analysis will be performed using the ASCAT algorithm, and base substitutions, small insertions and deletions using the CAVEMAN and Pindel algorithms, respectively. Statistical approaches including generalized linear models will be used to predict clinical variables such as maximum clinical response and duration of response using genetic data. Sanger and EBI to conduct analysis; Raw data and correlation with clinical endpoints to be analyzed by both EBI/Sanger and GSK (unique pipeline analyses to increase call confidence)

  Dataset EGAD00001001375

• Copy number analysis by SNP array

  Hybridization-based genomic profiling arrays were performed using Genome-Wide Human SNP Array 6.0 or the CytoScan HD array, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) now part of Thermo Fisher Scientific (Thermo Fisher Scientific, Inc.) Following the procedures of sample preparation, hybridization, and scanning, the CEL file of Genome-Wide Human SNP Array 6.0 was analyzed as previously described (Magrangeas et al. 2012) and the CEL file of CytoScan HD array was analyzed using the Chromosome Analysis Suite (ChAS) software (Thermo Fisher Scientific, Inc).

  Study EGAS00001005125

• RNA-Sequencing generated from 180 human putamen and substantia nigra

  Dataset EGAD00001005526

• GATCI RNAseq fastqs

  Raw RNA sequence data (fastq) for the GATCI project

  Dataset EGAD00001005810

• TCELL PILOT ATAC-SEQ

  This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001001317

• scRNA-seq

  This dataset gather scRNAseq data performed for MM.1S cell line in control and dex conditions at 4h and 24h

  Dataset EGAD00001011139

• Single-cell gene expression data from CD8+ T cells from two Austrian COVID19 patients stimulated with wildtype and mutant SARS-Cov-2 peptides

  The data contains single-cell gene sequencing data (10x Genomics) from FACS-purified CD8 T lymphocytes from two Austrian patients. The cells were stimulated with one MHC class I peptides obtained from a common (wild type) variant and an emerging mutant variant of the SARS-Cov-2 virus. Then the samples were multiplexed using hashtag oligos. We provide the raw and aligned sequence data for: i. The single-cell experiments ii. The PCR-amplified samples for enrichment of the hashtag oligo multiplexing barcodes iii. The PCR-amplified samples for enrichment of the T Cell Receptor (TCR) VDJ region for immuno-profiling. The samples and libraries were processed and obtained in collaboration between St. Anna Children's Cancer Research Institute (CCRI), CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, and the Medical University of Vienna. The cell barcodes and processed data has been submitted to the GEO database with GEO accession GSE166651.

  Dataset EGAD00001006995

• Whole genome sequencing

  Whole genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from 15 patients with homologous recombination deficiencies. The dataset includes fastq files from 56 HGSC tumours (1 primary, 1 relapse, 54 end-stage) and 15 matched normals. Sequence libraries were generated from tumour and matched normal genomic DNA using the KAPA HyperPrep PCR-free library preparation kit (Roche), or the Illumina TruSeq DNA Nano kit according to manufacturer’s instructions. Sequencing was carried out by the Kinghorn Centre for Clinical Genomics Sequencing Laboratory (Sydney, Australia) on the HiSeq X Ten System (Illumina) or by the Australian Genome Research Facility (Melbourne, Australia) on an Illumina NovaSeq to a minimum base coverage of 30-fold for normal DNA and 60-fold for tumour DNA samples.

  Dataset EGAD00001009746

• POETIC clinical Trial Ki67 Bookend Breast Cancer Targeted Exome and RNAseq Project

  Using RNAseq, we compare the 15% of poorest responders (PRs, n=177) as measured by proportional Ki67 changes after 2 weeks of neoadjuvant aromatase inhibitors to good responders (GRs, n=190) selected from the top 50% responders in the POETIC trial and matched for baseline Ki67 categories. In the POETIC trial, 4,480 postmenopausal women with primary ER+ BC were randomised 2:1 to receive either treatment with a non-steroidal AI (letrozole or anastrozole) for 2 weeks before and 2 weeks after surgery or to no perisurgical treatment. Only AI-treated patients with HER2- tumors, paired baseline and surgery Ki67 available, and baseline Ki67 immunohistochemistry (IHC) >10% (to minimise imprecision in proportional Ki67 falls) were included for selection. Data is baseline RNAseq and targeted exome DNA sequencing analysis of POETIC Good/Poor Responders to aromatase inhibitors based on change in Ki67.

  Dataset EGAD00001010919

• Single-cell ATAC-seq analysis for COVID19 patients

  While SARS-CoV-2 infection causes mild respiratory disease in most individuals, a small group of patients develops severe COVID-19. Dysfunctional innate immune responses have been identified to contribute to differences in COVID-19 severity, but the key regulators are still unknown. Here, we present an integrative single-cell epigenetics, transcriptomic, and genetics analysis of peripheral blood mononuclear cells from hospitalized and convalescent COVID-19 patients. In classical monocytes, we identified 41.3% of significantly up-regulated genes in hospitalized COVID-19 patients potentially induced by differential chromatin accessibility. Sub-clustering and motif-enrichment analyses of monocytes reveal disease condition-specific regulation by transcription factors, such as C/EBPs and SPI1, and their targets, including a long-noncoding RNA LUCAT1, which further regulates interferon responses and is associated with the need for oxygen supply of COVID-19 patients. The interaction between C/EBPs and LUCAT1 was validated through loss-of-function experiments. Finally, we investigated genetic risk variants that exhibit allele-specific open chromatin (ASoC) in promoters/enhancers of COVID-19 patients. Integrating our data with publicly available expression quantitative trait loci and chromosomal interactions indicates that ASoC SNP rs6800484-C is associated with lower expression of CCR2, which may contributeto higher viral loads in lungs and higher risk of COVID-19 hospitalization. Altogether, our study highlights the diverse genetic and epigenetic regulators that contribute to the innate immune responses of different COVID-19 patients.

  Study EGAS00001006559

• GoNL aligned sequence data in BAM format.

  We mapped the data to the UCSC human reference genome build 37 using BWA 0.5.9-r16. We first mapped each read pair separately using bwa aln. Then we used bwa sampe to map the paired reads together to a BAM9 file. The BAM file was then sorted by genomic position and indexed using PicardTools-1.32 SortSam. To prevent PCR artifacts from influencing the downstream analysis of our data, we used Picard to mark the duplicate reads, which were ignored in downstream analysis. We used GATK IndelRealigner on our data around known indels (from 1KG Pilot). The IndelRealigner creates all possible read alignments using the source and computes the likelihood of the data containing the indel based on the read pileup. Whenever the maximum likelihood contains an indel, the reads are realigned accordingly. Each base is associated with a phred-scaled base quality score. Calibration of Phred scores is crucial as they are used in some of the downstream analysis models. We used GATK to recalibrate the base qualities with respect to (i) the base cycle, (ii) original quality score, and (iii) dinucleotide context. To minimize issues stemming from mapping problems around indels, we decided to undergo a second round of indel realignment using the GATK IndelRealigner by family rather than by individual. For this second round, we considered two sources of possible indels: 1KG Phase 1 indels and indels aligned by BWA in the GoNL data.

  Dataset EGAD00001001038

• Whole exome and transcriptome analysis of UV-exposed epidermis and carcinoma in situ reveals early drivers of carcinogenesis

  Squamous cell carcinoma in situ (SCCIS) is a prevalent precancerous lesion that can progress to cutaneous squamous cell carcinoma (cSCC). Although SCCIS is common, its pathogenesis remains poorly understood. To better understand SCCIS development, we performed laser-captured microdissection of human SCCIS and adjacent epidermis to isolate genomic DNA and RNA for next generation sequencing. Whole exome sequencing (WES) identified UV-signature mutations in multiple genes including Notch 1-3 (GeneID:4851, GeneID:4853, GeneID:4854) in the epidermis and SCCIS and oncogenic TP53 (GeneID:7157) mutations in SCCIS. Novel gene families, including SCHLAFEN genes, contained UV/oxidative-signature disruptive (UVD) epidermal mutations that manifested positive selection in SCCIS. The frequency and distribution of NOTCH and TP53 mutations indicate that NOTCH mutations may precede TP53 mutations. RNA sequencing identified 1166 differentially expressed genes; the top 5 enriched GO biological processes included: 1) immune response, 2) epidermal development, 3) protein phosphorylation, 4) regulation of catalytic activity, and 5) cytoskeletal regulation. The NEURL1 ubiquitin ligase, which targets Notch ligands for degradation, was upregulated in SCCIS. Neuralized 1 protein was found to be elevated in SCCIS suggesting that increased levels could represent a novel mechanism for downregulating Notch during UV-induced carcinogenesis. The data from DNA and RNA sequencing of epidermis and SCCIS provide insights regarding SCCIS formation.

  Study phs002019

• DUX4 activates novel intergenic transcripts and isoforms in a tissue-specific context

  DUX4, a transcription factor driving zygotic genome activation during the embryonic cleavage stage in mammals, regulates the expression of genic and non-genic elements and modulates chromatin accessibility. Its misexpression in skeletal muscle causes Facioscapulohumeral muscular dystrophy (FSHD). The sporadic expression of DUX4 in FSHD muscle and the limitations of short-read RNA sequencing challenge, however, a comprehensive grasp of its consequences on the muscle transcriptome. Here, leveraging full-length isoform RNA sequencing with short-read RNA sequencing on DUX4-inducible myoblasts, we elucidated DUX4-induced transcriptomic changes within a myogenic context. DUX4 yields a complex transcriptome featuring numerous unannotated isoforms from known and novel loci. Moreover, we observed distinct isoform usage of DUX4 target genes between myogenic and embryonic cleavage states highlighting the distinct differences between DUX4 transcription factor activity in skeletal muscle and during the cleavage stage. We also identified ~1,400 unannotated intergenic isoforms predominantly originating from repetitive elements such as LTRs, LINEs, and SINEs. Integration with available datasets delineates the transcriptional and epigenetic landscape of these loci across myogenic and embryonic backgrounds. Like the cell type-specific isoform production, the usage of DUX4 binding sites at these intergenic loci is in part cell type-specific. Collectively, these findings demonstrate substantial and context-specific transcriptomic alterations induced by DUX4 further enriching our understanding of DUX4-induced muscle pathology.

  Study EGAS50000000503

• RNA Editing Exome

  Exome sequencing data for tumor and matched normal samples of the EGAS00001000495 project.

  Dataset EGAD00001000626

• RNA Editing AZIN1 amplicon sequencing

  AZIN1 amplicon sequencing data of the EGAS00001000495 project.

  Dataset EGAD00001000708

• Saliba Lab Data Access Committee

  DAC for data generated by Saliba Lab at Helmholtz institute for RNA-based Infection Research, Würzburg, Germany

  Dac EGAC50000000152