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• Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling

  Genomic sequencing has driven precision-based oncology therapy; however, genetic drivers remain unknown or non-targetable for many malignancies, demanding alternative approaches to identify therapeutic leads. Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Here, we mapped active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts. Enhancer regions revealed novel oncogenes, molecular targets, and pathways, which when subjected to small molecule inhibitor or shRNA treatment, increased survival and slowed proliferation in mouse and neurosphere patient-derived models of ependymomas. This study represents one of the largest enhancer mapping study of any cancer type to date, and provides a framework for target and drug discovery for other cancers recalcitrant to therapeutic development because of their lack of known genetic drivers.

  Study EGAS00001002696

• Predictor_ChemoNEAR_TNBC (2019-08-14)

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005255

• Profiling the Microbiome of Pediatric Gut with Metagenomic Short-Read Sequencing

  This dataset contains short-read metagenomic sequencing of stool, as well as intestinal tissue and tissue washes, from preterm infants. 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 EGAD00001016052

• Ovarian carcinosarcoma genomics and eribulin response

  Ovarian carcinosarcoma (OCS) is an aggressive and rare tumour type with limited treatment options. OCS is hypothesised to develop via the combination theory, with a single progenitor resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). In this study, we analysed DNA variants from isolated carcinoma and sarcoma components to show that OCS from 18 women is monoclonal. RNA sequencing indicated the carcinoma components were more mesenchymal when compared with pure epithelial ovarian carcinomas, supporting the conversion theory and suggesting that EMT is important in the formation of these tumours.

  Study EGAS00001006555

• Heart Failure: A Controlled Trial Investigating Outcomes of Exercise Training (HF-ACTION-BioLINCC)

  Accessing Data Please refer to “Authorized Access” below regarding accessing data through the BioData Catalyst ecosystem. The data from this accession is not available for download through dbGaP.ObjectivesThe HF-ACTION study examined whether exercise training reduces a composite endpoint of all-cause mortality or all-cause hospitalization for patients with left ventricular systolic dysfunction and heart failure symptoms. Background Heart failure (HF) is a major and growing cardiovascular syndrome that is the end result of many cardiovascular disorders. Although evidence-based drug and device therapies decrease mortality, hospitalizations, and HF symptoms and improve quality of life, many patients treated with these regimens often remain burdened by dyspnea and fatigue, diminished exercise tolerance, reduced quality of life, recurrent hospitalizations, and early mortality. Whereas rest was traditionally recommended for HF patients, there has been evidence that physical deconditioning may play a key role in the progression of symptoms and poor outcomes. Previous studies have shown positive effects of exercise training on exercise capacity, quality of life, and biomarkers and suggest that exercise training might improve survival and decrease HF hospitalizations. Nonetheless, there remains a safety concern regarding exercise training in HF and a large scale, multicenter, controlled clinical trial was needed to provide definitive clinical outcome data. Participants A total of 2,331 participants were randomized. 2,130 consented to share data with non-commercial entities, and 1,753 consented to share for commercial purposes. Design All participants underwent baseline cardiopulmonary exercise testing. Test results were reviewed by investigators to identify significant arrhythmias or ischemia that would prevent safe exercise training, to determine appropriate levels of exercise training, and to establish training heart rate ranges. Demographics, socioeconomic status, past medical history, current medications, physical exam, and the most recent laboratory tests were obtained prior to randomization. All participants received detailed self-management educational materials which included information on medications, fluid management, symptom exacerbation, sodium intake, and physical activity. Participants randomized to the exercise training arm first participated in a structured, group-based, supervised exercise program, with a goal of 3 sessions per week for a total of 36 sessions in 3 months. The primary exercises were walking, treadmill, or stationary cycling. Exercise was initiated at 15 to 30 minutes per session at a heart rate corresponding to 60% of heart rate reserve, and was increased after 6 sessions to 30 to 35 minutes duration and 70% of heart rate reserve. Participants began home-based exercise after completing 18 supervised sessions and were to fully transition to home exercise after 36 supervised sessions. The target training regimen for home exercise was 5 times per week for 40 minutes at a heart rate of 60% to 70% of heart rate reserve. Participants randomized to the usual care group were not provided with a formal exercise prescription. To provide comparable levels of attention from study personnel, all participants were called every 2 weeks for the first 9 months, monthly until 24 months of follow-up, and quarterly thereafter. Participants returned for clinic visits every 3 months for the first 2 years of participation and yearly thereafter for up to 4 years. Follow-up assessments included cardiopulmonary exercise testing, a 6-minute walk test, and a physical activity questionnaire. The primary end point was a composite of all-cause mortality or all-cause hospitalization. Secondary end points included all-cause mortality, the composite of cardiovascular mortality or cardiovascular hospitalization, and the composite of cardiovascular mortality or HF hospitalization. Conclusions After adjustment for highly prognostic predictors of the primary end point, exercise training was associated with modestly significant reductions for both all-cause mortality or hospitalization and cardiovascular mortality or heart failure hospitalization.

  Study phs003599

• Preferential infiltration of unique Vγ9Jγ2‐Vδ2 T cells into glioblastoma multiforme

  Glioblastoma multiforme (GBM) is clinically highly aggressive as a result of evolutionary dynamics induced by cross-talk between cancer cells and a heterogeneous group of immune cells in tumor microenvironment. The brain harbors limited numbers of immune cells with few lymphocytes and macrophages; thus, innate‐like lymphocytes, such as γδ T cells, have important roles in antitumor immunity. Here, we characterized GBM‐infiltrating γδ T cells, which may have roles in regulating the GBM tumor microenvironment and cancer cell gene expression. V(D)J repertoires of tumor‐infiltrating and blood‐circulating γδ T cells from four patients were analyzed by next-generation sequencing-based T-cell receptor (TCR) sequencing in addition to mutation and immune profiles in four GBM cases. In all tumor tissues, abundant innate and effector/memory lymphocytes were detected, accompanied by large numbers of tumor‐associated macrophages and closely located tumor‐infiltrating γδ T cells, which appear to have anti-tumor activity. The immune-related gene expression analysis using the TCGA database showed that the signature gene expression extent of γδ T cells were more associated with those of cytotoxic T and Th1 cells and M1 macrophages than those of Th2 cells and M2 macrophages. Although the most abundant γδ T cells were Vγ9Vδ2 T cells in both tumor tissues and blood, the repertoire of intratumoral Vγ9Vδ2 T cells was distinct from that of peripheral blood Vγ9Vδ2 T cells and was dominated by Vγ9Jγ2 sequences, not by canonical Vγ9JγP sequences that are mostly commonly found in blood γδ T cells. Collectively, unique GBM‐specific TCR clonotypes were identified by comparing TCR repertoires of peripheral blood and intra‐tumoral γδ T cells. These findings will be helpful for the elucidation of tumor-specific antigens and development of anticancer immunotherapies using tumor-infiltrating γδ T cells.

  Dataset EGAD00001004862

• VCF file from 16 patients affected by acute intermittent porphyria

  VCF file from 16 patients affected by acute intermittent porphyria. Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). BAM files were processed at the CNAG (Barcelona) with their pipeline, including GATK v3.6 for genotyping and other tools such as snpEff for annotating variants, to produce this VCF file with a total of 10,630,259 variants, out of which 8,731,523 are SNVs.

  Dataset EGAD00001006952

• Massive parallel RNA sequencing of highly purified mesenchymal cells derived from bone marrow specimens of 10 healthy donors

  Highly purified mesenchymal cells (CD45-/7AAD-/CD235a-/CD31-/CD271+/CD105+) were prospectively FACS-isolated from bone marrow specimens of 10 healthy donors (HDs). This data set is used as a baseline control to observe the differences between gene expression profiles (GEPs) of pre-leukemia cases (45 low-risk myelodysplastic syndrome, 4 Shwachman-Diamond and 3 Diamond-Blackfan anemia patients) and gene expression patterns observed in a normal, healthy context. Through differential expression and gene set enrichment analysis we determined that inflammatory signaling pathways are significantly more active in mesenchymal cells of pre-leukemia cases compared to their healthy counterparts. Finally, we determined through statistical modelling of healthy donor's GEPs which pre-leukemia cases have significantly more active inflammatory signaling and demonstrated a strong relation to survival statistics.

  Dataset EGAD00001002659

• Analysis of four key cell types (epithelial, fbroblast, myeloid and T cells)

  Alterations of the normal prostate epithelial cell genome trigger the emergence of carcinoma, however cancer-only analyses of genomic aberrations have resulted in little clinical translation. A deep understanding of the tumor microenvironment is likely to inform on key drivers of disease progression and novel therapeutic opportunities. We investigated the role of key cell types along disease progression, profiling the RNA abundance of 52 samples from 13 patients enriched for one of four key cell types, spanning a wide CAPRA-S risk score range. Using a novel differential transcription Bayes method, TABI, we avoided a priori patient stratification, and mapped transcriptional alteration events to specific risk scores. The developmental and cell-type resolution yielded a landscape of concurrent transcriptional alterations from the tumour microenvironment, including key hallmarks. These transcriptional signatures permitted the identification of a “high survival” patient cluster in an independent prostate cancer dataset. Most importantly, together with our integrated transcriptional analysis, differential tissue composition analysis provided evidence for a key role for monocytes and macrophages in prostate cancer progression and disease recurrence.

  Study EGAS00001003579

• Changes in AXL and/or MITF melanoma subpopulations in patients receiving immunotherapy

  Our data demonstrate large interpatient variability and variable therapy-induced changes independent of the type of therapy. We identify the presence of previously described AXL+ and MITF+ subpopulations in metastatic tissues both at the mRNA level and in situ at the protein level, and demonstrate that MITF+ melanoma cells are significantly decreased upon immunotherapy, while AXL+ melanoma cell numbers are stable. MITF+ tumor cells showed the most significant inverse correlation with CD8+ T cells. Our patient cohort also shows that immunotherapy-induced changes in the abundance of AXL+ or MITF+ tumor cells did not correlate with improved survival.

  Study EGAS50000001080

• Invariant patterns of clonal succession determine specific clinical features of Myelodysplastic syndromes (MDS)

  Myelodysplastic Syndromes (MDS) are heterogeneous myeloid neoplasms, characterized by stepwise acquisitions of multiple somatic mutations. Mutational configurations (e.g. bi-allelic) and specific distributions, timing of acquisitions corresponding to rank within the clonal hierarchy, and combinatorial spectrum are not elucidated. Therefore, we conducted targeted deep sequencing in a panel of the 36 most frequently mutated "myeloid" genes in terms more than of 500 patients with MDS or related myeloid neoplasms.

  Study phs001898

• Circulating tumor cell copy-number heterogeneity in ALK-rearranged non-small-cell lung cancer resistant to ALK inhibitors

  Gatekeeper mutations are identified in only 50% of the cases at resistance to Anaplastic Lymphoma Kinase (ALK)-tyrosine kinase inhibitors (TKIs). Circulating tumor cells (CTCs) are relevant tools to identify additional resistance mechanisms and can be sequenced at the single-cell level. Here, we provide in-depth investigation of copy number alteration (CNA) heterogeneity in phenotypically characterized CTCs at resistance to ALK-TKIs in ALK-positive non-small cell lung cancer.

  Study EGAS00001005301

• DAC for Human exome sequencing data from three family members reported in the publication

  Germline variants in UHRF1 are associated with multi-locus imprinting disturbance in humans and mice. Eguzkine Ochoa, Ilona Zvetkova, Sunwoo Lee, Nozomi Takahashi, Benoit Lan-Leung, Emma Hobson, Mahmoud Issa, Bryndis Yngvadottir, France Docquier, Fay Rodger, Dounia Foster-Hall, Graeme Clark, Ana Toribio, Ezequiel Martin, Leonardo Bottolo, Anne C Ferguson-Smith, Wolfgang Fischle, Miguel Constancia, Eamonn R Maher

  Dac EGAC50000000710

• Bottleneck Sequencing Of Human Tissue (Wgs) (2020-10-20)

  Bottleneck sequencing of human tissue including neurons, cord blood, sperm. 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/ . This dataset contains all the data available for this study on 2020-10-20.

  Dataset EGAD00001006459

• WES of breast and larynx cancer cases

  The dataset is based on 37 FFPE samples obtained from 12 patients diagnosed with breast or larynx cancer, For each patient 3 sample types were obtained P - primary tumor, L - malignant lymph node and C - benign lymph node (control). For patient G46 two malignant lymph nodes were used. DNA isolated from all samples was subject to exome selection using Agilent SureSelect Human All Exon V7. The obtained material was sequenced using NovaSeq 6000 platform with 2x150 reads. The sequencing was conducted by Novogene company.

  Dataset EGAD00001009081

• Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML

  Our aim was to identify regulators of the EVI1/MECOM gene, which is the most lethal oncogenic TF and is highly expressed in AML with chromosome 3q26 abnormalities.

  Study EGAS50000000347

• Whole Exome Sequencing and RNA-Seq to Characterize the Somatic Breast Cancer Landscape Among Latinas in California

  Somatic mutational profiles are increasingly being used to guide treatment. However, there is a dearth of data from non-European populations. To address this gap, we conducted paired tumor/normal whole exome paired-end sequencing and tumor RNA-Seq on 146 breast tumors from 140 Hispanic/Latina (H/L) women with breast cancer. We characterized somatic mutations, copy number alterations, tumor subtypes [Prediction Analysis of Microarray 50 (PAM50)], Catalogue Of Somatic Mutations In Cancer (COSMIC) mutation signatures and expression profiles, and compared them to breast tumors from non-Hispanic White (White) women in The Cancer Genome Atlas (TCGA). Using MutSigCV, we found that the most commonly mutated genes, including TP53, RUNX1, PTEN, PIK3CA, MAP3K1, GATA3, CDH1 and CBFB, were similar to those in breast tumors from non-Hispanic white women. Novel findings were that outliers of BLTP2 (aka KIAA0100) over-expression and COSMIC mutational signature 16 were more common in tumors from H/L women than White women. We also identified that the known germline APOBEC3A/B deletion variant was significantly more common in H/L women and was associated with indigenous American ancestry. Data available through dbGaP will be whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) data, as well as phenotypic data, including estrogen receptor, progesterone receptor, and HER2 receptor status, tumor histology, stage, and grade, and age at diagnosis.

  Study phs003218

• Decoding Human Heart Morphogenesis through Single-cell Multi-modal Analyses

  The heart, which is the first organ to develop, is highly dependent on its form to function. However, how diverse cardiac cell types spatially coordinate to create complex morphological structures critical for heart function remains to be elucidated. Here, we show that integration of single cell RNA-sequencing with high-resolution multiplexed error-robust fluorescent in situ hybridization (MERFISH) not only resolves the identity of cardiac cell types developing the human heart but also provides a spatial mapping of individual cells that enables illumination of their organization into cellular communities forming distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, supporting their specialization according to cellular ecosystem and anatomic region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and formed, with other cell subpopulations, several cellular communities. Interrogating cell-cell interactions within these communities revealed signaling pathways orchestrating the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis. In vivo conditional genetic mouse models and in vitro human pluripotent stem cell studies confirmed an intricate multicellular PLXN-SEMA crosstalk among specific ventricular cardiomyocyte, fibroblast and endothelial cell subpopulations that directs the compaction of the ventricular wall layers. Thus, these detailed findings into the cellular social interactions and specialization of cardiac cell types constructing and remodeling the human heart offer new insights into structural heart diseases as well as engineering complex multi-cellular tissues for human heart repair. Reprinted from Farah et al. (In press), with permission from Nature.

  Study phs002031

• Tocilizumab treatment leads to early resolution of myeloid dysfunction and lymphopenia in patients hospitalized with COVID-19

  Tocilizumab, an anti-interleukin-6 receptor inhibitor, is recommended in global treatment guidelines for patients hospitalized with severe COVID-19. Using proteomic and transcriptomic analysis, we characterized the immune profile and identified cellular and molecular pathways directly modified by tocilizumab in peripheral blood samples collected from patients enrolled in the COVACTA study, a phase 3, randomized, double-blind, placebo-controlled trial, to assess the efficacy and safety of tocilizumab in hospitalized patients with severe COVID-19 pneumonia. We identified factors predicting disease severity and clinical outcomes, including markers of inflammation, lymphopenia, myeloid dysfunction, and organ injury. Proteomic analysis confirmed a pharmacodynamic effect for tocilizumab. Transcriptomic analysis revealed that tocilizumab treatment leads to faster resolution of lymphopenia and myeloid dysfunction associated with severe COVID-19 thus supporting an underlying anti-inflammatory mechanism of action for the beneficial effects of tocilizumab in patients hospitalized with COVID-19.

  Study EGAS00001006688

• Combining transcription factor binding affinities with open chromatin data for accurate gene expression prediction

  The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid cost and labour intensive TF ChIP-seq assays.It is important to develop reliable and fast computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices.TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq, using either peaks or footprints as input.In addition to open-chromatin data, also Histone-Marks (HMs) can be used in TEPIC to identify candidate TF binding sites.TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength.Using machine learning techniques, we show that incorporating low affinity binding sites improves our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites.Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance.In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq datasets.Finally, we show that these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

  Study EGAS00001002073

• A novel orthotopic patient-derived xenograft model of radiation-induced glioma following medulloblastoma

  Radiation-induced glioma (RIG) is a highly aggressive brain cancer arising as a consequence of radiation therapy. We report a case of RIG that arose in the brain stem following treatment for paediatric medulloblastoma, and the development and characterisation of a matched orthotopic patient-derived xenograft (PDX) model (TK-RIG915). Patient and PDX tumours were analysed using DNA methylation profiling, whole genome sequencing (WGS) and RNA sequencing. While initially thought to be a diffuse intrinsic pontine glioma (DIPG) based on disease location, results from methylation profiling and WGS were not consistent with this diagnosis. Furthermore, clustering analyses based on RNA expression suggested the tumours were distinct from primary DIPG. Additional gene expression analysis demonstrated concordance with a published RIG expression profile. Multiple genetic alterations that enhance PI3K/AKT and Ras/Raf/MEK/ERK signalling were discovered in TK-RIG915 including an activating mutation in PIK3CA, upregulation of PDGFRA and AKT2, inactivating mutations in NF1, and a gain-of-function mutation in PTPN11. Additionally, deletion of CDKN2A/B, increased IDH1 expression, and decreased ARID1A expression were observed. Detection of phospho-S6, -4EBP1 and -ERK via immunohistochemistry confirmed PI3K pathway and ERK activation. Here, we report one of the first PDX models for RIG, which recapitulates the patient disease and is molecularly distinct from primary brain stem glioma. Genetic interrogation of this model has enabled the identification of potential therapeutic vulnerabilities in this currently incurable disease.

  Study EGAS00001004709

• Mannheim Liquid Biopsy Unit, Heidelberg University & DKFZ

  The dataset consists of sequenced cell free DNA (cfDNA) samples from colorectal cancer patients. The samples were sequenced on an Illumina MiSeq machine using a custom amplicon sequencing approach. These amplicons were designed to cover the most common mutation hotspots in colorectal cancer. The data include 138 cfDNA samples from 34 different patients. For each patient several samples are available derived from blood drawn at different time points during treatment. In addition the data include samples from 22 histology slides and 30 samples derived from HT29/HCT116 cell lines that were used as controls.

  Dataset EGAD00001004574

• A clinically applicable connectivity signature for glioblastoma includes the tumor network driver CHI3L1

  Tumor microtubes (TMs) connect glioma cells to a network with considerable relevance for tumor progression and therapy resistance. The determination of TM-interconnectivity in individual tumors has been challenging and the impact on patient survival unresolved. Here, a connectivity signature from single-cell RNA-sequenced (scRNA-Seq) xenografted primary glioblastoma (GB) cells has been established using a dye uptake methodology, confirmed with recording of cellular calcium epochs and validated with clinical correlations. Astrocyte-like and mesenchymal-like GB cells have the highest connectivity signature scores in scRNA-sequenced patient-derived xenografts and patient samples. In large GB cohorts, network connectivity correlated with the mesenchymal subtype and dismal patient survival. CHI3L1 has been identified and validated as a robust molecular marker of connectivity with functional relevance. The connectivity signature allows novel insights into brain tumor biology, provides a proof-of-principle that tumor cell TM-connectivity is relevant for patients’ prognosis, and serves as a robust prognostic biomarker.

  Study EGAS00001007611

• NCI Expanded Genome-Wide Association Study of Renal Cell Carcinoma

  The National Cancer Institute (NCI) expanded genome-wide association study (GWAS) of renal cell carcinoma (RCC) was a 2nd GWAS of this cancer performed by NCI to further investigate common genetic variants associated with RCC risk. The GWAS includes 2,781 cases and 2,940 controls of European background from 13 studies conducted in the US and Finland (10 cohorts, 2 case series, 1 hospital biorepository), scanned using the Illumina OmniExpress and Omni2.5 SNP arrays. SNP-level results from this GWAS were combined by meta-analysis with results from the earlier NCI RCC GWAS (phs000351.v1.p1; 1,311 cases and 3,424 controls) and others conducted by the International Agency for Research on Cancer (scan 1: 2,438 cases and 5,071 controls; scan 2: 2,781 cases and 2,940 controls), The University of Texas MD Anderson Cancer Center (893 cases and 556 controls) and the Institute for Cancer Research, UK (944 cases and 4,024 controls). Only data from the second NCI scan are included in this dbGaP submission. Data from 239 cases and 229 controls from this scan will be deposited in dbGaP separately under the Women's Health Initiative (phs000200).

  Study phs001736

• HuBMAP: Single-Cell Multiplex Chromatin and RNA Interactions in Aging Human Brain

  The study employs the Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) technique to concurrently profile multiplex chromatin interactions, gene expression, and RNA-chromatin associations within individual nuclei, revealing dynamically organized chromatin complexes in human frontal cortex samples from elderly donors. The MUSIC technique allows for the exploration of chromatin architecture and transcription at cellular resolution in complex tissues. The study includes 14 human cortex tissues and employs MUSIC to delineate diverse cortical cell types and states, revealing that nuclei with fewer short-range chromatin interactions correlate with an "older" transcriptomic signature and Alzheimer's pathology. Additionally, the study elucidates that specific cell types, characterized by chromatin contacts between cis expression quantitative trait loci (cis eQTLs) and a promoter, are particularly susceptible to the regulatory impact of these cis eQTLs on target gene expression. Furthermore, the female cortical cells exhibit highly heterogeneous interactions between the X-inactive specific transcript (XIST) non-coding RNA and Chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploring chromatin architecture and transcription at cellular resolution in complex tissues.

  Study phs003568