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• Single cell TCR sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell TCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.

  Dataset EGAD00001007674

• Single cell BCR sequencing

  Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell BCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.

  Dataset EGAD00001007673

• 5' single cell RNA sequencing

  Pared-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics 5' single cell RNA sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina HiSeq 4000 using recommended cycling parameters.

  Dataset EGAD00001007672

• ChIP-seq in colorectal cancer and paired adjacent normal mucosa

  This dataset includes ChIP-seq data for H3K27ac and H3K4me1 on 20 paired samples of colorectal cancer and adjacent normal mucosa. One tumor sample that failed QC is not available.

  Dataset EGAD00001007707

• CGH Array

  DNA samples were extracted from peripheral blood lymphocytes using commercially available kit (Puregene Core Kit A, Qiagen) according to manufacturer's protocol. Agilent SurePrint G3 Human CGH Microarray 180K platform was used for screening of copy number aberrations (CNAs) using array-CGH protocol recommended by manufacturer (Agilent Technologies), data mining and interpretation of array-CGH results was performed in same manner as in our previously published results.

  Dataset EGAD00001007743

• cfMeDIP data for 14 Barrier samples

  We analyzed the cell free DNA methylomes using 14 plasma samples from patients with mCRPC in the Barrier cohort. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.

  Dataset EGAD00001008712

• 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

• 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

• Dataset on keratinocytic gene expression pattern in Hidradenitis suppurativa

  Human skin samples were obtained from HS patients after informed consent (Ethical vote, University of Würzburg; No. 306/12). Lesional and perilesional were taken and epidermis and dermis separated. Isolated epidermal keratinocytes were further processed for RNA isolation. mRNA was extracted from five pairwise-matched lesional and perilesional epidermal HS pellets and RNA sequencing was performed.

  Dataset EGAD00001008005

• Feb2020 interim Genes and Health (28k) GSA imputed genotyped data

  Genotyped data for 28,022 British individuals with South Asian ancestry from the Genes and Health cohort (Feb2020), which were imputed with the GenomeAsia pilot reference panel.

  Dataset EGAD00001007815

• cfMeDIP data for 30 CPC-GENE samples

  We analyzed the cell free DNA methylomes using 30 plasma samples from patients with localized prostate cancer in the CPC-GENE project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.

  Dataset EGAD00001007972

• Finding structural variation and functional consequences from the Skin fibroblast at the single-cell level

  In this study, we aimed to identify somatic structural variation of Skin fibroblast at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of skin fibroblast sample from male donor.

  Dataset EGAD00001009307

• Molecular Characterization for Nasopharyngeal Carcinoma (NPC)

  Total RNA was isolated from 50 formalin-fixed paraffin-embedded nasopharyngeal cancer (NPC) specimens using the RecoverAll Total Nucleic Acid Isolation kit (Ambion). Tumor RNA libraries were prepared with 200ng RNA using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold, and sequenced with >80 million 100 bp paired-end reads.

  Dataset EGAD00001009047

• Cystic Fibrosis Varsity Project Multi-omics data

  This Dataset contains RNA-Seq, H3K27Ac ChIP-Seq, and ATAC-Seq data for 13 cystic fibrosis (CF) patients and 8 healthy volunteers (HV).

  Dataset EGAD00001009062

• Dataset for urologic_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 36 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008903

• Dataset for MCPlus_WGS

  WES/WGS sequencing data of 44 chromothriptic tumor and control runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009277

• Whole transcriptome sequencing of 38 follicular lymphoma tumours.

  This data set includes RNAseq from 38 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

  Dataset EGAD00001009650

• Paired RNA sequencing of 30 samples RRMM (multiple myeloma)

  Paired RNA sequencing of 30 samples RRMM using Illumina TruSeq stranded mRNA kit and either HiSeq2000 or HiSeq X Ten for sequencing.

  Dataset EGAD00001009680

• NABUCCO cohort 2 Whole Exome Sequencing (Tumor and Blood)

  Data from NABUCCO cohort 2 (NCT03387761). This dataset includes Whole exome DNA sequencing on bladder tumor samples matched with blood samples for patients from NABUCCO Cohort 2 (Cohort 2A and Cohort 2B). The data is pre-treatment

  Dataset EGAD00001009864

• Whole transcriptome sequencing of 78 follicular lyphoma tumours

  This data set includes RNAseq from 77 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

  Dataset EGAD00001010894

• analysis of the off target effect after Prime editing in IPSC line KCNQ2 R201C. Comparison of parental KCNQ2 R201C with two corrected clonal lines.

  Short read whole genome sequencing analysis of the off target effect after Prime editing in IPSC line KCNQ2 R201C. Comparison of parental KCNQ2 R201C with two corrected clonal lines (3samples in total). Dataset contains CRAM files and VCF files for the respective samples.

  Dataset EGAD00001010904

• SMARTer bulk RNA sequencing for highly purified CD271+ BMSCs from NBM and AML

  bulk RNAseq was conducted on highly purified CD45 - CD71 - CD235a - CD31 - CD271 + BMSCs isolated from a cohort of newly diagnosed 62 AML patients, uniformly treated within an intensive chemotherapy clinical trial and selected to represent the mutational landscape of AML

  Dataset EGAD00001011056

• 10x genomics RNAseq of an isogenic human iPSC model of SMA

  10x genomics single-cell RNAseq of an isogenic human iPSC model for SMA and control. The transcriptomic analysis was performed at 3 timepoints, day 4, day 20 and day 40. The analysis of this dataset was reported in the manuscript "An isogenic human iPSC model unravels neurodevelopmental abnormalities in SMA" from Grass et al.:

  Dataset EGAD00001011259

• Whole Exome Sequencing of One Nuclear Family with Non-syndromic Sensorineural Hearing Loss

  Our goal is to find genes responsible for non-syndromic sensorineural hearing loss. Blood samples were collected from the JS6 family affected with hearing loss. The family is of Caribbean Hispanic ethnicity. Family JS6 consisted of two deaf siblings, JS6.001 (Male) and JS6.002 (Female) and healthy parents, JS6.100 (mother) and JS6.200 (father). The siblings had no other medical findings. Audiometry tests and Rinne and Weber tuning fork tests identified sensorineural hearing loss in the two siblings. We performed whole exome sequencing of the four individuals and identified a recessive mutation, p.(Arg186Trp), in the CIB2 gene in the two affected siblings. Both parents were unaffected carriers.

  Study phs000969

• FaceBase Study of Facial Shape in Tanzania: CIDR

  The goals of this project are to identify loci that underlie major genetic determinants of orofacial shape, by means of a GWAS in a cohort of normal African children (from Tanzania) from whom we have collected 3D digitized facial morphometric scans, and a subsequent replication study of normal children from the same population. These studies are part of the NIDCR FaceBase initiative (https://www.facebase.org/). In addition to dbGaP, all study genotype and phenotype data (including primary facial scans and landmarks) will be available for data-sharing with qualified investigators via the NIDCR FaceBase Hub (www.facebase.org/), following approval by the NIDCR FaceBase Data Access Committee.

  Study phs000622

• Next Generation Mendelian Genetics: Familial Hemophagocytic Lymphohistiocytosis

  The NHGRI Next Generation Mendelian Genetics project uses exome resequencing to identify variants in unsolved Mendelian diseases. Familial hemophagocytic lymphohistiocytosis (fHLH) is a serious immune disorder that results from defective cytotoxic lymphocyte function. Autosomal recessive mutations in PFP1, UNC13D, STX11, STBP2, or RAB27, and hemizygous mutations in SH2D1A or BIRC4, account for known causes of the disease, but 30-70% of patients in North America lack a known genetic etiology. This project was designed to identify additional genetic abnormalities from HLH patients. The exome sequences of four unrelated individuals with a diagnosis of HLH, but without mutations in genes known to cause disease, were obtained by massively parallel DNA sequencing.

  Study phs000537

• Breast Cancer Risk Pathways

  We sought to identify genomic variants that differed between individuals who developed familial breast cancer and individuals who had a family history of breast cancer but who had not developed breast cancer. We aggregated these data at the pathway level to identify pathways that play a role in familial breast cancer development. We profiled peripheral blood cells, extracted DNA, and sequenced the DNA using exome-capture sequencing to identify genomic variants in these samples. For 34 of the 35 samples, we also profiled peripheral blood using Affymetrix Human Exon 1.0 ST Array microarrays. Those data can be found in Gene Expression Omnibus under accession identifier GSE47862.

  Study phs001044

• Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures

  We generated primary cultures from mechanically isolated kidney glomeruli (filtration unit of the nephron) which are composed of podocytes and mesangial cells. In parallel, we generated primary kidney cortex tubule cell cultures, which are composed primarily of proximal tubule cells. Early passage cultures of these two cell types were subjected to chromatin accessibility profiling (DNase-Seq) and gene expression profiling (RNA-Seq). We found thousands of dynamically regulated enhancers in both cell types that potentially regulate nearby and distal target genes that are differentially expressed. These data will be useful for understanding the epigenomic regulation of gene transcription in key kidney cell types.

  Study phs001720

• GWAS in Fibrosing Interstitial Lung Disease

  This study was a case-control genome-wide association study of 1616 non-Hispanic white cases and 4683 controls. Under an additive model for the minor allele at each SNP, we identified 19 SNPs, representing 7 chromosomal locations (5p15, 6p24, 7q22, 11p15, 15q14-15, 17q21, and 19p13), with genome-wide significant (P < 5x10-8) associations using the discovery samples included in this submission. We genotyped the 19 genome-wide significant SNPs in addition to 178 SNPs with 5x10-8 < P-value <.0001 and found 4 additional loci (3q26, 4q22, 10q24, and13q34) with genome-wide significant SNPs in the meta-analysis.

  Study phs000751

• Loss of IFN-gamma Signaling in Tumor Cells Associates with Primary Resistance to Anti-CTLA-4 Therapy

  Antibody blockade of the inhibitory CTLA-4 pathway has led to clinical benefit in a subset of patients with metastatic melanoma. Anti-CTLA-4 enhances T cell responses, including production of IFN-γ, which is a critical cytokine for host immune responses. However, the role of IFN-γ signaling in tumor cells in the setting of anti-CTLA-4 therapy remains unknown. Here we demonstrate that, based upon exome sequencing data, patients identified as non-responders to anti-CTLA-4 (ipilimumab) harbor a much higher genomic defects in the IFN-γ pathway genes than melanoma patients who had clinical response to ipilimumab therapy.

  Study phs001257

• DNA methylation in rhabdomyosarcoma PDX and PDX-derived primary cells

  Conditions to maintain primary tumor cells in culture are largely unknown for most tumor entities including rhabdomyosarcoma. In this collaborative study with Dr. Beat Schäfer's laboratory, we performed DNA methylation profiles of rhabdomyosarcoma patient-derived xenograft (PDX) and their matching PDX-derived primary cells (PPC), where the PPCs were developed and maintained under optimized culture conditions. We further compared DNA methylation profiles between these PDXs and PPCs. Exome sequencing and copy number analysis between these rhabdomyosarcoma PDXs and PPXs were also carried out. These analyses may help us to evaluate a feasibility of in vitro profiling of primary rhabdomyosarcoma cells from a genomic perspective.

  Study phs002051

• Mechanisms of Chemotherapy Resistance in T-ALL

  The goals of this study are to unravel the molecular mechanisms underlying leukemic transformation and chemotherapy resistance in T-cell acute lymphoblastic leukemia (T-ALL). Towards this end, a cohort of T-ALL lymphoblast specimens was collected at the time of initial T-ALL diagnosis (prior to the start of therapy) from children enrolled on contemporary clinical trials, Children's Oncology Group study AALL0434 and Dana-Farber Cancer Institute 05-001. Samples were analyzed using targeted exon sequencing and RNA sequencing analysis. Results of these analyses form the basis of studies that have been submitted for publication, and will be linked to this entry once published.

  Study phs001513

• DNA Methylation age and mortality in the Lothian Birth Cohorts of 1921 and 1936

  The study examined the association between DNA methylation age and mortality. Methylation age was estimated in 4 cohorts (including the Lothian Birth Cohorts of 1921 and 1936) and related to subsequent time-to-death. Across all four cohorts there was a strong correlation between predicted methylation age and chronological age. For individuals with a 5 year age acceleration (DNA methylation age - chronological age = 5), there was a meta analysed hazard ratio of mortality of 1.21 [1.14, 1.29]. Phenotype data associated with the study are available through dbGaP, the methylation raw data are available through the European Genome-phenome Archive (EGA; accession number EGAS00001000910).

  Study phs000821

• Genomics of Relapsed Small Cell Lung Cancer Progression

  Small cell lung cancer (SCLC) accounts for nearly 15% of all patients with lung cancer. Though the response to initial therapy is favorable in many patients, a majority of patients go on to develop recurrent disease which is very difficult to treat. The response rates to chemotherapy are very low and most patients succumb to relapsed SCLC within a few months. Virtually no progress has been made in the treatment of SCLC in the last three decades. In order to better understand the molecular alterations in relapsed SCLC, we have generated exome and RNA sequence from normal, primary tumor and relapse tissues of SCLC patients.

  Study phs001049

• NHLBI TOPMed: Genetics of Asthma in Latino Americans (GALA)

  This is a case pharmacogenetic study of bronchodilator drug response (Albuterol) among racially admixed Latino children with asthma between the ages of 8-40. Lung function testing was performed using the KoKo PFT system and each participant was administered albuterol dependent on age. Participants under 16 years of age, were administered 2 puffs of albuterol from a standard metered dose inhaler and 4 puffs for participants over 16 years old. The overall goal is to identify genetic factors which are predictive of drug response in children with asthma. The principal tools include a questionnaire and biological specimen collection. Participants with asthma have physician-diagnosed asthma, symptoms and medications.

  Study phs001542

• NHLBI TOPMed: Childhood Asthma Management Program (CAMP)

  The Childhood Asthma Management Program (CAMP) was designed to evaluate whether continuous, long-term treatment (over a period of four to six years) with either an inhaled corticosteroid (budesonide) or an inhaled noncorticosteroid drug (nedocromil) safely produces an improvement in lung growth as compared with treatment for symptoms only (with albuterol and, if necessary, prednisone, administered as needed). The primary outcome in the study was lung growth, as assessed by the change in forced expiratory volume in one second (FEV1, expressed as a percentage of the predicted value) after the administration of a bronchodilator. Secondary outcomes included the degree of airway responsiveness, morbidity, physical growth, and psychological development.

  Study phs001726

• Characterizing the secretome of licensed hiPSC-derived MSCs

  Although mesenchymal stromal cells (MSCs) from primary tissues have been successfully applied in the clinic, their expansion capabilities are limited and results are variable. MSCs derived from human-induced pluripotent stem cells (hiMSCs) are expected to overcome these limitations and serve as a reproducible and sustainable cell source. We have explored characteristics and therapeutic potential of hiMSCs in comparison to hBMSCs. Our data qualify hiMSCs as a promising source for cell therapy and/or cell-based therapeutic products. Additionally, the herewith generated database will add to our understanding of the mode of action of regenerative cell-based therapies and could be used to identify relevant potency markers.

  Study EGAS50000000389

• Assessing Individual Head and Neck Squamous Cell Carcinoma Patient Response to Therapy Through Integration of Functional and Genomic Data

  This study combines RNA sequencing (RNASeq), whole exome sequencing (WES), reverse phase protein array (RPPA) and copy number variation (CNV) data, along with a custom high throughput inhibitor assay to characterize tumor cells from patients with head and neck squamous cell carcinoma (HNSCC), in order to identify potential therapy targets on an individual patient basis. The data that will be available through dbGaP include the RNASeq, WES, RPPA and array CNV data for the tumor and matched normal samples. This study represents a proof-of-concept. No treatments were administered to patients as part of this study.

  Study phs003456

• Single-Cell Transcriptomic Characterization of Microscopic Colitis

  Patients with microscopic colitis (MC), chronic diarrhea without histological signs of MC, or unaffected controls were profiled using single-cell RNA sequencing (scRNA-seq; inDrops and 10X Genomics were used). One profiled patient without clinical symptoms was found to have histological signs of MC (asymptomatic MC). Some of the subjects from dbGaP study phs003418 are controls in this study. T-Cell Receptor sequencing (TCR-Seq) was also performed on a subset of patients. Individual transcriptomes were analyzed to characterize the cellular profile associated with MC and search for mediators of disease pathology. Raw reads and processed count matrices will be available through dbGaP.

  Study phs003876

• Atezolizumab monotherapy following dCRT indicated a promising cCR rate in patients with unresectable locally advanced esophageal squamous cell carcinoma (EPOC1802)

  The objective is to analyze tumor and normal cell exome sequencing of esophageal cancer patients participating in the Tenergy trial before treatment and RNA sequencing specimens of tumor biopsy specimens at three points before treatment, after radiation chemotherapy, and after atezolizumab administration, in order to search for biomarkers to predict treatment response. Exome sequencing of pretreatment tumor tissue (27 specimens) and normal tissue (27 specimens) from esophageal cancer patients participating in the Tenergy trial, and RNA sequencing of tumor biopsy specimens at three time points before treatment (28 specimens), after radiation chemotherapy (25 specimens) and after atezolizumab administration (25 specimens).

  Study JGAS000708

• Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions

  Alterations in the DICER1 and DGCR8 microprocessor genes confer risk to the development of benign and malignant thyroid lesions. The involvement of 2 miRNA biogenesis genes in benign and malignant thyroid tumors highlights the key role of miRNAs in the thyroid gland. We traced the progression from benignity to malignancy in DICER1- and DGCR8-mutated thyroid lesions by performing a multiomic characterization of these lesions aiming to uncover unique features characterizing either form for potential use as biomarkers. This multiomic characterization included whole exome sequencing (WES) (N=18), miRNA profiling (N=38), spatial transcriptomics (N=2) and/or methylome (N=281).

  Study EGAS50000001577

• "Elucidation of Immune Status and Its Clinical Significance in Patients with Solid Tumors, Including Gastrointestinal Cancers": A Phase II Clinical Trial of Lenvatinib Plus Pembrolizumab in Patients with Advanced Gastric Cancer

  The objective is to analyze tumor and normal cell exome sequencing of gastric cancer patients participating in the EPOC1706 trial before treatment and RNA sequencing specimens of tumor biopsy specimens at two points before treatment and after the combination therapy of Lenvatinib plus pembrolizumab, in order to search for biomarkers to predict treatment response. Exome sequencing from 10 gastric cancer patients participating in the EPOC1706 trial, and RNA sequencing of tumor biopsy specimens at two time points before treatment (9 patients) and after the combination therapy (8 patients) were obtained.

  Study JGAS000894

• scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment.

  We performed scRNAseq analysis of CD8 T cells infiltrating the bladder and tumor of 4 non-muscle-invasive bladder cancer patients, before and after BCG treatment. In order to identify tumor-specific T cells, we selected CD8 T cells that were enriched in the tumor of the patient. We also selected CD8 T cells appearing in the bladder after BCG treatment, with the hypothesis that BCG treatment stimulates tumor-specific CD8 T cells. Next, we cloned the TCR of these T cells in a Jurkat cell line and tested these TCR for recognition of tumor-specific antigens.

  Study EGAS50000001384

• Whole genome sequencing data of paediatric T cell acute lymphoblastic leukemia (T-ALL)

  T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy accounting for approximately 15–25% of pediatric and adult ALL cases. Despite significant therapeutic improvements over the last decade, the prognosis of T-ALL remains less favorable than that of B-ALL, with 5-year EFS and OS of around 76–82% and 80–88%, respectively, depending on the treatment protocol used. T-ALL patients often suffer from failure of induction therapy or early relapse, which is associated with a dismal prognosis. Approximately 10–15% of T-ALL patients experience relapse, and survival after relapse is poor.

  Study EGAS50000001387

• Multi-modal spatial characterization of tumor-immune microenvironments in diffuse large B-cell lymphoma

  We have leveraged spatial transcriptomics together with proteomic and genomic analysis to investigate the spatial immunology and pathobiology of DLBCL. We define distinct cellular niches that differ in frequency across tumors, related to both Epstein-Barr virus (EBV) infection status and the anatomical site of the tumor, and show that residence within different cellular niches is associated with divergent functional states of T-cells and tumor B-cells due to different patterns of cell-cell communication. This provides a framework for understanding stereotyped patterns of spatial organization in DLBCL and immunological interactions associated with heterogeneity in immune cell infiltration and function across patients.

  Study EGAS50000001146

• The_GENCODE_exome___sequencing_the_complete_human_exome

  We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an addition 5,594 genes and 10.3 Mb compared to current sets which mainly target the CCDS database. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed covers 47.9Mb and performed well in sequence capture experiments with HapMap and clinical samples. Samples within this study are prepared with either the CCDS or GENCODE exome products.

  Study EGAS00001000016

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model – 2D versus 3D co-culture comparison

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions (each as biological triplicates): - wild-type cells from 2D or 3D co-cultures after 3 months of culturing (2D_WT, 3D_WT) - knock-in cells from 2D or 3D co-cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (2D_KI, 3D_KI) - 2D and 3D KI cultures treated with Bumetanide (KI_bum) or BACE IV (KI_bace) inhibitor

  Study EGAS50000001392

• Extracellular vesicles from TGF-β-activated cancer-associated fibroblasts remodel the tumor microenvironment through EV surface-associated proteins.

  In this study, we explored the function of extracellular vesicles (EVs) derived from non-activated cancer-associated fibroblasts (CAFs) and TGF-β-activated CAFs. We tested these two types of EVs on other cell types in the tumor environment, including cancer cells, CD8+ T cells, and CAFs. We further explored the protein cargo in EVs altered by TGF-β treatment using quantitative proteomics, and selected several highly upregulated proteins for further analysis. We found that the majority of these proteins were presented on the EV surface, and they regulated the target cells in an EV-cell contact dependent manner.

  Study EGAS50000000922

• Gene expression profiling by RNAseq of multiple cell types derived from patients with LSD1 mutations and healthy controls, and in isogenic cell lines with LSD1 mutation introduced by CRISPR-Cas9

  Cell lines (fibroblasts, reprogrammed from them hiPSCs and differentiated from hiPSCs endoderm, mesoderm and neuronal cells) derived from two male CPRF patients carrying distinct LSD1 mtuations and their healthy fathers as controls were subjected to gene expression analysis by bulk RNAseq to identify mis-regulated genes. Some cell lines were subject to treatment with HDAC inhibitor valproic acid (VPA) or DMSO as controls and also underwent RNAseq analysis. Two isogenic LSD1 mutant hiPSC lines with CRISPR-edited Family B LSD1 mutation were also used for RNAseq analysis (after endoderm differentiation, with or without VPA treatment).

  Study EGAS00001008240